Varian GC-MS - Saturn 2000 MS Operators Manual

Varian, Inc.
2700 Mitchell Drive

Walnut Creek, CA 94598-1675/USA
Varian, Inc. 2003-2009 Printed in U.S.A. 03-914979-00:5

Saturn 2000 GC/MS
MS Workstation
Version 6

Operation Manual
NOTICE: Varian, Inc. was acquired by Agilent
Technologies in May 2010. This document is provided
as a courtesy but is no longer kept current and thus
will contain historical references to Varian. For more
information, go to www.agilent.com/chem.

1
Contents
Getting Started........................................................................................................................11
About this Manual/Help ............................................................................................................................................11
Additional Manuals/Help...........................................................................................................................................11
MS Workstation Toolbar ........................................................................................................13
Overview...................................................................................................................................................................13
Elements of the MS Workstation Toolbar.................................................................................................................14
Launching Applications from the MS Workstation Toolbar................................................19
Using the Application Icon Buttons...........................................................................................................................19
Using the Data File and Method Quick Link buttons................................................................................................19
MS Workstation Toolbar Options..........................................................................................21
Moving the MS Workstation Toolbar ........................................................................................................................21
The MS Workstation Toolbar Options Menu ............................................................................................................21
2000 MS Module Control ........................................................................................................25
Starting System Control the First Time ....................................................................................................................25
Configuring the Instrument .......................................................................................................................................25
Configuring the 3800 or 3900 GC Communication (No Company Network) ...........................................................32
Configuring the GC for a Company Network............................................................................................................34
Using a Password to Protect BOOTP Settings ........................................................................................................39
Adding a GC and Varian MS to the Instrument in System Control ..........................................................................41
2000 MS Instrument Control Command Reference .............................................................47
Saturn Module Dialogs .............................................................................................................................................47
2000 Module Window...............................................................................................................................................48
2000 MS Instrument Window.................................................................................................59
The 2000 MS Instrument Window............................................................................................................................59
Status and Control Window......................................................................................................................................73
3800 GC System Control Window.........................................................................................99
The Instrument Window............................................................................................................................................99
The 3800 GC Status and Control Window.............................................................................................................100
Documenting Module Information ..........................................................................................................................104
3800 GC Injecting a Single Sample.....................................................................................107
Overview.................................................................................................................................................................107
Using the Inject Single Sample Dialog Box............................................................................................................107
Specifying the Data File Name and Path ...............................................................................................................108

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Specifying Per-Sample Data Handling Parameters ...............................................................................................109
Specifying a RecalcList ..........................................................................................................................................110
Monitoring the Status of the Run............................................................................................................................110
Using QuickStart.....................................................................................................................................................111
3800 GC Injecting Multiple Samples ...................................................................................113
Introduction.............................................................................................................................................................113
Using a SampleList in System Control ...................................................................................................................113
Changing Default SampleList Entries.....................................................................................................................117
Reading Vial Positions from an 8200 AutoSampler ...............................................................................................117
Monitoring the Status of Runs ................................................................................................................................118
Saving SampleLists for Later Use..........................................................................................................................119
Using More Than One Method for Injections..........................................................................................................119
3900 GC System Control Window.......................................................................................123
The Instrument Window..........................................................................................................................................123
The 3900 GC Status and Control Window.............................................................................................................124
Documenting Module Information ..........................................................................................................................128
3900 GC Injecting a Single Sample.....................................................................................131
Overview.................................................................................................................................................................131
Using the Inject Single Sample Dialog Box............................................................................................................131
Monitoring the Status of the Run............................................................................................................................133
Using QuickStart.....................................................................................................................................................134
3900 GC Injecting Multiple Samples ...................................................................................137
Introduction.............................................................................................................................................................137
Using a SampleList in System Control ...................................................................................................................137
Monitoring the Status of Runs ................................................................................................................................141
Saving SampleLists for Later Use..........................................................................................................................142
System Control Menus.........................................................................................................145
File Menu................................................................................................................................................................145
Edit Menu................................................................................................................................................................146
Inject Menu .............................................................................................................................................................147
Automation Menu....................................................................................................................................................147
Recalculate Menu...................................................................................................................................................148
Instrument Menu.....................................................................................................................................................148
Windows Menu.......................................................................................................................................................149
Help Menu ..............................................................................................................................................................150

3
System Control Toolbar .......................................................................................................151
Main Toolbar...........................................................................................................................................................151
2000 MS Method Basic Scan Functions .............................................................................153
Introduction.............................................................................................................................................................153
2000 MS Method Chemical Ionization.................................................................................155
Introduction.............................................................................................................................................................155
The Chemical Ionization Scan Function.................................................................................................................155
Ion Formation By Chemical Ionization....................................................................................................................157
The CI Parameters .................................................................................................................................................158
Chemical Ionization Using Fixed Parameters ........................................................................................................162
Using Liquid CI Reagents.......................................................................................................................................162
Adjusting the CI Reagent Gas Pressure for Gases Other Than Methane.............................................................165
Tuning for CI Operation..........................................................................................................................................166
Low-Pressure CI vs. High Pressure CI...................................................................................................................166
Recommended Reading.........................................................................................................................................167
2000 MS Method Command Reference...............................................................................169
Spreadsheet editing................................................................................................................................................169
The CI Parameters .................................................................................................................................................175
CI Fixed Parameters...............................................................................................................................................176
Ion Storage (SIS) Parameters ................................................................................................................................177
Customize SIS........................................................................................................................................................177
The MS/MS Ion Prep Method.................................................................................................................................178
The MS q Calculator ............................................................................................................................................178
Ion Preparation MS/MS ..........................................................................................................................................183
MS
n
.........................................................................................................................................................................185
2000 MS Method Electron Ionization ..................................................................................189
The Electron Ionization Scan Function with Automatic Gain Control (AGC) .........................................................189
Ion Formation..........................................................................................................................................................190
AGC Prescan..........................................................................................................................................................190
Mass Scanning.......................................................................................................................................................191
Basic Equation of the AGC Software .....................................................................................................................192
Software Parameters..............................................................................................................................................193
2000 MS Method Ion Preparation ........................................................................................199
The Ion Preparation Method...................................................................................................................................199
Theory of Operation of the SIS Option...................................................................................................................201
Selected Ion Storage (SIS) Parameters.................................................................................................................202
Customize SIS........................................................................................................................................................203
Tips for Using SIS...................................................................................................................................................205
2000 MS Method MS/MS Option: Theory of Operation.....................................................207
Overview.................................................................................................................................................................207
The MS/MS Ion Prep Method.................................................................................................................................212
Customize Non-resonant Method...........................................................................................................................214
Customize Resonant Method................................................................................................................................217

4
Tandem Mass Spectrometry (MS/MS) ...................................................................................................................219
Automated Methods Development .........................................................................................................................221
MS/MS....................................................................................................................................................................224
Unit Resolution Selected Ion Storage ....................................................................................................................224
MS/MS/MS..............................................................................................................................................................224
2000 MS Method Section......................................................................................................227
Overview.................................................................................................................................................................227
Using Star Assistant to Create a New Method.......................................................................................................227
The Method Builder Window ..................................................................................................................................230
The 2000 MS Method Windows .............................................................................................................................231
The Flow Sampling Segment .................................................................................................................................233
2000 MS Method System Control ........................................................................................235
The Startup Method................................................................................................................................................235
Editing Methods from the Saturn Status and Control Window...............................................................................236
Changing Method End Time from the Saturn Control and Status Window............................................................236
Importing Method Sections.....................................................................................................................................237
Deleting Method Sections.......................................................................................................................................238
Printing the Method ................................................................................................................................................239
Password Protecting a Method ..............................................................................................................................239
3800 GC Method Command Reference...............................................................................241
3800 GC AutoSampler ...........................................................................................................................................241
3800 GC Sample Delivery......................................................................................................................................248
3800 GC Injector ....................................................................................................................................................249
3800 GC Flow/Pressure .........................................................................................................................................253
3800 GC Column Oven ..........................................................................................................................................256
3800 GC Detector...................................................................................................................................................257
3800 GC Output......................................................................................................................................................265
3800 GC Data Acquisition ......................................................................................................................................266
3800 GC Method Section......................................................................................................267
Overview.................................................................................................................................................................267
The 3800 GC Method Windows .............................................................................................................................271
Sample Delivery Window........................................................................................................................................274
Injector Window......................................................................................................................................................276
Flow/Pressure Window...........................................................................................................................................281
Column Oven Window............................................................................................................................................285
Detector Window....................................................................................................................................................286
Output Window.......................................................................................................................................................294
Data Acquisition Window........................................................................................................................................295
Autosampler Window..............................................................................................................................................296
Auto-Configuring the Method to Match the 3800 GC Hardware ............................................................................297
Uploading the Method from the 3800 GC...............................................................................................................297
Editing Methods from the 3800 Status and Control Window..................................................................................298

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3800 GC System Control Command Reference.................................................................303
Status and Control Window....................................................................................................................................303
Setup Ethernet Ports Dialog Box............................................................................................................................327
8400/8410 SampleList Window Extensions ...........................................................................................................330
3900 GC Method Command Reference...............................................................................333
3900 GC AutoSampler ...........................................................................................................................................333
3900 GC Injector Section .......................................................................................................................................341
3900 GC Flow/Pressure Section............................................................................................................................343
3900 GC Column Oven Section.............................................................................................................................344
3900 GC Method Section......................................................................................................345
Overview.................................................................................................................................................................345
The 3900 GC Method Windows .............................................................................................................................349
GC Control Window................................................................................................................................................352
Autosampler Window..............................................................................................................................................356
Auto-configuring the Method to Match the 3900 GC Hardware.............................................................................357
Uploading the Method from the 3900 GC...............................................................................................................357
Editing Methods from the 3900 Status and Control Window..................................................................................358
3900 GC System Control Command Reference.................................................................363
Status and Control Window....................................................................................................................................363
Setup Ethernet Ports Dialog Box............................................................................................................................377
8200 AutoSampler Instrument Control Command Reference ..........................................381
8200 AutoSampler Status and Control Window.....................................................................................................381
8200 SampleList Window Extensions ....................................................................................................................385
8200 Method Command Reference .....................................................................................389
8200 Configuration Window ...................................................................................................................................389
Automated MS Report Generation......................................................................................393
Overview.................................................................................................................................................................393
Automation File Editor Command Reference ....................................................................395
Menus.....................................................................................................................................................................395
Main Toolbar...........................................................................................................................................................397
Open Automation File Dialog Box ..........................................................................................................................398
Save Automation File As Dialog Box......................................................................................................................399
Print Setup Dialog Box ...........................................................................................................................................400
Edit Notes Dialog Box.............................................................................................................................................401
RecalcList Window.................................................................................................................................................402
SampleList Window................................................................................................................................................408

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Sequence Window..................................................................................................................................................414
Automation File Editor .........................................................................................................415
Overview.................................................................................................................................................................415
Accessing the Automation File Editor.....................................................................................................................415
Editing or creating a RecalcList ..............................................................................................................................415
Editing or creating a SampleList.............................................................................................................................417
Editing or Creating a Sequence .............................................................................................................................423
GC Batch Report...................................................................................................................425
Overview.................................................................................................................................................................425
Method Selection....................................................................................................................................................426
Generating Reports ................................................................................................................................................427
Changing Report Commands.................................................................................................................................427
GC Data Handling Calibration .............................................................................................429
Types of Calibration................................................................................................................................................429
Preparing the Method for Calibration .....................................................................................................................429
Automated Calibration............................................................................................................................................430
Inspecting Calibration Curves ................................................................................................................................431
Generating Calibration Block Reports....................................................................................................................433
Calibration Verification............................................................................................................................................434
GC Data Handling Fundamentals........................................................................................435
Introduction.............................................................................................................................................................435
Performing a Pilot Run ...........................................................................................................................................435
Peak Detection .......................................................................................................................................................436
Identifying Peaks ....................................................................................................................................................439
Building a Calibration Curve...................................................................................................................................439
External Standard Calibration.................................................................................................................................440
Internal Standard Calibration..................................................................................................................................441
Normalized Percent Calibration..............................................................................................................................441
Choosing a Calibration Type ..................................................................................................................................441
GC Data Handling Method Command Reference...............................................................443
Integration Parameters...........................................................................................................................................443
Peak Table..............................................................................................................................................................445
Calibration Setup....................................................................................................................................................447
Calibration Curve Window......................................................................................................................................450
Verification Setup....................................................................................................................................................454
Time Events Table..................................................................................................................................................455
GC Interactive Graphics Dialog Boxes ...............................................................................459
Open Multiple Data Files Dialog Box......................................................................................................................459
Open Method File Dialog Box.................................................................................................................................462
Open Original/Recalc Dialog Boxes.......................................................................................................................463

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Save Method As Dialog Box...................................................................................................................................464
Saturn Printer Setup Dialog Box.............................................................................................................................465
Preferences Dialog Box..........................................................................................................................................465
Reintegration List Dialog Box .................................................................................................................................471
Fill Peak Table Window..........................................................................................................................................473
Exact View Dialog Box ...........................................................................................................................................474
GC Interactive Graphics Menus ..........................................................................................475
File Menu................................................................................................................................................................475
Edit Menu................................................................................................................................................................476
View Menu..............................................................................................................................................................476
Results Menu..........................................................................................................................................................477
Edit Method Menu...................................................................................................................................................478
Help Menu ..............................................................................................................................................................479
GC Interactive Graphics Toolbars.......................................................................................481
Toolbar Overview ...................................................................................................................................................481
Main Toolbar...........................................................................................................................................................481
Method Quick Link Toolbar.....................................................................................................................................482
Chromatogram Toolbar ..........................................................................................................................................482
GC Interactive Graphics Window........................................................................................485
Locator Window......................................................................................................................................................485
Main Window..........................................................................................................................................................486
Info-Panels..............................................................................................................................................................489
Visual Method Edit Window....................................................................................................................................491
GC Interactive Graphics.......................................................................................................497
Viewing Chromatograms in Interactive Graphics...................................................................................................497
Elements of the Interactive Graphics Window........................................................................................................498
Changing Viewing Options .....................................................................................................................................501
Selecting a Method.................................................................................................................................................504
Changing the Data Handling Parameters...............................................................................................................507
Filling the Peak Table.............................................................................................................................................510
Interactive Editing of Timed Events........................................................................................................................511
Moving Peak Start and End Points.........................................................................................................................513
Calculating Results.................................................................................................................................................513
Viewing Results ......................................................................................................................................................515
Viewing Calibration Curves ....................................................................................................................................516
Printing and Copying the Chromatogram Display..................................................................................................517
GC Standard Report Method Command Reference...........................................................519
Print Options...........................................................................................................................................................519
Results Format .......................................................................................................................................................521
Chromatogram Format ...........................................................................................................................................522
Calibration Block Report Format ............................................................................................................................524
Generating GC Standard Reports .......................................................................................525
The Standard GC Reports Method Section............................................................................................................525
Automated Report Generation................................................................................................................................528
Automated Printing to Multiple Printers ..................................................................................................................529

8
Batch Report Printing without Recalculating ..........................................................................................................530
Viewing a Report for a Single Run .........................................................................................................................531
Method Builder Dialog Boxes..............................................................................................535
Create/Open Method File Dialog Box.....................................................................................................................535
Open Method File Dialog Box.................................................................................................................................536
Save Method File As Dialog Box............................................................................................................................537
Add Password Dialog Box......................................................................................................................................538
Change Password Dialog Box................................................................................................................................539
Print Method Sections Dialog Box..........................................................................................................................540
Star Printer Setup Dialog Box.................................................................................................................................541
Delete Method Sections Dialog Box.......................................................................................................................542
Import Method File Sections Dialog Box ................................................................................................................543
Star Assistant Wizard .............................................................................................................................................543
Method Builder Menus .........................................................................................................549
File Menu................................................................................................................................................................549
Edit Menu................................................................................................................................................................550
View Menu..............................................................................................................................................................550
Window Menu.........................................................................................................................................................550
Help Menu ..............................................................................................................................................................551
Method Builder Toolbars .....................................................................................................553
Overview.................................................................................................................................................................553
Main Toolbar...........................................................................................................................................................553
Directory Toolbar ....................................................................................................................................................554
Window Toolbar......................................................................................................................................................555
Method Builder Window.......................................................................................................557
Overview.................................................................................................................................................................557
Method Directory ....................................................................................................................................................558
Method Parameters ................................................................................................................................................559
Module Information Editor ...................................................................................................561
Module Information Editor ......................................................................................................................................561
Creating a Section..................................................................................................................................................562
Deleting a Section ..................................................................................................................................................562
Renaming a Section ...............................................................................................................................................562
Adding an Entry to a Section..................................................................................................................................563
Deleting an Entry from a Section............................................................................................................................563
Editing an Entry or Renaming an Item ...................................................................................................................563
Creating a Default Module Information Template ..................................................................................................564
Designing Documentation Structures.....................................................................................................................564
Retrieving Information from Data Files...................................................................................................................565
Commands .............................................................................................................................................................565
Dialog Boxes...........................................................................................................................................................566
Security Administration .......................................................................................................569
Overview.................................................................................................................................................................569
Passwords ..............................................................................................................................................................569
Application Locking.................................................................................................................................................571

9
File Revision Settings .............................................................................................................................................572
Standard GC Reports Command Reference ......................................................................575
File Menu................................................................................................................................................................575
Search Menu ..........................................................................................................................................................575
Font Menu...............................................................................................................................................................575
View Menu..............................................................................................................................................................576
Options Menu .........................................................................................................................................................576
Windows Menu.......................................................................................................................................................576
Help Menu ..............................................................................................................................................................577
Standard GC Reports Dialog Boxes....................................................................................579
Open Data File Dialog Box.....................................................................................................................................579
Print Dialog Box......................................................................................................................................................580
Printer Setup Dialog Box ........................................................................................................................................581
Title Dialog Box.......................................................................................................................................................581
Chromatogram Options Dialog Box........................................................................................................................582
Results Options Dialog Box....................................................................................................................................584
Find Dialog Box ......................................................................................................................................................585
Standard GC Reports Format Descriptions .......................................................................587
Results Report ........................................................................................................................................................587
Verification Report ..................................................................................................................................................593
Standard GC Reports Toolbar .............................................................................................595
Main Toolbar...........................................................................................................................................................595

10

11
Getting Started
About this Manual/Help
This manual/help system contains information about how to acquire data, build
methods, and operate the Saturn GC/MS through the Varian MS Workstation.
This manual also describes the configuration of the 3800 and 3900 GCs for
standard Ethernet communication with the Saturn 2000 and MS Workstations
System Control application. Use this manual in conjunction with the other
manuals supplied with your MS Workstation and your 3800 GC or 3900 GC. All
of the information included in this manual is also available in the On-Line Help
section of the software.
Additional Manuals/Help
Other sources of information are available to help you get the most from this
product.
2000 GC/MS Hardware Reference Manual/Help
The Hardware Reference Manual/Help system provides the necessary
information for installing, maintaining, using and repairing your Saturn GC/MS
System. All of the information included in this manual is also available in the On-
Line Help section of the software.
MS Workstation Manual/Help
This Manual/Help provide a practical way to quickly learn how to perform basic
tasks using the MS Workstation Software. While these tutorials use Saturn 2000
ion trap files, they can easily be adapted to your instrument configuration.
3800 and 3900 GC Operators Manuals
These manuals are included on the Varian MS Workstation CD-ROM and
describe the GC Method, instrument operation, and the process of connecting
your GC to a PC or to an existing network.
Context Sensitive Help
The MS Data Review, Method Builder and System Control sections of the
software contain Context Sensitive Help. Help can be obtained simply by
positioning the mouse pointer on the item of interest, clicking the right mouse
button and selecting "What's This".

12

13
MS Workstation Toolbar
Overview

Saturn GC/MS Workstation is a suite of applications for controlling
chromatographs, collecting data from chromatograph detectors, and analyzing
those data. The MS Workstation Toolbar provides quick and easy access to the
Saturn GC/MS Workstation applications. When activated, the MS Workstation
Toolbar behaves very much like the Windows Taskbar. It can be docked on any
of the four sides of the display screen and other Windows programs will not
cover or go behind it when they are opened in full screen mode.
If the MS Workstation Toolbar is not already opened on your Saturn GC/MS
Workstation, you can start it from the Windows Start Menu.

14
Elements of the MS Workstation Toolbar
Application Buttons for immediate access to the selected application.

Tooltip shows the application name when the cursor rests on the Application
Button.
Quick Link Buttons provide menu selections of operations to be performed on the
listed file.
Application Descriptions give a brief description of the application that will be opened
when the cursor rests on the Application Button.

15
Application Buttons

Used to monitor instrument status, perform automated
injections, and perform batch recalculations.

Used to view and edit instrument operation, data
acquisition, and data handling methods.

Used for off-line editing of SampleLists, RecalcLists and
Sequences.

Used to review chromatograms and spectra, perform library
searches, and review and process quantitation results.

Used to create, edit, and view standard MS reports.

Used to create, edit, and view customized MS reports.

Used to convert data files between DOS and Windows
formats.
Used to review standard GC chromatograms, interactively
edit data handling parameters, and recalculate results.

Used to preview standard chromatogram and results
reports.

Used to generate standard reports for a group of Data Files
by dragging and dropping them on the Batch Report
Window.

Used to run a sample without a Sample List.

Used to set Saturn GC/MS Workstation security options and
passwords.
In addition, other application buttons may be added to the MS Workstation
Toolbar when you install additional Saturn GC/MS Workstation options, such as
StarFinder and Star Custom Report Writer.

16
Quick Link Buttons

Most Recently Used Data File. A menu of operations that can be performed on
the Most Recently Used Data File are displayed when the button is pressed. A
different data file can be selected from a list of most recently used files.

Most Recently Used Method. Menu of operations that can be performed on the
Most Recently Used Method will be displayed when the button is pressed. A
different method can be selected from a list of most recently used methods.

17
MS Workstation Toolbar Options

Right-click the bar to display the Toolbar Options. A menu of MS Workstation
Toolbar configuration options and operations that may be performed will be
shown.

18

19
Launching Applications from the
MS Workstation Toolbar
Using the Application Icon Buttons

Saturn GC/MS Workstation applications appear as icon buttons on the MS
Workstation Toolbar. As you move the mouse over these buttons, the name of
the application is shown in a tooltip window below the cursor.
Click any icon in the MS Workstation Toolbar to launch the corresponding
application.
Using the Data File and Method Quick Link buttons

The two buttons to the right of the application buttons are Quick Link buttons.
These two Quick Link buttons correspond to recently used Data Files and
Methods. On each Quick Link button is the name of the file associated with that
button. When you click the Quick Link button, a menu is displayed showing
operations that can be performed on the corresponding file.
The Quick Link buttons in the MS Workstation Toolbar are always updated with
the most recently used Data File and Method. If the Data File or Method you wish
to use is not displayed in the Quick Link button, you can choose from the eight
most recently used files by selecting Pick a different Data File (or Method) from
Quick Link buttons menu.

20

21
MS Workstation Toolbar Options
Moving the MS Workstation Toolbar
The MS Workstation Toolbar can be moved to any edge of the Windows screen.
Click a portion of the MS Workstation Toolbar that does not contain application or
Quick Link buttons and drag the toolbar to the edge of the screen that you desire.
When you release the mouse, the toolbar will remain on that edge. The MS
Workstation Toolbar remembers its location the next time it is started.
Additionally, you can display the MS Workstation Toolbar as a Windows Taskbar
icon. To do so, select Move to Windows Taskbar from the MS Workstation
Toolbar options menu. Taskbar icons appear in the lower right (or bottom) of the
Windows Taskbar (the bar on which the Start button appears). When displayed
as a Taskbar icon, the toolbar no longer takes up space on the screen. When
you click the MS Workstation Toolbar icon, the options menu is displayed.
The MS Workstation Toolbar Options Menu

When you move the mouse over an area of the MS Workstation Toolbar not
containing application or QuickLink buttons, you may right-click to display an
option menu.

22
Move to Windows Taskbar
You can display the MS Workstation Toolbar as a Windows Taskbar icon.
Taskbar icons appear in the lower right (or bottom) of the Windows Taskbar (the
bar on which the Start button appears). When displayed as a Taskbar icon, the
toolbar no longer takes up space on the screen. When you click the MS
Workstation Toolbar icon, the options menu is displayed.
Show/Hide Applications on Toolbar
Selecting this option displays the Show and Hide Applications on Toolbar dialog
box.

This dialog box allows you to select which Saturn GC/MS Workstation
applications are represented by icons on the MS Workstation Toolbar. The top
list box shows all applications that are currently displayed in the toolbar. The
bottom list shows all applications that are installed but not displayed in the
toolbar. To remove an icon from the toolbar, select it from the top list and click
Remove. To add an icon to the toolbar, select it from the bottom list and click
Add.
Enable/Disable Instrument Modules
Selecting this option displays the Enable/Disable Instrument Modules dialog box.

23

This dialog box allows you to select which Saturn GC/MS Workstation instrument
modules are available from this Workstation. When an instrument module is
available, it will appear in System Control if the corresponding instrument is
connected and powered-on, you will be able to create a Method section for it,
and you will be able to format reports for it.
The top list box shows all instrument modules that are currently installed and
enabled in the Saturn GC/MS Workstation. The bottom list shows all instrument
modules that are installed but not enabled. To disable an instrument module,
select it from the top list and click Disable. To enable an instrument module,
select it from the bottom list and click Enable.
Application Descriptions

When this menu item is checked, application descriptions are displayed when
you move the mouse over application buttons in the MS Workstation Toolbar.
Small Buttons on Toolbar

When this menu item is checked, the MS Workstation Toolbar is reduced in size.

24
Run Application
This hierarchical menu item lists all applications showing on the MS Workstation
Toolbar. When you select an item from this list, the corresponding application is
launched.
Help on
This hierarchical menu item lists all applications showing on the MS Workstation
Toolbar. When you select an item from this list, the online help corresponding to
the application is displayed.
Pick Data File for Quick Link Button
This hierarchical menu item lists the eight most recently used Data Files in order
of use. When you select a Data File from this list, the Data File currently
displayed in the Quick Link button is changed to the selected file.
Pick Method for Quick Link Button
This hierarchical menu item lists the eight most recently used Methods in order of
use. When you select a Method from this list, the Method currently displayed in
the Quick Link button is changed to the selected file.
Help on MS Workstation Toolbar
Displays the help you are now using.
Product Support Web Site
If you have Internet access and a web browser installed on your computer, this
option will automatically open the Saturn GC/MS Workstation Product Support
Web Site. Here you will find the latest software and documentation updates for
the Saturn GC/MS Workstation suite of products, along with additional notes,
tips, and answers to frequently asked questions.
You may wish to visit this site periodically to see if new information is available
that may be pertinent to you.
About MS Workstation Toolbar
Displays the About Box for the MS Workstation Toolbar. The About Box contains
information about the software version, installation information, and a list of the
instrument control modules that you have installed.
Quit
Quits the MS Workstation Toolbar application. If you elected to run the MS
Workstation Toolbar automatically when Windows starts, the MS Workstation
Toolbar will reappear the next time you start Windows.

25
2000 MS Module Control
Starting System Control the First Time
Before you enter System Control for the first time, confirm that the proper
instrument modules have been enabled and that any instrument modules that
are not part of the system have been disabled. To enable or disable instrument
modules refer to the section of the MS Workstation Toolbar, Enable/Disable
Instrument Modules.
Configuring the Instrument
Before beginning the configuration process, you should know whether you will be
attaching your Workstation and 3800 or 3900 GC to a company network or an
isolated network only used for instrument control. If you have a Network
Administrator on site, you may wish to ask which configuration is recommended.
Use this table to determine the order in which you should read the following
sections.
1. If an Ethernet card has not been installed and configured on your PC, read
Installing and Configuring the Ethernet Card in Your PC and one of the
following:
- No Company Network: Configuring TCP/IP Parameters with no
Company Network.
- Company Network: Configuring TCP/IP Parameters for a Company
Network.
2. Read Connecting Your 3800 or 3900 GC to Your PC or Network.
3. If you have not already installed the Varian MS Workstation, do so before
proceeding.
- No Company Network: Read Configuring the 3800 or 3900 GC
Communication (No Company Network).
- Company Network: Read Configuring the GC for a Company Network.
4. Continue reading the rest of the sections, starting with Adding a GC and
Varian MS to the Instrument in System Control.
5. Installing and Configuring the Ethernet Card in Your PC.
NOTE: The following section describes a procedure that is relatively generic;
consult your Windows documentation and that of the Ethernet cards
manufacturer for more detailed explanations.

26
Refer to the installation instructions packaged with your Ethernet card for
information on installing the Ethernet card in your computer. Before proceeding,
your Ethernet card should be recognized by your Windows version. When done,
the Network Neighborhood icon should appear on your Windows desktop.
NOTE: For the following procedure, the use of disks other than the ones that
were used for the original Windows installation may result in a Ethernet driver
version mismatch that keeps Windows from starting. Should this occur, it may be
necessary to remove the Ethernet Board from the computer to remove the
incorrect Ethernet drivers.
You must configure your computers network settings to allow communication
with the 3800 or 3900 GC. You do so by running the Windows Control Panel.
1. Run the Control Panel by selecting it from the Start menu (under Control
Panel or Settings).
The Control Panel window is displayed.

2. Double-click the Network icon to set your Network options.

27
The Network dialog box is displayed.

3. If TCP/IP is already listed in the list of network components, skip to the Note
after step 5, otherwise, click Add.
The Select Network Component Type dialog box is displayed.

4. Select Protocol and click Add.

28
The Select Network Protocol dialog box is displayed.

5. Select Microsoft as the manufacturer. Select TCP/IP as the protocol. Click
OK. The protocol is added to your installed network Component list.
NOTE: If you are not connecting your Workstation to a company network (that
is, you are not assigned an IP address by a Network Administrator), follow the
next three steps. If you are connecting your Workstation to a company network,
skip to Configuring the GC for a Company Network.
Configuring TCP/IP Parameters with no Company
Network
The following three steps assume you have completed steps 1 through 5 from
the previous procedure.
1. Select TCP/IP from the network components list and click Properties. The
TCP/IP properties dialog box is displayed.

29

Enter an IP address in the range 10.2.128.1 through 10.255.255.254. Note that if you
are adding more than one Workstation to this network, each Workstation PC must
have a unique IP address within this range. The Subnet Mask will be automatically
set to 255.0.0.0. Do not change this value.

30
Ensure that no entries have been made in your Gateway, and that Domain Name
Server (DNS) and WINS Configuration have been disabled. These entries are not
used in an isolated network and may cause problems if they are present. Delete
any settings that may have been entered from a previous configuration.
2. Click OK. Reboot Windows for the changes to take affect.
NOTE: Refer to Communication Problems in the Diagnostic and
Troubleshooting section for information about diagnostic tools to verify that your
network installation is correct.
Configuring TCP/IP Parameters for a Company
Network
The following three steps assume you have completed steps 1 through 5 from
the previous table.
3. Select TCP/IP from the network components list and click Properties. The
TCP/IP properties dialog box is displayed.

Enter the IP address to be used by this Workstation. Contact your Network
Administrator (or whoever assigns IP addresses in your network) to get the
appropriate address. Note that each Workstation PC must have a unique IP
address. Enter the appropriate Subnet Mask to be used with this IP address.
4. Your Network Administrator may instruct you to obtain an IP address
automatically by selecting the appropriate radio button.

31

Contact your Network Administrator (or whoever assigns IP addresses for your
network) to see what the appropriate settings are for your Gateway, and whether
Domain Name Server (DNS) and WINS Configuration are needed.
5. Your Network Administrator may also instruct you to specify parameters in
the Bindings and Advanced tabs.
6. Click OK. Reboot Windows for the changes to take affect.
NOTE: Refer to Communication Problems in the Diagnostic and
Troubleshooting section for information about diagnostic tools to verify that your
network installation is correct.
Connecting Your 3800 or 3900 GC to Your PC or
Network
Refer to the Installation Instructions for the 3800 GC Communications Board
(packaged with the 3800 GC Communications Kit) for details on adding the
communications board to your 3800 GC (if not previously installed). Also, refer to
the Communications section of the 3800 GC Operators Manual or 3900 GC
Operators Manual for instructions on connecting your GC to the PC or a
company network. Before proceeding, your GC should be connected to your PC
or network.

32
Configuring the 3800 or 3900 GC Communication (No
Company Network)
Use the following instructions if either a 3800 or 3900 GC and Varian MS
Workstation PC are being connected to an isolated network, that is, a network
dedicated to Varian MS Workstations and the instruments they control. In this
case, a Network Administrator will not be involved in assigning IP addresses.
NOTE: If you are connecting your 3800 GC and Varian MS Workstation PC to a
multi-purpose company network managed by a Network Administrator, refer to
Configuring the 3800 or 3900 GC Communication (No Company Network).
You may connect one 3800 GC directly to one Workstation

After you have configured your computers network settings start System Control.

Click System Control/ Automation.
When System Control has started for the first time, the Star Assistant
Communication Configuration Wizard will appear to guide you through the setup
and network connections of your 3800 GC. Use the following procedure for
configuring the IP address for your GC.
The first time the Star Assistant guides you through the setup of your 3800 you
will get the following messages:

Read the description presented in each window and click Next.

33

From the Setup Ethernet Ports, click Setup for IP Address Management [BOOTP
Server].

Click Setup.
When the Setup BOOTP Server dialog box is displayed, turn on the 3800 or
3900 GC that has been connected to the network.
NOTE: If more than one Workstation is being connected on the same network,
only one Workstation should manage the IP addresses for all GCs connected (all
others should have the Manage IP addresses from this Workstation checkbox
unchecked). If more than one Workstation is managing IP addresses, naming
conflicts may arise.
As the GC is powered on, an entry is added to the table. For each entry, an IP
address is automatically assigned. For each GC, you provide a host name that
will be used to identify it in the Varian MS Workstation.

34

Click the Manage IP addresses from this Workstation checkbox to manage your
GCs IP address from this Workstation. As the GC is turned on, its Ethernet address
is added to the list.. The IP address is automatically generated. Enter a host name for
each GC. This name is used to identify the GC in the Workstation. You cannot
connect to a GC until you provide it a name. Click OK after entering host names
for each GC.
NOTE: Proceed to Using a Password to Protect BOOTP Settings.
Configuring the GC for a Company Network
Use the following instructions if either a 3800 or 3900 GC and Varian MS
Workstation PC are being connected to a company network, that is, a multi-
purpose network used for services in addition to instrument control. In this case,
a Network Administrator will be involved in assigning IP addresses. If the GC and
Varian MS Workstation computer are the only devices being connected together,
refer to Configuring the 3800 or 3900 GC Communication (No Company
Network).
You may connect virtually any number of 3800 and 3900 GCs and any number of
Varian MS Workstation computers to a company Ethernet network.
Depending upon your network configuration, all Varian MS Workstations will be
able to control all 3800 and 3900 GCs on the network.
After you have configured your computers network settings start System Control.

35
Click System Control/Automation.
When System Control has started for the first time, the Star Assistant
Communication Configuration Wizard will appear to guide you through the setup
and network connections of your GC.
NOTE: Before proceeding with this section, consult your Network Administrator
about whether a central BOOTP Server is available on the network.
1. If IP addresses are managed by a central BOOTP Server, then proceed
to Specifying IP Addresses from a Central BOOTP Server.
2. If IP addresses are specified by a Network Administrator but not centrally
managed, then continue reading Specifying IP Addresses from System
Control.
Specifying IP Addresses from System Control
The Varian MS Workstation can be used to specify IP addresses to 3800 and
3900 GCs attached to the network.
Use the following procedure to manage IP addresses form System Control.
The first time the Star Assistant guides you through the setup of your GC you
will get the following messages:

Read the description and click Next.

36

From the Setup Ethernet Ports dialog box select Setup to display the BOOTP
Server dialog box.

Select Setup to display the BOOTP Server dialog box.
The BOOTP Server dialog contains a table listing all 3800 and 3900 GCs to
which IP addresses may be assigned.

37
NOTE: If more than one Workstation is being connected on the same network,
only one Workstation should manage the IP addresses for all GCs connected (all
others should have the Manage IP addresses from this Workstation checkbox
unchecked). The Workstation acting as BOOTP Server must remain running all
the time to allow other Workstations to connect to GCs. If more than one
Workstation is managing IP addresses, naming conflicts may arise.

Check this box to enable the BOOTP Server.
If 3800 or 3900 GCs are already connected to the network and powered on, their
Ethernet addresses will appear in this table.
You must enter a name for each GC. The IP address will not be assigned to the
GC until a name is entered.
You may manually assign any IP address to any GC. When this item is selected, type
the IP addresses directly into the table. Select OK when all addresses and names
have been entered.

38
When the Assign # IP addresses starting from: #.#.#.# radio button is selected,
the bottom portion of the dialog changes.

You may select to consecutively assign IP addresses beginning from a particular
address. Enter the number of IP addresses you want to assign automatically. Enter
the starting address here. As 3800s are powered on, IP addresses are automatically
assigned starting with this address.
NOTE: Proceed to Using a Password to Protect BOOTP Settings.
Specifying IP Addresses from a Central BOOTP
Server
If IP addresses are managed by a Network Administrator from a central source,
the 3800 and/or 3900 GCs must be added to the list of devices requiring IP
addresses. IP addresses must be assigned to GCs using a BOOTP Server. A
BOOTP Server lists Ethernet addresses (which are unique to each
communication card installed in each 3800 and 3900 GC) along with the IP
addresses that are to be assigned to the corresponding device. You may obtain
the Ethernet address for each GC from the GCs front panel or the label on the
Ethernet card within the 3800 GC. Turn on the 3800 GC and press any key to
allow it to start in local mode. The Ethernet address will be automatically loaded
into the BOOTP Server list for 3900 GCs.
ENTRY
TABLE EDIT
PAGE CURSOR
NEW
LINE
HELP UNDO
DELETE
LINE
CLEAR
TABLE
ENTER DECR INCR
SAMPLE
DELIVERY INJECTOR
GC CONTROL INSTRUMENT
FLOW/
PRESSURE
COLUMN
OVEN DETECTOR OUTPUT
METHOD SEQUENCE
SELECT/
EDIT
PRIORITY SAMPLE
SUSPEND RESUME
METHOD
AUTOMATION
ACTIVATE
SINGLE METHOD
EDIT MENU
NOT
READY READY RUN
START STOP
STATUS SETUP
MENU

When the GC has completed its initialization process, press the menu button.

39
The Instrument menu is displayed. Press 1 to select the Remote/ Local Control
screen. The Ethernet address, IP address and Alias (which may not yet be
assigned) are displayed.
ACTIVE
METHOD
EDIT
METHOD
CTRL RUN
TIME
END
TIME
Method 1 Method 1 0.00 20.00
REMOTE / LOCAL CONTROL
Enable
Ethernet Address: XX:XX:XX:XX:XX:XX
IP Address: XXX.XXX.XX.XXX
Alias: 3800A

Use the Ethernet address shown here when setting up the BOOTP Server. The IP
Address and Alias (host name) are assigned by the BOOTP Server.
If the BOOTP Server that you are using automatically updates its table with
Ethernet addresses broadcast by devices on the network, then the Ethernet
addresses from 3800 and 3900 GCs connected to your network and powered on
will automatically appear. Note that the frequency with which these addresses
are broadcast by the GC decreases over time to a maximum rate of once per
minute. This means that the BOOTP Server may not receive an Ethernet
address for up to a minute from any given GC.
If you are using a 3800 GC on a 2000R system and the BOOTP Server that you
are using does not automatically update its table with Ethernet addresses
broadcast by devices on the network, then the Ethernet address can be obtained
from the label on the Ethernet card in the 3800 GC.
Once you have entered the Ethernet address for each GC on the network to the
BOOTP Server, power each GC off then on again. Check that the IP address
shown on the front panel of each GC (in the Remote/Local Control screen)
matches the intended address entered into the BOOTP Server. If they do not
match, verify the Ethernet address, updating the BOOTP Server if necessary.
Powering the GC off and on will update the IP address.
NOTE: When IP addresses are managed from central location by a Network
Administrator, the BOOTP Server on your workstation must be disabled. Verify
that the Manage IP addresses from this Workstation is unchecked in the Setup
Ethernet Ports dialog box.

Using a Password to Protect BOOTP Settings
You may wish to restrict access to the BOOTP Server dialog box to avoid
inadvertent or unauthorized changes to IP address assignments. To do so,
enable password protection in the BOOTP Server dialog box. If the Setup

40
Ethernet Ports dialog box is not displayed, select the Setup Ethernet
Communications menu item from the Instrument menu to display the Star
Assistant Communication Wizard. Click Next.

Select Setup to display the BOOTP Server dialog box.
The BOOTP Server dialog is displayed.

Check this box to enable password protection.
The next time you enter the BOOTP Server dialog box from the Setup Ethernet
window, you will be prompted for a password.

Enter a password here. Once successfully entered, you may change the password
below. Enter a new password here twice.
The initial password is blank (no password). To set your password initially, enter
the desired password in the Enter new password and Re-enter new password
fields. Subsequent entry into the BOOTP Server will require this password.
NOTE: Refer to Recovering a Lost Password for BOOTP Server Access in the
Diagnostics/Troubleshooting section for instructions on resetting the password.

41
Adding a GC and Varian MS to the Instrument in System
Control
Once you have configured your Workstation computer and 3800 or 3900 GC for
network communication, you may select one GC to be controlled from each
Varian MS Workstation.
If it is not already running, start System Control. The Star Assistant
Communication Configuration Wizard will be displayed if you have not yet
configured your GC Ethernet connections. Click Next.

Click Address to attach to a 3800 GC on the Ethernet network.
When the Address button is selected, the Module Selection dialog box is
displayed.

Select the GC that you wish to connect to the address (44). Click OK.
NOTE: If you are running on a company network, only GCs on the same local
subnet appear in the Select Available Modules dialog box. To connect to a GC in
a different subnet, type its IP Address directly into the IP address field in the
Setup Ethernet Ports dialog box. Consult your Network Administrator about
subnets on your network.
After you have completed your selection, the Setup Ethernet Ports Dialog Box
shows the 3800 GC connected to your Workstation.

42

This 3800 GC is connected to Port 44. The status indicates the availability of the GC.
The IP address of the GC is shown here. Click OK, and wait for the 3800 to connect.
When the GC connects to System Control, it will be represented by an icon at the
bottom of the Configuration Window. The icon will have a label reading 3800.44,
and will include the Host Name of the GC appended to the label. The number 44
is a System Control communication addresses that correspond to the Ethernet
port connected to the device. The same principles are true for the 3900 GC.
Modules and Instruments Defined
The Varian MS system consists of two modules, the 3800 GC and the 2000 MS.
Additionally, a third module is present if you have the 8200 AutoSampler (Note
that the CP-8400 and CP-8410 AutoSamplers will not have a separate icon but
will be included on the 3800 or 3900 Status and Control Window). These
modules also have addresses and the message logs frequently refer to the
module and address. The modules and allowed addresses are listed below.

Module Name Address
Mass Spectrometer 2000 40
Gas Chromatograph 3800 44
AutoSampler 8200 26

Other communication addresses are used for different types of communication
hardware: 16,18,20,22 for Varian ADC Boards; 17,19,21,23 for Varian 3400 and
3600 GCs, and 24 - 39 for Serial Port devices.
If an 8200 AutoSampler is attached to the J4-SID1 connector on the 3800 GC,
the 8200 icon will also appear with the Host Name of the corresponding GC
appended to the label.
NOTE: Refer to the 8200/SPME AutoSampler for 3800 GC Manual for
information about configuring your 8200 for use with the 3800 GC.

43
Elements of the Configuration Screen
After the 3800 or 3900 connects to System Control, configure it in an Instrument
by moving its icon from the bottom of the Configuration Window into the
Instrument Area. System Control will remember where to put the icon the next
time that the 3800 connects.
If the 3800 is to be operated with an 8200, make the 8200 the AutoControl
Module. Place the GC icon in the AutoControl Module if either a CP-8400 or CP-
8410 AutoSampler will be used with the GC. If the 3800 or 3900 is to be
operated without an AutoSampler controlled from the Varian MS Workstation,
leave the AutoControl Module box empty. If you are using a sampling device with
the 3800, the device must be connected to the synchronization port of the GC.

The Varian MS is usually configured into 2 modules, the 2000 and the GC.
Additionally, an 8200 AutoSampler can also be part of the system. After each
module connects to System Control, configure it in an Instrument by moving its
icon from the bottom of the Configuration Window into the Instrument Areas.
System Control will remember where to put the icon the next time that the system
connects.

44

Instrument Parameters, Instrument Name, Operator Name, and Instrument status are
listed here. AutoStart Module area. Place the 8200 AutoSampler Module icon in this
box. Module icon showing that 3800 GC Module 44 has been configured to
Instrument #1. Click button to enter or change the Instrument Name, Operator Name,
and Maximum allowable error count. Modules that have logged in and are available
for configuration into an instrument are displayed here.
Once the modules are in place you are ready to proceed.
Setting Instrument Parameters
Some parameters used by the Instrument are set in the Instrument Parameters
dialog box accessed from the Configuration window.

The instrument name appears on reports and in the instrument window. The
operator name appears on reports. The Ready File is used only with older Varian

45
software versions (i.e. the forth software system). When the maximum number of
non-fatal errors is exceeded during automation, the automation sequence halts.
Setting this value to zero disables this feature. You are optionally prompted for
this information when you start an automated sequence of injections or
recalculations.
Running an MS Method Without a GC Method
To run an MS method without the GC module or GC method, open System
Control. Under the menu Instrument, select Configuration. Move the GC icon
from the mid field to below the bar labeled Available Modules, by click, drag and
dropping the icon . When a MS method is activated, the GC method will not be
downloaded. To activate the GC and AutoSampler modules, click-drag-drop the
icons into the active field.
NOTE: If an AutoSampler icon is present: click, drag and drop the AutoSampler
icon in the Available Modules area.

46

47
2000 MS Instrument Control
Command Reference
Saturn Module Dialogs
Saturn Module Keypad Dialog

This dialog can be hidden by clicking on Hide Keypad.

48
Spectrum Toolbar

Click the green arrow t hide the toolbar. Click the upper left of the full
screen display to restore the toolbar.
Click full scale to normalized to chromatogram. Double-clicking the
chromatogram does the same.
Click to return the xy axes to the previous scale.
Click spectrum plot to open a preview of the spectrum.
Click scale to choose between Auto Scale and Fixed Scale Intensity.
Click mass range to choose between Acquired Mass Range, Fixed
Mass Range, or Maximum.
Click to switch graphics or text displays of ion intensity and status
information.
Click select preferences to change the color of the chromatogram display,
labels, axes, font, and other features.
Click Report Preferences to choose the chromatogram and spectra
options for the standard report.
2000 Module Window

49
Item Description
Manual Control Click the Manual Control to turn on or off the trap controls (rf,
Filament, and Multiplier) and to open the CI and Cal gas valves.
Also adjust the rf response, the CI gas pressure, and the Cal
gas pressure. This mode is also used to select the current trap
filament and to adjust the axial modulation voltage. Although
scans may be taken and displayed under method conditions of
any one of the MS Method segments, data may not be acquired
while in this mode. To acquire data, Acquisition Mode must be
selected.
Auto Tune Tune the instrument, including the multiplier setting, mass
calibration, and trap function calibration.
Temperatures Change the temperature of the ion trap or transfer line. Do
bakeout to remove volatile materials absorbed on electrode
surface.
Diagnostics Check the system for status and faults.
Shutdown Shutdown for routine maintenance or for an extended period.
Acquisition Acquire data for a single sample or an automated list .
Manual Control

Ion trap schematic
Item Description
On/Off Turn on or off the ion trap (the filament, rf and multiplier).

Turn on or off the rf

Turn on or off the filament.

Turn on or off the multiplier.

Open the valve to turn on the CI gas.

Open the valve to turn on the Cal gas.
Hide Keypad Remove the upper portion of the screen display so that the
lower portion is expanded.
Display Selection Select from to view the spectrum in profile or centroid mode.

50
Instrument Settings

Item Description
Method button Opens the Method Editor program.
Segment # box Select the current segment of the active method.
Scan Mode Ionization mode of the current segment, such as EI-Auto.
Ion Prep. Ion preparation method of the current segment, such as
MS/MS.
Setpoints tab

Item Description
Filament Selection Click to select the current filament. Saturn has 2 filaments so
the system can be used if one burns out.
Axial Modulation
Voltage
Select the voltage to apply to the upper end caps. Recalibrate
the mass axis when you change this value.
Apply button Apply changes you make to the Axial Modulation Voltage. If the
voltage edit control has the focus, press enter to apply the
changes.
Adjustments tab

51
Item Description
Adjust Cal Gas Click to adjust the cal gas pressure.
Adjust rf Ramp Change the rf setting for the instrument by turning the screw at
the bottom front panel.
Adjust Set the proper CI reagent pressure for CI analysis. The
pressure is very dependent on the reagent gas used.
Reagent Gas
Selection Box
Choose which CI gas you are using.
Done Used when you complete your adjustment.
Status

Item Description
Mode State Indicates what function the Saturn MS is currently performing, such as
scanning or adjusting cal gas.
Fault State Indicates if a fault has occurred.
Ion Time Indicates the ionization time of the last scan.
Ion Count Indicates the ion count of the last scan.
Auto Tune

52

Item Description
Start Auto Tune Begins the event sequence that will tune the instrument. Only
checked boxes will be executed.
Reset Stops the auto tune process.
Continue Starts the next selected function if the single step option has been
checked.
Hide Keypad Causes upper portion of the screen to be removed so that the lower
portion can be expanded in the display.
Display
Selection
Select the display.
Method

Item Description
Air/Water Check Measures the air and water content of the trap, to
determine if there is a leak.
Electron Multiplier Tune Autoset the electron multiplier voltage.
FC-43 Mass Calibration Calibrate the mass axis. Choose Straight Line or FC-43.
Trap Function Calibration Calculate the waveforms for CI, MS/MS and SIS.
Single Step Observe each step in the auto tune process. Use Continue
to proceed after each step.
Set Points

53

Item Description
Electron Multiplier Voltage Manual adjustment of the Final Gain Setting determine
from the Auto Tune check.
SIS Amplitude Adjust
Factor
Adjust each trap system for optimum ion sensitivity and
ejection. The voltage adjustment range is between 50 to
200%. The default is 100%.
Temperatures

Item Description
Start Bakeout Execute the bakeout conditions, which removes volatile
material from the ion trap surface.
Reset End a bakeout before the specified time.
Hide Keypad Hide the upper portion of the screen and expand the lower.
Analysis Conditions Set temperature for trap, manifold and transfer line. Click
Apply to initiate conditions.
Bake out Conditions Hold Time specifies the number of hours for bake out. Under
Trap, set the bake out temperature, such as 220 C. The
manifold bakeout temperature is fixed. The transfer line
bakeout temperature matches the analysis temperature.
Diagnostics Mode

54

Item Description
Start Click Start to execute the desired test
Reset Cancel a test executed with Start.
System Test

Item Description
Run To Completion Click to run all tests without stopping.
Halt On Error Halts the system checks when an error is detected.
Detailed test of the heater zones

Item Description
Trap Tests the Ion Trap heater element May take up to 13.5
hours to complete.
Manifold Tests the Manifold Heater element.
Transfer Line Tests the Transfer Line heater element.

55
Monitor Window

Item Description
Multiplier check box Display the voltage (center left) on the
multiplier when on.
rf check box For Service Engineers.
Filament check box Display the status of the system filaments
(upper right).
Ion gauge check box View the vacuum status using the filament
selected by the Filament Radio Button.
Filament Select a filaments and view the ion gauge
vacuum system test.

Shows current temperature readings for each zone

56
Shutdown Mode

Item Description
Shutdown button Shuts down the system in an orderly manner. The pump
speed is slowly reduced and the heaters are turned off so
that the system slowly cools.
Reset button Brings the system back to a ready state if the Shutdown
procedure was started. This restarts the pumps and turns
on the heaters.
Diffusion Pump Shutdown Sequence

NOTE: The Diffusion Pump System shutdown sequence takes at least 30
minutes:
- The Saturn GC/MS heaters are turned OFF.
- The GC temperature zones should be cooled downed before maintenance is
performed.
- The diffusion pump heater is turned OFF while the Peltier Baffle cooler is
kept on. The DIFFUSION PUMP STATUS changes from NORMAL to
COOLING. After 15 minutes, when there is no pump vapor to contaminate
the system, the Peltier Baffle cooler is turned OFF. After another 15 minutes,
the cooler has warmed to the point that it wont condense water vapor, and
the pump is considered to be off. The DIFFUSION PUMP STATUS then
changes from COOLING to OFF.
NOTE: If the word FAULT! is displayed in the Vacuum Status box, click
Diagnostics for detailed information.
The Vacuum Status represents the state of the diffusion pump. To precisely
identify the problem, the USER should go to the Diagnostics mode and run
"System Test to Completion. Fault messages may appear on startup or during
normal operation.

57
Turn OFF main power by placing switch at rear of system into OFF (down)
position. Manually vent the system for at least 5 minutes using the lever on front
panel.
NOTE: DO NOT ATTEMPT to VENT SYSTEM by any other method (via transfer
line, foreline vacuum clamps, etc.). Rapid, improper venting of the system will
cause diffusion pump fluid to backstream into the manifold and ion trap.
Maintenance procedures SHOULD NOT BE attempted until the shutdown
program has finished!
Acquisition Mode

Item Description
Start Acquisition button Click to start the analysis.
Reset button Will end the acquisition and reset the
conditions to their initial conditions.
End time button Click to increase or decrease the end time of
the analysis.
Hide Keypad button Causes the upper portion of the screen to be
removed so that the lower portion can be
expanded in the display.
Display Box Selector Allows you to choose among chromatogram,
spectra, or both.
Method button Used to open the Method Editor with the
active method. You can edit the method and
then return to this screen for analysis.

58

59
2000 MS Instrument Window
The 2000 MS Instrument Window

System Control has four major sections: the System Control Menu bar, System
Control Toolbar, Saturn Keypad Dialog, Chromatogram and Spectrum Toolbar,
and Spectrum Display.
File Menu

60
Activate Method allows you to choose a method from those already prepared.
This will set the conditions for the GC, MS, AutoSampler and data handling.
Other sections will also be activated if they are part of the method.
Upload Active Method from Modules will allow you to get the conditions from the
existing modules to be saved in a new method. Whichever method is active will
now be converted to the conditions of the active modules.
New Sample List allows you to open the dialog box to create a sample list.
Open Sample List allows you to select and activate an existing sample list. The
sample list dialog box is shown below.

New Recalc List allows you to open the dialog box to create a recalculation list.
Open Recalc List allows you to select and activate an existing recalculation list.
The Recalc list dialog box is shown below.
NOTE: You may process a Recalc List either in System Control (by clicking the
Begin button) or in SaturnView. In SaturnView use the menu command
Quantitation Process/Review Recalc List to access this feature. Also note
that processing of a Recalc List takes more time when done from System Control
but has the advantage of allowing AutoLink functions such as automated
reporting with SaturnWriter templates.

New Sequence List allows you to open the dialog box to create a sequence list.
Open Sequence List allows you to select and activate an existing sequence list.
The sequence dialog box is shown below.

61

Edit Menu
Click the Edit menu and highlight Edit Module Info.

Each module in your system (3800GC, 2000MS, 8200 AutoSampler) contains its
own message log and documentation screen. The Module Documentation
screen shown below allows you to keep a record of performance, maintenance,
hours used, or any other comments you wish to make.

Use the Add, Edit, and Delete buttons to record any information you wish about
the MS module.

62
Inject Single Sample Menu

The command will allow you to give the sample information prior to an injection.
The dialog box below will appear when this command is invoked. The 2000
module window must be in acquisition mode for the system Not Ready to convert
to Ready and then a manual injection can be made. If an AutoSampler is used,
click Inject in the bottom left corner.

The sample type can be changed by double clicking in the field below Sample
Type. The following displays your choices.

The same procedure can be used for injection notes. Any notes that you wish to
enter here will be saved with the data file. The AutoLink button works in the same
way. Note the picture below.

A command can be entered here to execute a program once the data file
acquisition is completed. For example, this can be a program to activate Saturn
Writer to print the sample reports. To run a SaturnWriter report in automation
enter the directory path and the name of the SaturnWriter template (for example
C:\VarianMS\EPA525.swt). Note that SaturnWriter templates should always be
stored in the VarianWS directory. The browse command can be used to select
the command executable file. Select OK when you have made your selection.

63
Automation Menu
Below is a picture of the Automation pull down menu and a description of the
functions.

Begin Sample List will cause an automation to start at line 1 and end at the last
line.
Begin Sequence will allow you to change methods and sample list during an
automation. An example of this might be to run a set of samples using EI and
then the same set of samples using a different MS method for CI.
Begin At starts an automation at a particular line and runs until the last line is
completed.
Suspend Automation stops an automation at its last completed sample.
Resume Automation starts the automation after it has been suspended. It starts
where it was suspended.
Stop Automation ends the automation action.
Reset Modules brings the various modules to there ready states.
Enable Automated Printing allows the printer functions to work during an
automation.
Recalculate Menu

The above picture highlights the Recalculate pull down menu. Note that
recalculation may be performed here in System Control or in SaturnView under
the menu command Quantitation Process/Review Recalc List. Also note
that processing of a Recalc List takes more time when done from System Control
than in SaturnView but has the advantage of allowing AutoLink functions such as
automated reporting with SaturnWriter templates.

64
Begin RecalcList will allow you to start an automated recalculation. A
recalculation list must already be prepared and selected to do this. A New Recalc
list may need to be made.
Begin at Selected RecalcList Line allows you to process a recalculation list
starting with a chosen line and proceeding with the rest of the list.
View Calibration Curves will allow you to view any of the curves for the calibrated
compounds in the active method. An example of the calibration curve screen is
given below. For a complete explanation of this screen, go to the Quantitation
section.

Instrument Menu
The pull down Instrument menu:

Saturn GC/MS #1 denotes that this is the instrument configured.
Configuration allow you to add new modules to the existing instrument. This is
necessary if additional hardware is added such as an additional GC detector.

65
Instrument 1 Faults allows you to see if there are any faults in any of the modules
contained in Instrument 1. An example of this screen is shown below. The
update key will allow you to periodically check for new faults without opening and
closing the dialog box. 2000 faults are not reported in this window.

Setup Ethernet Communication will allow you to set up the communication
between the 3800 GC and System Control.
Windows Menu
The pull down menu titled Windows allows you to view any of the windows
associated with the system control. This list is shown in the picture below.

Show Module Windows allows you to see all of the module windows that are
configured in the instrument. In this example the module available is the 2000.
Iconize Module Windows causes the individual module windows to become icons
at the bottom of your screen.
Show Automation Windows allows you to view any of the automation screens.
These are the Sample list, Recalc list, and Sequence list.
Arrange Icons arranges the icons, if any, in a row at the bottom of the System
Control window.
Sequence List allows you to display the active sequence list.
Sample list allows you to display the active sample list.
Recalc list allows you to display the active recalculation list.

66
Instrument 1 Status allow you to view the status of the modules connected to the
system.
Message Log allows you to view the event log for the MS module. The log
display is shown below. All error messages for the Saturn Module will show up
here.

2000 module allows you to display the Saturn module control screen.

Help Menu

Click an item in the Contents box to open online help.

67

In the Help dialog box, from the Index tab, you can select a particular topic. Click
the selection, go to the bottom of the screen and click Display.

68

System Control Toolbar
The system control toolbar is located near the top of your screen. A picture of
this toolbar is displayed below.

Clicking on this button will allow you to create a new automation file.
Clicking on this button will allow you to select a new automation file.
Clicking on this button will allow you to view/edit or print a
method.
Clicking this button will allow you to activate a method.
Clicking on this button will allow you to edit notes for an automation file.
Clicking on this button will allow you to edit module information for any
module that is online such as the 2000, 3800GC, or 8200 AutoSampler.
Clicking on this button allows you to inject a single sample.
Clicking on this button allows you to start a recalculation list if you have one
active.

69
Clicking on this button allows you to start a sample list that you have
created. The list must already be selected.
Clicking on this button allows you to start a sequence list that has been
created.
Clicking on this button allows you to suspend a list that is running.
Clicking on this button allows you to begin a list.
Clicking on this button is used to stop a list that is already running.
Saturn Module Keypad Dialog

This dialog can be hidden by clicking on Hide Keypad.

Click Show Keypad to display Saturn Module Modes : Manual, Auto Tune,
Temperatures, Diagnostics, Shutdown, and Acquisition. See Saturn Module
Modes for details.

70
Spectrum Toolbar

Click the arrow to hide the toolbar. Click the upper left of the screen to
restore the toolbar.

Click full scale to normalize the chromatogram in the vertical and horizontal
directions. Double-click the chromatogram to do the same.
Click this to return the xy axes to the previous scale.
Clicking on the spectrum plot button will cause a window previewing the
spectrum to be displayed.
Clicking on the scale button allows you to choose between Auto Scale
Intensity and Fixed Scale Intensity.
Clicking on the mass range button allows you to choose between
Acquired Mass Range, Fixed Mass Range, or Maximum.
This button allows you to switch between graphics and text displays of
ion intensity and status information.
Configuring the Real-Time Chromatogram Display
Before performing an analysis the MS module window must be in acquisition
mode. To enter this mode, click Acquisition. During an analysis, observe the
chromatogram in the system control screen. From the following list box ,select
the Chromatogram, Spectrum, or both to be displayed.

71
Choosing the Chromatogram only option will allow you to see a live
chromatogram as in the example below.

Click Hide Keypad to expand the chromatogram. Notice in the following picture
the text information at the top is hidden.

To bring the keypad display back, click Show Keypad.
Configuring the Real-Time Spectrum Display
During an analysis it is possible to observe the spectrum in the system control
screen. However, if there are insufficient processor resources, the spectrum
control will not be updated until those resources become available. Selecting the
time selector mode in the chromatogram display will also stop the real-time
update of the spectrum display. In the picture below the drop down list box allows
the selection of Chromatogram, Spectrum, or both to be displayed.

72

Choosing the Spectrum only will allow you to see a live spectrum as in the
example below.

Click hide keypad to expanded the display.

73

Click Show Keypad to display the keypad.
Status and Control Window
You are now ready to program the GC/MS to perform fully automated data
acquisition. Initially the MS Module Window will look similar to the figure below. If
you do not see this screen, go to the pull down menu labeled Instrument, and
select the item Saturn GC/MS.

The upper left side of the window shows the ion trap schematic, which allows the
ion trap to be turned on. If the trap is displayed in red, it is currently disabled. The
trap is disabled if the current segment is a filament/multiplier delay segment, one
with an ionization mode of none, or if a fault has occurred. If the ion trap icon is
not currently disabled, clicking in the center of the ion trap will turn on the trap.
The black schematic will turn green to denote that it is on, as displayed below.

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You must select a method segment that is not a Filament/multiplier delay
segment for the ion trap to be enabled. This method and segment selection is
located in the center of the screen. This center section deals with the active
method and the instrument set points.
The ion trap symbol is a pictorial representation of the ion trap showing the
endcaps (two horizontal curved lines), the rf-voltage ring electrode (two vertical
curved lines), the electron multiplier (a curved cone), the filament (a triangle), the
tank for the CI reagent gas, and the reservoir for the calibration compound. By
clicking on the appropriate part of the ion trap symbol, or by clicking on the
corresponding button, you can turn on and off the various parameters shown in
the symbol (i.e. click triangle to turn on filament). Click in the center of the trap
and the Cal Gas bulb, a spectrum of PFTBA will be displayed.

Method

Now notice the three tabs in the center of the System Module: Method,
SetPoints and Adjustments. There is always an active method controlling the
GC/MS system. This method is the last method selected from a previous use or
the default method if the instrument is just being configured. In the default
method, the first MS Method Segment defines a "Filament/Multiplier Delay."
When such a segment is active, the trap controls are forced off and scans are
not taken to protect the trap from solvent peaks that elute shortly after injection.
This kind of segment is specified in the method by selecting an Ionization Mode
of "None." When such a segment is active in Manual Control, the trap icon
appears red, indicating that the trap is off and that its state cannot be changed.
To actually take (and display) scans, an MS Segment must be specified that has
an Ionization Mode of other than "None." Once this is done, the color of the trap
icon will return to black and the trap may again be turned on by clicking on the
trap icon. (Note that the trap icon may also temporarily appear red while the
system is initializing). Below the method button is the segment number. Click the
up arrow to select segment 2. See Saturn Method Editor for more information on
methods.

75

The informational fields displayed in the above dialog are taken from the
currently executing method.
The Scan Mode describes the ionization mode of the current segment, for
example, EI-Auto.
The Ion Prep. is the ion preparation method of the current segment, such as
MS/MS.
The Range will show the mass range being scanned by the current segment.
Operating Conditions
The Operating Conditions located to the far left of the Saturn Module window
allows you to observe the current instrument information.

The Mode State will indicate what function the Saturn MS is currently performing
such as scanning or adjusting cal gas.
The Fault State will indicate if a fault has occurred.
The Ion Time indicates the ionization time of the last scan.
The Ion Count indicates the ion count of the last scan. If profile mode is selected,
this is the total ion count. If centroid mode is selected, this is the reconstructed
ion count.
SetPoints
The SetPoints tab allows us to select the filament and the axial modulation
voltage. Clicking on that tab will bring up the following screen.

76

Two filaments are provided to reduce down time for maintenance. The selection
of the filament is made by choosing the radio button. The Axial Modulation
voltage can be changed by using the up/down arrows and then clicking the apply
button.
The Axial Modulation Voltage is applied to the endcap electrodes as described in
the section Saturn Method Editor. Proper setting of this voltage is critical to
resolution and sensitivity in the ion trap. In most cases, the best Axial Modulation
voltage is the lowest value at which there is still good resolution of the 131/132
and 414/415 cal gas peaks. For most instruments this value will be between 2
and 4 volts.
The Axial Modulation voltage must be adjusted to its proper value before the
AGC target TIC is determined and before the mass calibration is done.
If the value of the Axial Modulation voltage is too low, high molecular weight ions
will not be observed. If the value for the Axial Modulation voltage is too high, the
peak widths for low molecular weight ions will be broadened and mass
misassignments may occur.
NOTE: The mass calibration must be done if the axial modulation setting is
changed. See the autotune section for mass calibration.
Adjustments
The third tab is the Adjustments tab. Clicking on this tab will bring up the screen
below.

This tab is used to adjust the Cal gas pressure, the CI reagent gas pressure,
select the CI reagent, and to adjust the rf ramp.
When you select Adjust rf Tuning Ramp, you obtain a screen from which you
can determine if the rf voltage is in tune throughout the entire mass range of the
Saturn GC/MS. This is done by observing the rf modulator response.

77

When the rf Modulator Response screen is displayed, it shows a real time view
of the rf modulator response from 20 to 650 m/z. The vertical axis of the display
is in percentage of counts, and the horizontal axis is mass units. One scan, over
the entire mass range, requires about 1s.
The Counts are displayed as Average rf modulator response and Highest rf
modulator response in counts.
To monitor the rf voltage, observe the displayed ramp. If the rf voltage generator
circuit is properly tuned, the ramp will rise gradually in a generally straight line
from low mass to high mass without any sudden rises in the ramp, and the
Average number counts will be less than 1000. If the rf voltage generator is not
tuned properly all the way to 650 m/z, the end of the ramp will rise sharply at the
mass above which the generator is out of tune, and the Average number of
counts might be above 1000. If this is the case, the rf voltage amplitude must be
adjusted.
The text just to the left of the rf button will tell you if an adjustment is necessary. If
the rf voltage is tuned throughout the entire mass range, you will receive the
following message:
rf response within limits
continue adjustment to minimize highest reading
If the rf voltage is out of tune, you receive the following message:
rf response out of range adjust the rf screw
for a linear response
The rf coil is tuned by adjusting its resonant frequency to match that of the output
of the rf generator board. This is done as follows.
Open the front door and insert a flat head screwdriver into the tuning rod within
the hole labeled rf ADJUSTMENT on the lower part of the front panel.
Slowly turn the screw clockwise until the slope of the ramp increases, then turn
the screw counterclockwise until either the slope of the ramp is at its lowest or
there is a sudden rise at the end of the ramp. At that point, turn the screw three
turns clockwise and verify that the Average number of counts is less than 750
and the Highest number of counts is less than 1500. If they are, the coil is
successfully adjusted. If not, run Diagnostics and call a qualified service
representative.

78
When it is properly adjusted, the dialog will say the rf response is within limits.
When you are finished, select the Done button.
To adjust the Cal gas pressure click Adjust Cal Gas. You obtain a screen from
which you can check and adjust the setting of the calibration compound needle
valve.

When adjusting the cal gas, the following happens automatically. The filament,
electron multiplier, and rf voltage are turned on; the calibration compound
solenoid operated valve is opened; and the scan range is set to display
calibration compound peaks from 45 to 135 m/z. Then, the program determines if
the calibration compound pressure in the vacuum manifold is too low, too high, or
satisfactory.
Under Control and Status dialog box, messages are displayed that indicate the
status of the calibration compound pressure in the vacuum manifold. The
messages are listed below.
Below the dialog box, a progress bar display that shows the status of the
pressure visually.
If the pressure is satisfactory, you will receive the following message:
The calibration gas pressure is OK. Allow time for the gas to flow and the
emission current to equilibrate.
In this case, click Done.
If the calibration compound pressure is too low, you receive the following
message:
Increase calibration gas pressure by adjusting the calibration needle valve.
Allow time for the gas to flow and the emission current to equilibrate.
In this case, turn the calibration compound needle valve 1/4 turn
counterclockwise. Wait for about 30 seconds for the instrument to equilibrate.
Then, note the message again.
If the pressure is too high, you will receive the following message:
Decrease calibration gas pressure by adjusting the calibration needle
valve. Allow time for the gas to flow and the emission current to
equilibrate.
In this case, turn the calibration compound needle valve 1/4 turn clockwise. Wait
for about 30 seconds for the instrument to equilibrate. Then, note the message
again.
If you are using Chemical Ionization you will need to select a CI reagent gas
and adjust its pressure. Select the reagent gas you are using by clicking on the
arrow below the word Adjust.

79

In CI, as in EI, the Saturn GC/MS is tuned to achieve the best combination of
maximum peak height (sensitivity), optimum resolution of peaks, and smooth
peak shape. And in CI, as in EI, the key to proper tuning is to optimize the
number of ions in the ion trap: Too few ions, sensitivity suffers; too many ions,
resolution and peak shape suffer.
In CI, the two main factors that affect the number of ions in the ion trap are the
ionization time and the reaction time. (Once again, the emission current is an
important third factor.)
The CI ionization time is the time that energetic electrons, emitted from the
filament, are allowed to interact with reagent gas to form reagent ions. The
reaction time is the time that reagent gas ions are allowed to react with sample
molecules to form ions.
To a first approximation, the number of reagent ions formed is directly
proportional to the ionization time, and the number of sample ions formed is
directly proportional to the reaction time.
Once you have selected methane as the CI reagent gas it is time to adjust the
flow rate of the gas into the mass spectrometer. Make sure that the gas tank is
open and connected to the back of the instrument. Select the adjust button. This
will open the CI valves, turn on the filament and multiplier. You will see the
screen below. This is an example of the CI gas spectrum for methane, when the
CI gas pressure is too low and needs to be increased. Notice the resolution and
relative ratio between masses 10 and 30. See the Chemical Ionization
section in the Hardware Manual for setup and CI gas adjustment.

80
Increase the CI gas pressure by adjusting the CI needle valve on the front of the
2000. Turn the knob clockwise to increase the pressure. When the pressure is
correct you will see the picture below.

If you increase the pressure too much, you will see a picture like the one below
and you will have to decrease the pressure until you get the picture above.

Once the pressure is adjusted properly you are finished and ready to perform
chemical ionization experiments.
Autotune Mode
It is necessary to perform an auto tune when the instrument is first setup.
Additionally, you must recalibrate the mass axis (FC-43 Mass Calibration)
whenever the temperature, axial modulation, or rf adjustment is changed. Each
time the system is shut down the auto tune must be performed when it is
restarted.

There are four major sections to the Auto Tune window: the Control and Status
display, the Method & Set Points, the Operating Conditions display and the
Spectrum and Event Message window.

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Control and Status
The Auto Tune methods are started from this display by clicking on the Start
Auto Tune button. The method maybe stopped by clicking on the Reset button.
The State displays whether the Saturn MS is currently executing an auto tune
function or is idle.
The Function shows which tuning function is currently being performed.

Method and Set Points

There are four auto tune checks to automatically set up, tune and calibrate the
mass spectrometer. Air/Water check, Electron Multiplier Tune, Mass Calibration
and Trap Function Calibration.

Set Points are for manual adjustment of the Electron Multiplier Voltage and
the SIS Amplitude Adjust Factor.
NOTE: The Air/Water Check will use the last 10
5
Electron Multiplier Setting and
not the manual setting. If the electron multiplier is replaced, the autotune of
Electron Multiplier Tune must be done before the Air/Water Check.
Operating Conditions
The operating conditions of the auto tune display will vary depending on the
currently executing auto tune function. The display will show the current results
of the function.

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An example: The dialog for the air/water check is shown below.

The mass 28 peak width is used to determine if air is present in the trap. The
progress bar labeled Air Level is a graphical representation of the peak width.
The mass 19/18 ratio value is used to determine if water is present in the trap.
The progress bar labeled Water Level is a graphical representation of the ratio.
Spectrum and Event Message Window
On the left side of the auto tune screen you will see the picture below. You can
select what information you wish to see displayed during the auto tune tests by
clicking on the arrow and selecting from the display options drop down list box.
The Hide Keypad button will cause the upper portion of the screen to disappear
and for the lower portion to be expanded.

The Current Module Attributes is the information stored from the last auto tune.
When you are finished performing the auto tune you can view this information
which is stored in an auto tune log.

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Auto Tune Checks
In the top center of the screen you will see 4 check boxes. These are the auto
tune steps that are to be performed. If your system does not contain SIS, or
MS/MS the Trap Function Calibration does not need to be performed. To perform
the auto tune click the check boxes and click Start Auto Tune.

Each one of the items that you selected in the check boxes will now be executed.
If you checked the single step button, a single step will be executed but will not
proceed to the next until the continue button is clicked. You can stop the auto
tune at any time by clicking on the Reset button.
Air/Water Check
When you select Air/Water Check, you obtain a screen from which you can
determine the relative amount of air and water vapor in the vacuum manifold.
When you display the Air/Water screen, the following happens automatically: The
filament, electron multiplier, and rf voltage are turned on; AGC is turned off; and
the scan range is set to display the air/water spectrum (14 to 44 m/z). To
determine the air background, the width of the peak for mass 28 at 10% peak
height is calculated. To determine the water background, the ratio of mass 19 to
mass 18 is calculated.

84

On the left side of the dialog box is an progress bar that indicates the relative
amount of AIR in the system. A message is displayed below the bar.
If the display reads OK, there is essentially no air leak in the system. If the
message MAYBE is displayed, there is a small air leak. The system can be
operated, but performance might not be optimum.
If the display reads HIGH, there is a significant air leak. The leak must be found
and corrected before the system can be operated.
On the right side of the dialog box is an progress bar that indicates the relative
amount of WATER in the system. A message is displayed below the bar.
If the meter reads OK, there is very little water in the system and the system can
be operated.
If the display reads MAYBE, there is a small amount of water, and the system
can be operated, but performance might not be optimum. If the meter reads
HIGH, there is a comparatively large amount of water present in the system, and
the system must be bake out to remove the water before the system can be
operated. (A relatively high water background is generally observed immediately
after you have vented the instrument. It will usually go away within a few hours of
restoring the instrument to its normal operating conditions.)
NOTE: The Air/Water Check uses the electron multiplier voltage giving a 10
5

gain and not the manual setting. If the electron multiplier is replaced. The
autotune of Electron Multiplier Tune must be done before the Air/Water Check.
Electron Multiplier Tune

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The Electron Multiplier Tune will determine three proper settings: the Integrator
Zero, the 10
5
gain for the Electron Multiplier and the Electron Multiplier voltage
boost for optimum peak intensity and resolution.
The Integrator Zero Set obtains the average value of the signal level coming
from the Integrator Circuitry when the filament is off. When the filament is off, the
major source of signal coming from this circuitry is electronic noise. The
Integrator zero is adjusted such that the average value of electronic noise is
slightly greater than zero.
NOTE: The average value for the integrator zero; it should be between 0.20 and
0.80 counts. The Setting can range between 0 and 255.
The Electron Multiplier Tune program can automatically set the electron
multiplier voltage, such that the electron multiplier gain is approximately 10
5

electrons per ion. The program to set the electron multiplier voltage should only
be run when there is no sample of any kind in the instrument. For example, you
should wait at least 30 minutes after you close the calibration compound valve
before you run the program.
For the determination of 10
5
gain, Electron Multiplier Tune program runs in two
phases. In the first phase, the electron multiplier is set to a low test voltage, the
message PRE-ADJUSTMENT PHASE is displayed. The electron multiplier
voltage is increased by 100V increments until a signal is detected coming from
the electron multiplier. The electron multiplier voltage is then set to 300V less
than the value at which a signal was first detected. This ends the first phase.
In the second phase of the program, the electron multiplier voltage is increased
by 100V increments beginning with the final value of the first phase of the
program. In this phase, the Locate Low Voltage End where 10
5
gain is not
achieved and Locate High Voltage Start where 10
5
gain is exceeded.

NOTE: The electron multiplier is approaching the end of its lifetime when the
voltage setting nears 3000 volts.
The final determination is the Electron Multiplier boost, which determines the EM
voltage and AGC Target value for optimum peak intensity and resolution. It uses
the calibration compound peak at mass 131. The program adjusts the target TIC
value to a level that provides reasonable resolution of the major peak and its first
isotope peak. The program determines the height and area of the major peak of
interest, the height and area of the isotope peak, the height of the valley between
the two peaks, and ratio of the height of the valley and the height of the isotope
peak. The Final Gain setting will reflect any increase in the voltage for optimal

86
sensitivity and resolution. This setting is also the value displayed in the Set
Points dialog, in the Electron Multiplier voltage field.
Mass Calibration
The mass calibration function adjusts the rf Scale for a coarse full mass range
calibration and, then locates several FC-43 masses for a multi-point calibration
curve.

To initiate mass calibration based on FC-43, click the button to the left of FC-43
Calibration. When you initiate the program, the calibration compound valve is
opened, and the electron multiplier, filament, and rf voltage are turned on
automatically. The program then automatically uses the calibration compound
peaks at masses 69, 131, 264, 414, 464, 502, and 614 to create a calibration
curve.
Factors Affecting the Mass Calibration:
- The program also uses the air peak at mass 28 for the calibration of low
masses. Any air leak results in a distorted calibration at low mass. Therefore,
do not run the Mass Calibration program if your instrument has an air leak.
- If one or more of the mass peaks are not found by the program, the rf voltage
amplitude might need to be adjusted.
- Temperature changes can adversely affect the mass calibration and this
procedure should be initiated after the manifold has reached its equilibrium
point (i.e., approximately 3 hours after the set-point temperature has been
established).

An ideal slope (that of a straight line calibration) is 6.300 steps per atomic mass
unit. You will generally obtain a slope of 6.3 0.1. The standard deviation should
be 0.15 steps per atomic mass unit or less. (If the standard deviation you obtain

87
is outside of these limits, check if the rf voltage amplitude is adjusted properly
over the entire mass range).
Straight Line Mass Calibration
To initiate a straight line mass calibration, click Straight Line Calibration and Start
Auto Tune. A straight line calibration assumes a linear relationship between DAC
steps and mass. It is used for certain hardware adjustments. When you initiate
the program, a straight line calibration curve is calculated with the zero DAC step
set equal to 0 m/z and 4095th DAC step set equal to 650 m/z.
Trap Function Calibration
When the mass calibration has completed, the trap function calibration can be
performed, if an MS/MS or SIS key is installed on the SAP/Wave Board. This
calibration determines parameters which are required for the operation of ion
preparation methods such as MS/MS and SIS. It takes several minutes to
complete and the Trap Function calibration should be done each time a mass
calibration is done. If you are not using any ion preparation methods, the trap
function calibration does not have to be done. However, before you activate an
ion preparation method, you must then repeat the mass calibration with a trap
function calibration.

At the completion of Trap Function Calibration, the Event Message Window
displays the secular frequency values for the two trap function calibration points.
Nominal values are 257 and 255, respectively. These values can vary up to 4
KHz between instruments.
Set Points
x
The electron multiplier voltage and the SIS amplitude adjust factor can be set by
either changing the value in the edit box or by clicking on the up/down arrows.
The values are not set until the apply button is clicked and will be reset to their
previous values if the setpoints tab is left before clicking the apply button. If one
of the edit controls has the focus, the enter key can be pressed instead of the
apply button.
Electron Multiplier Voltage. Final Gain Setting determine from the Auto Tune
check of EM.

88
SIS Amplitude Adjust Factor. Each trap system must be adjusted for optimum
ion sensitivity and ejection. See Tutorial on SIS Calibration for your system.
The voltage adjustment factor may be set between 50 to 200%. The default is
100%.
Temperatures Mode
The temperature settings to control the Saturn and the transfer line are
accessible by clicking on the Temperature button located in the top center of the
instrument control screen. When you select this a screen like the following
opens.

Click any temperature to change it. After you change a setting, the Apply button
becomes active and you must click this for the changes to occur.

Manifold temperature (range 0C to 120C; default = 40C), the Trap heater
(range 0C to 250C; default = 150C), and the Transfer Line temperature (range
0C to 350C; default = 170C).
The manifold heater is primarily used for baking out the analyzer and should not
exceed 50C when performing acquisition. The default temperature of 40C is
recommended. The transfer line temperature should be adjusted so that its
temperature is no lower than that of the trap or the GC oven.
NOTE: DO NOT heat the transfer line above the maximum temperature
specified for the capillary column.
Whenever any temperature is changed, 2 to 3 hours should be provided to allow
the system to equilibrate after the temperature has reached its setpoint. Once
equilibrium is reached, the rf tuning should be checked, and adjusted if
necessary.
The Start Bakeout button will cause the Bakeout Conditions (time and
temperature) to be activated. The reset button will end the bakeout session. The
manifold bakeout temperature is fixed at 120 C. The transfer line bakeout
temperature defaults to its Setpoint temperature.

89

Whenever you execute changes, the event log at the bottom of the screen will be
updated with the time and the event that has occurred. The screen below is an
example.

At the conclusion of the bakeout, the trap, and manifold temperatures will return
to the set point values. New setpoint values can be applied during a bakeout. A
bakeout must be halted, by clicking the reset button, before a new bakeout
duration or new bakeout temperatures can be set.
Diagnostics Mode
Click Diagnostics in the top center of the screen.

The upper portion of the screen is divided into 3 sections: Control and Status,
Diagnostic Method, and Monitor States.
An automated diagnostics can be initiated by clicking on the Run to Completion
Box and clicking the Start

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The Monitor and Event Message window will detail results of the basic system.

If a fault had occurred, the message would indicate what test failed and the
source of the problem.

A more detailed test of the heater zones can be done by clicking in the box of the
zone to be tested under Heater Test. To complete these tests can take up to
13.5 hours for the trap, 2 hours for the manifold, and three hours for the transfer
line. The manifold and transfer line tests can be run simultaneously.

At the far right of the window is a dialog box of Monitor States, which allows you
to monitor the multiplier, rf, Filament, and Ion Gauge if present. Click the check
box to activate the selection. Some elements of the diagnostic display are active
if some trap components are not on.

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Also, present temperature values for each of the heating zones is displayed.

Monitoring diagnostics on startup will identify any problems. Please refer to the
Trouble Shooting section of the Hardware manual for additional information.
Shutdown Mode
The shutdown procedure is used to shut the system down in an orderly fashion.
The screen is shown below and it is accessed by clicking on the top button
labeled Shutdown.

After you see the screen and you want to shut down the GC/MS system, click
Shutdown in the left center of the screen, just above the Reset button. This

92
action will cause the heaters to be turned off and the system will begin to cool.
Additionally, the turbo pump will be slowly turned off. In the screen below the
shutdown command has been activated. Notice that the turbo pump speed is
being reduced as the temperature is being cooled.

Should you wish to restart the system after you have activated the shutdown,
simply hit the reset button on the left side of the screen above. This will restart
the pumps and turn on the heaters.
After the temperature zones have cooled, turn OFF main power by placing switch
at rear of system into OFF (down) position. Manually vent the system for at least
5 minutes using the lever on front panel.
Diffusion Pump Shutdown
NOTE: During the SHUTDOWN procedure, the MS temperature zones are
reduced (<80C). The system is manually vented to atmosphere when the trap
temperature is less than 80C.
From System Control click Shutdown. The Shutdown display appears, click
Shutdown above the reset button.
The shutdown procedure and capabilities for the Diffusion Pump system are
similar to the turbomolecular system.

Shutdown Page
NOTE: The Diffusion Pump System shutdown sequence takes at least 30
minutes:
- The Saturn GC/MS heaters are turned OFF.
- The GC temperature zones should be cooled down before maintenance is
performed.
- The diffusion pump heater is turned OFF while the Peltier Baffle cooler is
kept on. The DIFFUSION PUMP STATUS changes from NORMAL to
COOLING. After 15 minutes, when there is no pump vapor to contaminate
the system, the Peltier Baffle cooler is turned OFF. After another 15 minutes,

93
the cooler has warmed to the point that it wont condense water vapor, and
the pump is considered to be off. The DIFFUSION PUMP STATUS then
changes from COOLING to OFF.
NOTE: If the word FAULT! is displayed in the Vacuum Status box, click on the
Diagnostics mode button for detailed information on the cause of the fault.
The vacuum status represents the state of the diffusion pump. To precisely
identify the problem, the USER should go to the Diagnostics mode and run
"System Test to Completion. Fault messages may appear on startup or during
normal operation.
Turn OFF main power by placing switch at rear of system into OFF (down)
position. Manually vent the system for at least 5 minutes using the lever on front
panel.
NOTE: DO NOT ATTEMPT to VENT SYSTEM by any other method (via transfer
line, foreline vacuum clamps, etc.). Rapid, improper venting of the system will
cause diffusion pump fluid to backstream into the manifold and ion trap.
Maintenance procedures SHOULD NOT BE attempted until the shutdown
program has finished!
Diffusion Pump Startup
NOTE: The Diffusion Pump System Startup sequence takes at least 30 minutes:
First, the Peltier Baffle cooler is turned on while the pump heater is left off. This
step lasts 15 minutes and allows the cooler to drop in temperature before any
pump vapors are created. When the foreline pressure reaches proper vacuum
(~500 mTorr), the pump heater is turned on. When the heater has reached
operating temperature, after approximately 15 minutes, the ion trap electronics
can be turned on.
If a diffusion pump fault occurs the system will go to the shutdown mode. The
USER may check for faults on Startup by going to the Diagnostics mode and
checking the Vacuum Status field for "Fault". "Run Tests to Completion" and
check the event window for messages.

Diagnostics Page to Determine Diffusion Pump Status

94
NOTE: The Vacuum System status should be periodically checked during
Startup for foreline pressure. The pressure should read below 500 mTorr in 5
minutes and < 100 mTorr after 45 minutes. Higher values may indicate a leak.
Refer to the Troubleshooting chapter in the Hardware manual.
Acquisition
Selecting the Acquisition button activates the 2000 module for analysis. When
you first go into this screen the module will load the information for the active
method so that it is ready to collect data according to the conditions prescribed in
the method. You will see a screen similar to the one below on the left side of your
monitor.

Within a few moments you will see the red lights turn to green. This is an
indication that the Saturn module is ready for analysis. If the GC and/or
AutoSampler are not ready you will see a Not Ready message at the top of the
screen. Once the GC and AutoSampler come to a ready state, the not ready
message will change to Ready. To determine the individual ready states of the
components you can go the top pull down menu under Windows and see the
states for the 2000, 3800, and 8200 modules. Once all components are ready,
you are ready to start an analysis.
An analysis can be run as a single sample or through an automated sequence.
To run a single sample, go to the top pull down menu called Inject. Select inject
single sample. You will see a screen similar to the one below.

All of the fields in the picture above are editable for your particular sample. Be
sure to give the correct information about sample name, vial position and
injection volume if an AutoSampler is used, and data file path. Once this
information has been entered correctly, select the inject button in the bottom left
corner. If no AutoSampler is used, inject the sample the sample manually when
the GC ready light illuminates on the GC keyboard. If an AutoSampler is used, it
will now be activated and make the injection for you. Refer to the Tutorial Manual
or Help for more information on injection.

95
In the above screen there are additional buttons which allow you to browse or
check data files that already exist to make sure that you are not overwriting an
existing file. Prior to making the injection any of these buttons can be selected
and checks can be made.
The sample type can be changed by double clicking in the field below Sample
Type. Note the picture below for the selections that can be made.

The same procedure can be used for injection notes. Any notes that you wish to
enter here will be saved with the data file. The AutoLink button works in the same
way. Note the picture below.

A command can be entered here to execute a program once the data file
acquisition is completed. This can be a program to activate Saturn Writer to print
the sample reports, for example. The browse command can be used to select the
command executable file. Select OK when you have made your selection.
The RecalcList button can be used to create a list of samples for data processing
from the injection that you are making. This will save you some time in creating
the list manually. See the picture below.

96
Select one of the 3 radio buttons and name the recalculation list you are using if
appropriate.
In order to perform automated injections of a group of samples you must first
build a sample list and then a sequence list. An example of a sample list is
displayed below. This screen can be activated from the pull down menu under
File, New Sample List. You must create the list from the empty table you see on
your screen. All of the entry fields are the same as the previous information in
this section for single sample injections. Be especially sure that the AutoSampler
vial information is correct in your sample list.

Once the sample list is created, it is time to create the sequence which will cause
the injections to be made. An example is given below. Select Inject for action,
type the name of the method that you wish to run, and type the name of the
sample list you wish to be injected. When this is completed you are ready to
inject your samples. Use the begin button to start the sequence.

General Parameters that Affect EI Operation
Electron Multiplier Gain
Normal Saturn GC/MS operation assumes that the electron multiplier gain is set
up to produce approximately 10
5
electrons per ion. This is accomplished
automatically with Auto Tune.
The AGC software operates on information derived from the prescan
measurement of the TIC (the AGC peak).
(See Main Method Editor in the Saturn Method Manual for details of scan
function). Unlike the ionization time or filament emission current that can alter the
actual number of ions created in the ion trap, changing the electron multiplier
gain only alters the amplification of the ion current signal of ions after they are

97
scanned out of the ion trap. Thus, when the multiplier gain is changed, there is
no change in the actual quantity of ions formed and measured in the prescan
measurement, but the peak area of the AGC peak will be changed. The AGC
software will misinterpret this change in peak area as a real change in the
number of ions created in the ion trap and will adjust the ionization time
accordingly. An incorrect ionization time may cause a change in mass resolution.
The AGC software is dependent on the multiplier gain remaining constant in
order to measure the quantity of ions in the ion trap correctly and set the proper
ionization time.
Under certain circumstances (low background, small signal) increasing the
electron multiplier gain by +100 or +200 volts above the 10
5
gain can decrease
the detection limit. As explained in the note above, the same multiplier gain must
be used for determining the calibration curve and analyzing unknown samples.
Axial Modulation
The number of ions stored in the ion trap cavity is proportional to the ionization
time and the filament emission current. Although the maximum ion-storage
capacity of the ion trap is approximately 10
6
to 10
7
ions, space-charge repulsion
occurs when the number of ions exceeds 10
4
to 10
5
. Space-charge interactions
cause a loss in unit mass resolution. To overcome this limitation, a small ac
voltage, the axial modulation voltage, is applied to the endcap electrodes.
The axial modulation voltage is applied at a fixed frequency and amplitude during
the ramp of the rf voltage. The frequency of the axial modulation voltage is 485
kHz, which is about one-half of the frequency of the rf voltage. Only when an ion
is about to be ejected from the ion trap cavity is it in resonance with this
frequency. When an ion comes into resonance with this frequency, it moves
away from the center of the trap, where the field generated by the rf voltage is
zero (and space-charge effects are strong), into a region where the field
produced by the rf voltage is strong (and space-charge effects are small). As a
result, the ejection of the ion is facilitated, and mass resolution is significantly
improved. The default axial modulation voltage is 4.0. Once the optimum axial
modulate ion amplitude has been set for a given instrument, it need not be
changed.
Emission Current
The number of ions formed in the trap is a function of both the ionization time
and the intensity of the electron beam. In general, increasing the filament
emission current increases the quantity of ions produced. The relationship
between the filament emission current and the measured TIC (i.e., the number of
ions generated in the ion trap) is not a strictly linear one. In particular, the
emission current and the measured TIC do not vary linearly for emission current
values above 40 A and at high sample concentration.
In certain cases, a high emission current can be used to increase the sensitivity.
One of these is EI/MS/MS where the MS/MS isolation step eliminates the higher
background that would normally arise from a high emission current.
Ion Trap Temperature
After the system has been shut down and the ion trap vented to the atmosphere,
we recommend an initial trap temperature of 220C for the rapid removal of water
vapor. After this period, a reduction in trap temperature to 150-175C will extend
the turbomolecular vacuum pump lifetime. Some applications may require higher

98
temperatures and this is okay. In general use the lowest temperature which
provides acceptable chromatography. The manifold bakeout functions can be
used to do this overnight and reset the temperatures to operating conditions
automatically.
The trap temperature value selected should be high enough so that
chromatographic performance is not affected. We have found trap temperatures
can be 50-75C below the ending temperature for the GC column temperature
ramp, without compromising chromatographic performance.
Certain compounds (e.g., straight chain hydrocarbons) will show more
fragmentation at hotter ion trap temperatures.
AGC Target TIC Value
In EI mode with AGC on, the target TIC value determines how many ions AGC
allows into the ion trap during the calculated ionization time. While increasing the
target TIC value will increase peak heights, increasing it too far will result in a
loss of mass resolution. This would be observed as mass misassignments and/or
incorrect isotope abundance ratios. For full-scan EI operation, a target TIC of
20,000 is a good starting point. Under special circumstances, e.g., MS/MS, a
much lower target TIC is required. As the m/z distribution of the stored ions
becomes smaller, fewer ions can be trapped without a loss of resolution.

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3800 GC System Control Window
The Instrument Window
Once you have configured your 3800 GC in an instrument, you may view the
Instrument Window. The instrument window allows you to monitor the status of
all modules assigned to the instrument, perform injections of one or more
samples, and perform batch recalculations.

Double-click in this area or select the instrument from the Instrument menu to
view the 3800 GC Status and Control window.

If the Status and Control Windows for the modules configured in the instrument
are not currently displayed, you can select Show Module Windows from the
Windows menu.

100
Elements of System Control Toolbar
System Control Toolbar provides you with buttons to do the most common tasks
performed in System Control. Most Toolbar buttons correspond to a menu
command. You can find what each button does by resting the pointer on the
button. Note that the buttons controlling the SampleList, Sequence and
RecalcList become available after you activate a corresponding automation file.

Click on the Active Method button for additional options
The 3800 GC Status and Control Window
You are now ready to program each 3800 to perform fully automated data
acquisition. Initially the 3800 Module Window will look similar to the figure below.
The left side of the window shows the 3800 Operation parameters: RunTime,
EndTime, Method State, and Fault State. The Start, Reset, and Method buttons
control the 3800 GC.

Displays the 3800 Setup dialog. Selects the detector signals to view. Selects the
component status to view.
The detector signals viewed in the real time chromatogram display can be
selected.

101

Multiple detectors can be viewed horizontally or vertically.
The component status display can be changed to view detailed status of each
component in the GC.

Click on a temperature zone entry to select the corresponding component status
or select the component status from the list. Detailed component status is
displayed.
The 3800 Setup dialog is accessed from the View Setup button.

102

Installed hardware is listed here. The setup is changed from the 3800 GC front
panel.
The 3800 Setup dialog for the Saturn 2000R/3800 is also accessed from the
View Setup button and shows a different display.

The setup is changed from the Varian MS Workstation.
The Real-Time Chromatogram Display
All detectors installed on the 3800 GC display their chromatographic signals in
real time. Configuration of the chromatogram display for all detectors is the
same.

103

Show only the chromatogram display. Continue to view the signal after the run
Select the detector(s) to view.

Hide/unhide the Toolbar.
Set both the amplitude and time axes to full scale.
Set the amplitude axis to full scale.
Set the time axis to full scale.
Use these buttons to move between stored scalings.
Enable/disable the Auto Scale feature.
Enable/disable the cursor display.
Select the background color for the display.
Drag an area of the display to view a more detailed section of the plot, or zoom in
both axes by pressing and holding the left mouse button on the spot you wish to
enlarge. (Holding the Shift key down will allow you to zoom out.)

104
Adjust zero offset. Adjust amplitude scale.

Adjust time scale.
Hide/unhide vertical amplitude scale slider.
Documenting Module Information
You may wish to document the configuration of your modules, their installation
and most recent service dates, and other information pertinent to your
instrument. To do so, use the Module Information Editor accessed from the Edit
menu in the instrument window.

Click on the module window to give it the focus.
Select Edit Module Info.

The Module Information Editor window is displayed.

105

You may add and edit sections and items in sections.
The injections value is updated each time an injection is performed.
Select Help for details on creating and editing module information.
Click on Done to close the window.
Module information is copied into Data Files generated after injections and can
be included in the Run Log portion of the results report.

106

107
3800 GC Injecting a Single Sample
Overview
By now you should have your 3800 GC configured and a basic Method built for
data acquisition. If this hasnt been done, please refer to the previous sections for
instructions on doing this.
Using the Inject Single Sample Dialog Box
You can inject a single sample from System Control by using the Inject Single
Sample dialog box.

Display the Inject Single Sample dialog by selecting it from the Inject menuor
by clicking on the Inject Single Sample button on the toolbar.
The Inject Single Sample dialog box is displayed.

Specifies the number of injections of this sample.
Enter notes about the sample.
Refer to the Specifying Data Handling Parameters section in this manual.
Enter information about the sample.
The fields in the table change depending on the type of sampling device
configured in the instrument.
Select the Method to use for the run.
Change the location and name of the Data Files
Click Inject to start the run.
If you have an 8200 or 8400 AutoSampler or 8410 AutoInjector configured as
part of your instrument, there is a shortcut available to you. Instead of going to

108
the Inject Single Sample, double-click on the vial position you wish to inject from
in the carrousel display. This will bring up the Inject Single Sample dialog box
with the vial number already entered.
Specifying the Data File Name and Path
Data File names can be up to 255 characters long. Sample ID, injection date,
module name, and injection number can be embedded in the file name making
the Data File name correlate with each sample injection. When you click on the
Data Files button, the Data Files Generation dialog box is displayed. This
dialog box allows you to select the path and the filename specification for the
data file.
The left side of the Data File Generation dialog box allows you to select the drive
letter and subdirectory (path) where the data files are to be stored.

The right side of this dialog box allows you to create a filename specification.
You can combine text entry with the % variable symbols shown to specify
filenames that contain sample injection specific information. An example of the
filename is dynamically updated as you type in the filename specification. This
makes it easy to see how a Data File created with this filename specification
would appear.

109
Specifying Per-Sample Data Handling Parameters
Most Data Handling parameters are specified in the Method used during the
injection. Some parameters may vary on a per-sample basis, and are therefore
specified when you perform the injection. The following Data Handling
parameters can be specified on a per-sample basis:
Unidentified Peak Factor
Multiplier
Divisor
Amount Standard when one Internal Standard is being used

Refer to the Varian MS Workstation Data Handling and Reports Manual for a
brief description of these parameters. Refer to the Regulatory Compliance
Manual for a complete description of how these parameters are used to calculate
results.
Not only can you specify these parameters on a per-sample basis, but you can
specify them on a per-detector channel basis. This is useful if, for example, you
have different detectors installed on your 3800 GC. In addition, if you are using
multiple internal standards, you can also specify their amounts on a per sample
and per detector channel basis.
To access these extended Data Handling parameters, click on the button in the
Multi-Channel Multi-Standard column in the Inject Single Sample dialog box. The
Data Handling Channels dialog box is displayed. When you select the detector
channel to in the Data Handling Channels dialog box, the calculation type,
internal standard peaks and amounts are read from the active Method. Be sure
the Method you will be using is already active before you enter detector-
specific parameters.

Select specific detector channels here (up to 4).
An amount may be entered for each internal standard peak in the Method.
Use these buttons to edit the corresponding sections of the active Method.

110
Specifying a RecalcList
You can choose to create a new RecalcList, append to an existing RecalcList, or
not create nor update a RecalcList. To select the RecalcList option that you want,
click on the RecalcList button. The RecalcList Generation dialog box is
displayed.

If you choose to create a new RecalcList, this automatically generated RecalcList
will not overwrite an existing RecalcList. If a RecalcList with the same filename
exists, the newly created RecalcList will have number appended to its filename to
make it unique and to prevent the older RecalcList from being overwritten.
Monitoring the Status of the Run
After an injection is performed, the status of the run can be monitored in the
instrument window.

Module status is shown in the status and control windows and on the toolbar.
The total number of injections completed is shown in the Instrument Status
window.

111
List of Data Files generated in System Control, and a Quick Link button above
provides access to the selected file.
Automation actions and errors are logged in the Message Log.
The chromatogram is displayed as it is acquired.
When you double-click on the status bar at the bottom of the instrument window,
the entire Message Log window is displayed.

All Message Log entries are stamped with the time they occurred.
Using QuickStart
QuickStart is a fast way to inject a single sample without having to use System
Control directly. QuickStart can be customized and is ideal when setting up
instruments for routine use. Refer to the on-line help in QuickStart for further
details.
This button on
the MS Workstation Toolbar opens QuickStart for doing injections of routine
samples.
QuickStart first starts System Control and waits until all modules have logged in.
When ready, the QuickStart window is displayed.

112

Choose the instrument for the injection.
Enter the name of the Method you wish to use.
Enter the name of the stand-by Method. This Method is downloaded to the
modules after the run is complete, and is used to specify the stand-by state of
the instrument.
Enter sampling information. This information is specific to the type of sampling
device installed.
Refer to the on-line help for more details on the QuickStart screen.
Press Start to begin.

113
3800 GC Injecting Multiple
Samples
Introduction
Using a SampleList in System Control
You can inject multiple samples from System Control by using the SampleList.

Choose to open either a New SampleList or an existing SampleList from the File
menu..

or by clicking on the New or Open Automation File button on the toolbar.
The SampleList window for the open SampleList is displayed. It contains fields
that are specific to the sampling device configured in the instrument. In this case,
if a sampling device such as the 8200 AutoSampler is configured, the
corresponding SampleList is used.

114

Spreadsheet columns can be sized by dragging their border using the left mouse
button. Right click on the column headers for formatting options.
Enter post-run operations to be performed.
Enter information about the samples and the injections you wish to perform.
Select the location and name for the Data Files generated by the SampleList.
Specify RecalcList generation options.
Press the Begin button to start injecting samples.
When the table is scrolled to the right, the Sample Name column doesn't scroll so
you can easily tell for which sample you are entering additional parameters.
Commonly used data handling parameters, the amount for single internal
standard calculations, the unidentified peak factor, a multiplier, and a divisor, can
be entered directly into this table. If you have more complex requirements, such
as multiple internal standards or multiple detectors requiring different entries for
these data handling parameters, click on the button in MultiChannel
MultiStandard column.

Click here to enter extended data handling parameters
If you need to add several similar lines to the sample list, click on the Add
Lines button. You can then enter the common information in the dialog box.

115
For sequentially numbered Sample names, enter the starting number and the
number of entries to add to the SampleList. The Sample Names will have these
numbers appended to them.
When you press the Begin button, you are prompted for the Method to use.

Enter the Method to use for the runor browse for the Method file.
After you click on OK, the Method is downloaded to the 3800 GC and the run will
begin. If you are using a manual injector or a sampling device that is not
controlled by the Varian MS Workstation, you will need to start the device
manually.
data file.


116
makes it easy to see how a Data File created with this filename specifications
would appear.
Multiplier
Divisor
Refer to the Data Handling and Reports Manual for a brief description of these
parameters. Refer to the Regulatory Compliance Manual for a complete
description of how these parameters are used to calculate results.
specify them on a per-detector channel basis. This is useful if, for example, you
have more than one detector installed on your 3800 GC. In addition, if you are
using multiple internal standards, you can also specify their amounts on a per
sample and per detector channel basis.
MultiChannel MultiStandard column in the 8200 SampleList. The Data Handling
Channels dialog box is displayed. When you select the detector channel in the
Data Handling Channels dialog box, the calculation type, internal standard peaks
and amounts are read from the active Method. Be sure the Method you will be
using is already active before you enter detector-specific parameters.

displayed.

117

Changing Default SampleList Entries
When you add a new row into a SampleList, default values are used for each
cell. To change the default values, click on the Defaults button in the open
SampleList window. The following dialog box will be displayed. Enter the desired
default values and click on Save.

Reading Vial Positions from an 8200 AutoSampler
The 8200 AutoSampler can read the position of vials present in its carrousel.
This information can then be used to build a SampleList containing entries for
each vial in the AutoSampler.

118
Click on the Carrousel button.
The Carrousel dialog box is displayed.

Click on the button to perform the desired operation.
The SampleList is then updated with the vial information from the AutoSampler.
Default values are used for each entry added to the SampleList.
Refer to the 8200/SPME AutoSampler for 3800 GC Manual for details about use
of the 8200 AutoSampler with the 3800GC.
Monitoring the Status of Runs
instrument window.

Module status is shown in the status and control windows and on the Toolbar.
window.

119
List of Data Files generated in System Control, and a Quick Link button above to
access the selected file.

Saving SampleLists for Later Use
When you make changes to the open SampleList, the changes are automatically
saved to the SampleList file and will be used for the automated runs that are in
progress. If you want to edit a SampleList other than the open SampleList, use
the offline Automation File Editor application described in the next section of this
manual.
Using More Than One Method for Injections
The Varian MS Workstation allows you to perform automated injections using
more than one Method. There are two ways in which this can be accomplished.
The first is by changing the active Method from within the SampleList. The
second is by using a Sequence.
Changing the Method in the SampleList
You may change the Method used during injections by activating a Method in a
SampleList row.

120
Select Activate Method from the Sample Type cell.
Click on the AutoLink button. The Activate Method dialog box is displayed.

Enter the name of the Method to useor pick the Method from a list of files.

When this line is encountered during automated injections, the specified Method
is activated.
You may specify any number of Methods to be used in the SampleList.
Using the Sequence Window
The Sequence window allows you to specify multiple Methods and SampleLists
to be processed during automation.

Choose to open either a New Sequence or an existing Sequence from the File
menu..


121
The Sequence window for the open Sequence is displayed.

Enter the Method and SampleList to use. You may enter any number of
Sequence lines.
Choose the action to be done in that step of the Sequence from the drop down
box.
Browse for a Method or SampleList file in the active cell.
Press Begin to start the automation.

122

123
3900 GC System Control Window
The Instrument Window
Once you have configured your 3900 GC in an instrument, you may view the
Instrument Window. The instrument window allows you to monitor the status of
all modules assigned to the instrument, perform injections of one or more
samples, and perform batch recalculations.

Double-click in this area or select the instrument from the Instrument menu to
view the 3900 GC Status and Control window.

If the Status and Control Windows for the modules configured in the instrument
are not currently displayed, you can select Show Module Windows from the
Windows menu.

124
Elements of System Control Toolbar
System Control Toolbar provides you with buttons to do the most common tasks
performed in System Control. Most Toolbar buttons correspond to a menu
command. You can find what each button does by resting the pointer on the
button. Note that the buttons controlling the SampleList, Sequence and
RecalcList become available after you activate a corresponding automation file.

Click on the Active Method button for additional options
The 3900 GC Status and Control Window
You are now ready to program each 3900 to perform fully automated data
acquisition. Initially the 3900 Module Window will look similar to the figure below.
The left side of the window shows the 3900 Operation parameters: RunTime,
EndTime, Method State, and Fault State. The Start, Reset, and Method buttons
control the 3900 GC.

Displays the 3900 Setup dialog. Selects the detector signals to view. Selects the
component status to view.
The detector signals viewed in the real time chromatogram display can be
selected.

125

Multiple detectors can be viewed horizontally or vertically.
The component status display can be changed to view detailed status of each
component in the GC.

Click on a temperature zone entry to select the corresponding component status
or select the component status from the list. Detailed component status is
displayed.
The 3900 Setup dialog is accessed from the View Setup button.

126

Installed hardware is listed here. The setup is changed from the 3900 GC front
panel.
The 3900 Setup dialog for the Saturn 2000R/3900 is also accessed from the
View Setup button and shows a different display.

The setup is changed from the Varian MS Workstation.
The Real-Time Chromatogram Display
All detectors installed on the 3900 GC display their chromatographic signals in
real time. Configuration of the chromatogram display for all detectors is the
same.

127

Show only the chromatogram display. Continue to view the signal after the run
Select the detector(s) to view.

Hide/unhide the Toolbar.
Set both the amplitude and time axes to full scale.
Set the amplitude axis to full scale.
Set the time axis to full scale.
Use these buttons to move between stored scalings.
Enable/disable the Auto Scale feature.
Enable/disable the cursor display.
Select the background color for the display.
Drag an area of the display to view a more detailed section of the plot, or zoom in
both axes by pressing and holding the left mouse button on the spot you wish to
enlarge. (Holding the Shift key down will allow you to zoom out.)

128

Adjust zero offset. Adjust amplitude scale.

Adjust time scale.
Hide/unhide vertical amplitude scale slider.
Documenting Module Information
You may wish to document the configuration of your modules, their installation
and most recent service dates, and other information pertinent to your
instrument. To do so, use the Module Information Editor accessed from the Edit
menu in the instrument window.

Click on the module window to give it the focus.

129
Select Edit Module Info.
The Module Information Editor window is displayed.

You may add and edit sections and items in sections.
The injections value is updated each time an injection is performed.
Select Help for details on creating and editing module information.
Click on Done to close the window.
Module information is copied into Data Files generated after injections and can
be included in the Run Log portion of the results report.

130

131
3900 GC Injecting a Single Sample
Overview
Using the Inject Single Sample Dialog Box
You can inject a single sample from System Control by using the Inject Single
Sample dialog box.

Display the Inject Single Sample dialog by selecting it from the Inject menuor
by clicking on the Inject Single Sample button on the toolbar.
The Inject Single Sample dialog box is displayed.

Specifies the number of injections of this sample.
Refer to the Specifying Data Handling Parameters section in this manual.
The fields in the table change depending on the type of sampling device
configured in the instrument.
Select the Method to use for the run.
Change the location and name of the Data Files
Click Inject to start the run.

132
data file.

would appear.
Multiplier
Divisor
Refer to the Varian MS Workstation Data Handling and Reports Manual for a
brief description of these parameters.

133
displayed.

Monitoring the Status of the Run
instrument window.

Module status is shown in the status and control windows and on the toolbar.

134
window.

Using QuickStart
QuickStart is a fast way to inject a single sample without having to use System
Control directly. QuickStart can be customized and is ideal when setting up
instruments for routine use. Refer to the on-line help in QuickStart for further
details.
This button on
the MS Workstation Toolbar opens QuickStart for doing injections of routine
samples.
QuickStart first starts System Control and waits until all modules have logged in.
When ready, the QuickStart window is displayed.

135

Choose the instrument for the injection.
Enter the name of the Method you wish to use.
Enter the name of the stand-by Method. This Method is downloaded to the
modules after the run is complete, and is used to specify the stand-by state of
the instrument.
Enter sampling information. This information is specific to the type of sampling
device installed.
Refer to the on-line help for more details on the QuickStart screen.
Press Start to begin.

136

137
3900 GC Injecting Multiple
Samples
Introduction
Using a SampleList in System Control
You can inject multiple samples from System Control by using the SampleList.

Choose to open either a New SampleList or an existing SampleList from the File
menu..

The SampleList window for the open SampleList is displayed. It contains fields
that are specific to the sampling device configured in the instrument. In this case,
if a sampling device such as the 8400 AutoSampler is configured, the
corresponding SampleList is used.

138

button. Right click on the column headers for formatting options.
Enter information about the samples and the injections you wish to perform.
Select the location and name for the Data Files generated by the SampleList.
Press the Begin button to start injecting samples.
be entered directly into this table. If you have more complex requirements, such
as multiple internal standards or multiple detectors requiring different entries for
these data handling parameters, click on the button in MultiChannel
MultiStandard column.

Click here to enter extended data handling parameters


139
When you press the Begin button, you are prompted for the Method to use.

Enter the Method to use for the runor browse for the Method file.
After you click on OK, the Method is downloaded to the 3900 GC and the run will
begin. If you are using a manual injector or a sampling device that is not
controlled by the Varian MS Workstation, you will need to start the device
manually.
data file.

140
makes it easy to see how a Data File created with this filename specifications
would appear.
Multiplier
Divisor
displayed.


141

Monitoring the Status of Runs
instrument window.

Module status is shown in the status and control windows and on the Toolbar.

142

Saving SampleLists for Later Use
When you make changes to the open SampleList, the changes are automatically
saved to the SampleList file and will be used for the automated runs that are in
progress. If you want to edit a SampleList other than the open SampleList, use
the offline Automation File Editor application described in the next section of this
manual.
Changing the Method in the SampleList
SampleList row.


143

Enter the name of the Method to useor pick the Method from a list of files.

is activated.
Using the Sequence Window
The Sequence window allows you to specify multiple Methods and SampleLists
to be processed during automation.

Choose to open either a New Sequence or an existing Sequence from the File
menu..


144

Sequence lines.
box.
Press Begin to start the automation.

145
System Control Menus
File Menu

Menu Item Description
Activate Method Displays the Activate a System Control Method File dialog box to
activate a Method and download the Instrument Control sections
to the modules.
Upload Active Method
from Modules
Displays the Save a System Control Method File dialog box to
allow you to name the Method that will receive the instrument
control sections uploaded from all modules connected to the
instrument.
New SampleList Displays the Create a New System Control SampleList File
dialog box to name a new SampleList.
Open SampleList Displays the Open a System Control SampleList File dialog box
to open an existing SampleList .
New RecalcList Displays the Create a New System Control RecalcList File dialog
box to name a new RecalcList.
Open RecalcList Displays the Open a System Control RecalcListFile dialog box to
open an existing RecalcList.
New SequenceList Displays the Create a New System Control Sequence File dialog
box to name a new Sequence.
Open SequenceList Displays the Open a System Control Sequence File dialog box
to open an existing Sequence.
Print Prints the contents of the active window in System Control.
Printer Setup Opens the Star Print Setup Dialog Box to select a printer and set
options for it. You can open the Print Setup dialog box from the
Star Printer Setup dialog box. The Varian MS Workstation only
uses the printer for instrument 1.

146
Remember Last Open
Files
When checked, upon startup System Control will restore the
active Method and any automation files that were open when
System Control was last closed.
Exit Closes System Control. If System Control is in the process of
performing a critical operation, you may be prompted before the
application is closed.
Edit Menu

These commands are for use with Sequences, SampleLists, and RecalcLists.
Cut Deletes a selection and copies it to the Clipboard. Used to remove
or move a selected part of a spreadsheet.
Copy Copies a selection to the Clipboard. Used to duplicate a selection
and place the duplicate in a new place (using Paste).
Paste Inserts previously cut or copied information that was stored in the
Clipboard into a spreadsheet.
Clear Deletes a selection but leaves the Clipboard unchanged.
Add Adds a new line in a Sequence, SampleList or RecalcList.
Insert Inserts a new line in a Sequence, SampleList or RecalcList.
Select All Selects all lines in a Sequence, SampleList or RecalcList.
Fill Down Causes the contents of the top cell in a series of highlighted cells
to be copied to the cells below it. Used to edit all the cells in a
column quickly.
Edit Notes... Opens the Edit Notes Dialog Box to permit editing of the notes
associated with the Sequence, SampleList, RecalcList, or Method
file displayed in the active window.
Edit Module Info... Opens the Module Information Editor Dialog Box to permit editing
of the Module Information associated with the module displayed in
the active window.

147
Inject Menu

Inject Single
Sample...
Opens the appropriate Inject Single Sample Dialog Box for your
system. Used to inject a single sample without building a
Sequence and SampleList manually.
Automation Menu

Begin
SampleList
Begins execution of the currently open SampleList.
Begin Sequence Begins execution of the currently open Sequence.
Begin at
Selected
SampleList
Line...
Begins the open SampleList at the selected SampleList line. This item
is enabled when a SampleList is open. Upon selecting this menu item,
a prompt for the line in the SampleList appears. This is useful when
recovering from a power failure that interrupted automation in
progress.
Begin at
Selected
Sequence Line...
Begins the open Sequence at the selected Sequence line. This item is
enabled when a Sequence is open. Upon selecting this menu item, a
prompt for the line in the Sequence appears. This is useful when
recovering from a power failure that interrupted automation in
progress.
Suspend
Automation
Suspends execution of automation after the current run has been
completed.
Resume
Automation
Resumes execution of automation after it has been suspended.
Stop Automation Stops the current run, resets all modules simultaneously and
suspends automation.

148
Reset Modules Stops the current run, resets all modules simultaneously. Automation
proceeds to the next injection after all the modules go to the Ready
state.
Enable
Automated
Printing
(checked or
unchecked)
Turns on or off the printing of reports automatically generated during
any automation action. This is useful when you wish to disable printing
(if the printer is out of paper, for example) without having to modify the
Print Options portion of the Report Method.
Recalculate Menu

Begin RecalcList... Begins recalculation of the open RecalcList using the active
Method.
Begin at Selected
RecalcList Line...
Begins the open RecalcList at the selected RecalcList line. This
item is enabled when a RecalcList is open. Upon selecting this
menu item, a prompt for the line in the RecalcList appears. This is
useful when recovering from a power failure that interrupted
automation in progress.
View Calibration
Curves...
Opens the Open a Method File to View Curves dialog box to view
calibration curves that are stored in a Method file.
Instrument Menu

The Instrument Menu commands are used to switch the display between the
configuration screen and the instrument.

149

#:instrument name Displays the Instrument Status window and Status and Control
windows for the named Instrument. i.e. Saturn GC/MS #1
Configuration Displays the Configuration window.
Instrument # Faults Displays the Instrument Faults dialog box, showing recent and self-
test messages and faults. The list of faults may be printed from this
dialog box.
Setup Ethernet
Communications
Available if an optional module driver is installed that uses Ethernet
to communicate with the device. See the Operation Manual for
your module driver for a detailed description if applicable. Allows
set-up of the communication between the 3800 GC and Mass
Spectrometer
Setup COM Ports Available if an optional module driver is installed that uses Serial
I/O to communicate with the device. See the Operation Manual for
your module driver for a detailed description if applicable, such as
the 3400 GC.
Setup ADC Board
Ports
Opens the Setup ADC Board I/O Ports Dialog Box to configure the
ADC Board base address and determine the Switch S1 settings for
each ADC Board. Applicable only if the ADC Board module driver
is installed.
Windows Menu

Show Module Windows Opens the Status and Control windows for all the
modules in the Instrument. It is disabled when all
the windows are open, even if some are hidden
under others.
Iconize Module Windows Iconizes the Status and Control windows for all the
modules in the Instrument. It is disabled when all
the windows are iconized.
Show Automation Windows Opens the windows for all the automation files open
in the Instrument. It is disabled when all the
automation windows are open, even if some are
hidden under others.
Iconize Automation Windows Iconizes the windows for all the automation files in
the Instrument. It is disabled when all the windows
are iconized.

150

Arrange Icons Arranges the icons, if any, in a row at the bottom of
the System Control window.
Sequence:,
SampleList:,
RecalcList:

Opens the window for the selected file or moves it to
the front. Used to display the open Sequence,
SampleList, or RecalcList.
Instrument Status,
Message Log,
Configuration Log
(only if Configuration window is
open)

Displays the corresponding window for the
instrument or moves it to the front. Used to see the
instrument status, Message Log, or Configuration
Log.
Module Window
(name varies depending on
module)
Displays the Status and Control window for the
chosen module or brings it to the front.
Help Menu

Help Topics Displays the help you are now viewing.
Product Support Web Site If you have Internet access and a web browser
installed on your computer, this option will
automatically open the Varian MS Workstation
Product Support Web Site. Here you will find the
latest software and documentation updates for the
Varian MS Workstation suite of products, along with
additional notes, tips, and answers to frequently
asked questions.
You may wish to visit this site periodically to see if
new information is available that may be pertinent to
you.
About System Control Displays the About Box for the System Control
application. The About Box contains information
about the software version, installation information,
and a list of the instrument control modules that you
have installed.

151
System Control Toolbar
Main Toolbar

The System Control main toolbar appears at the top of the Configuration and
Instrument Windows.

Item Description

Creates a new automation file (RecalcList, SampleList
or Sequence). You are prompted for the name of the
new file.

Opens an existing automation file. Displays the Open
Automation Dialog Box.

Active Method QuickLink button. When clicked,
displays operations that may be performed on the
active method, including re-activation (which
downloads the method to any modules attached to the
instrument).

Activates a Method. Displays the Active Method
Dialog Box.

Displays the Edit Notes Dialog Box. Notes are
displayed in the Open File dialog box and are included
in the automation file printout

Displays the Module Information Editor Dialog Box.
Module information is logged in data files generated by
the instrument and can be included in reports.

Inject a single sample. Displays the Inject Single
Sample Dialog Box.

Begins the RecalcList currently open in the instrument.
This item is disabled unless a RecalcList has been
opened.

Begins the SampleList currently open in the
instrument. This item is disabled unless a SampleList
has been opened.

Begins the Sequence currently open in the instrument.
This item is disabled unless a Sequence has been
opened.

Pause automation. The current run will complete and
then automation will be suspended.

152

Resume automation after a pause. Automation will
continue at the point that it was suspended.

Stop automation. Stops the current run, resets all
modules simultaneously and suspends the Sequence.

Instrument status indicator. Shows whether the
instrument is not ready, running, computing or printing.
When the instrument is ready but not running (idle), no
status is shown.

153
2000 MS Method Basic Scan
Functions
Introduction
The Saturn GC/MS analyzes the gas-phase ions formed from a sample in terms
of their mass-to-charge (m/z) ratios and their relative abundances in the resulting
spectra. The mass spectrum is a graphical representation of the ion intensities
versus the mass-to charge ratio.
The Saturn GC/MS creates the mass spectrum with an ion-trap analyzer. This
type of analyzer differs from beam transport analyzers such as magnetic sectors,
quadrupoles, and time-of-flight instruments where the ions to be separated pass
through a sequence of fixed electromagnetic fields. Instead, the ion trap confines
the ions within a single region where they experience time-dependent
electromagnetic fields.
Sample analysis with an ion trap analyzer may be divided into several steps:
Sample Introduction: Compounds are introduced from the transfer line to the ion
trap analyzer through the direct coupled capillary column.
Sample Ionization: The compound is ionized in the mass spectrometer by either:
- destabilizing its molecular structure, causing an electron to be removed from
somewhere on the molecule (Electron Impact/Ionization) (EI).
- pressuring the MS with a selected reagent gas; e.g., methane, performing EI
on the gas to form reagent ions, and allowing ion-molecule reactions to occur
between the compound and the reagent ion (Chemical Ionization) (CI).
Sample Fragmentation: Depending on the compounds original structure and the
excess destabilizing (internal) energy present in the structure, the ionized
compound (molecular ion) breaks apart (fragmentation). This process forms
fragment ions and neutral fragments.
Ion Storage: The ions (molecular and fragment ions) which were just produced
are stored and stabilized in the ion trap cavity, where they travel in defined orbits.
Helium buffer gas is also present in the cavity. It helps to focus the ions into more
compact orbits which produce sharper mass peaks as they are scanned out.
Helium is used because it does not ionize as readily as the analyte molecules.
While helium ions are the most dominant species in the trap, they are not stored,
but are pumped away as soon as they are formed.
Ion Analysis: The ions are analyzed by applying a radio frequency (rf) (1.1 MHz)
voltage to the ring electrode encircling the trap cavity. As the voltage increases
on the ring electrode, ions are sequentially ejected from the trap according to
their mass-to-charge ratio. A small AC voltage (axial modulation voltage) of fixed

154
frequency and amplitude is also applied to the endcap electrodes during the
analysis to improve ion injection and unit mass resolution.
The Saturn GC/MS has two techniques for generating sample ions in the ion
trap. Consequently there are two basic scan functions, i.e., the electron
ionization scan function and the chemical ionization scan function. A scan
function is a representation of the timing sequence for ion trap operation. It
shows the variations in time of the rf potential applied between the ring electrode
and the end cap electrodes, as well as any supplementary waveforms applied to
the cap electrodes.

155
2000 MS Method Chemical
Ionization
Introduction
Chemical ionization (CI) provides mass spectral data that complement electron
ionization (EI) data for the analysis of complex compounds. In the CI mode of
operation, a CI reagent gas is introduced into the ion trap analyzer. The reagent
gas is ionized by EI. Then, the sample molecules are ionized by ion molecule
reactions with the reagent gas ions.
CI is a softer ionization technique than EI. That is, CI imparts less energy to the
sample molecules than does EI. Thus, the ionized sample molecule undergoes
less fragmentation, and an ion indicative of the molecular weight is more likely to
be observed. In addition to molecular weight confirmation, CI mass spectra often
provide other significant structural information that may not be available from EI
mass spectra.
The Chemical Ionization Scan Function
EI space charge control uses the integrated ion current from a fixed ion time
prescan to calculate the analytical scan ionization time. In contrast, CI space
charge control does not use a fixed ionization time prescan to measure the
charge formed. CI uses a portion of the ions detected during the previous
analytical scan to calculate the ionization and reaction times for the next
analytical scan.

156
The figure below shows the scan function for chemical ionization.

A Reagent gas ionization, time determined by the previous scan
B Ejection of unwanted ions (i.e., non-reagent ions) using SECI waveform
C Reaction of reagent gas ions with sample molecules, time determined from
previous scan
D Ejection of ions with masses lower than that of the background mass
E Acquisition of CI mass spectrum
CI Scan Function
Chemical ionization occurs by forming reagent ions by electron impact, which
react with the sample to form product ions by ion molecule reactions. The
ionization and reaction storage rf are maintained at the same level. Unwanted
sample ions formed by electron ionization during the formation of the reagent
ions are ejected using a low frequency waveform prior to the chemical ionization
step.
The ion trap operates in a pulsed mode. The supply of reagent ions is created
during the ionization pulse and consumed during the reaction period to form
analyte ions. The number of analyte ions depends on the concentration of the
analyte, the initial reagent ion intensity, and the reaction time.
Because the spectral intensity is proportional to sample concentration and
reaction time, linear calibration curves can be obtained.
Then, during the analytical scan, the following steps occur:
1. The reagent gas is ionized for the length of time determined by the previous
scan.(A)
2. All ions with a mass greater than the reagent ions are ejected, i.e., all EI ions
from the sample. ( B)
3. Reagent gas ions react with sample molecules to form sample ions. (The
reaction time was determined by the previous scan.) (C)

157
4. Reagent gas ions are ejected. (D)
5. The CI mass spectrum is acquired for the sample ions. (E)
SECI ejects all ions above a cutoff mass by applying a waveform between the
ionization and reaction periods. This is the preferred mode of operation on the
Saturn GC/MS, since all EI artifact ions are eliminated. It should be noted that
fragmentation can still be observed in CI spectra due to energy imparted when
the proton is transferred from the reagent ion to the sample molecule.
Ion Formation By Chemical Ionization
In CI, ionization of sample molecules is a two-step process. In the first step,
reagent gas ions are formed as the reagent gas is ionized by interaction with
electrons emitted by the filament.
In the second step, the reagent gas ions react with sample molecules in the ion
trap to form sample ions. There are four principal reactions between reagent gas
ions and sample molecules. They are:
(A) Proton transfer: (RH)
+
+ M (MH)
+
+ R
(B) Hydride abstraction: R
+
+ M [M-H]
+
+ RH
(C) Association: R
+
+ M (MR)
+

(D) Charge transfer: R
+
+ M M
+
+ R
where R
+
is the secondary reagent gas ion and M is the neutral sample
molecule.
For methane CI, proton transfer (A) is the major reaction, and hydride abstraction
(B) is the next most often observed reaction. In both cases the resulting even-
electron ions are often relatively stable, and the observation of strong (M+1) or
(M-1) ions is possible even if the EI spectrum of the same component shows no
molecular ion. The exothermicity of the reactions determines the amount of
energy deposited; therefore, the degree of fragmentation can be controlled by
the choice of a suitable CI reagent gas. The proton affinities of some common
reagent gases of this type, known as proton transfer agents or Bronsted acids,
range from 130 kcal/mol to 200 kcal/mol in the following order: methane, water,
isobutane, and ammonia (with ammonia resulting in the softest ionization). By
choosing a suitable reagent gas, you can obtain high specificity (i.e., less
efficient detection of background or matrix interferences compared to the
analyte) as well as molecular weight information for the compounds of interest.
The association or clustering reactions (C) typically have very low reaction rates,
and the reaction products require rapid collisional stabilization. They are typically
seen on the Saturn GC/MS at much lower abundance then the (M+1) ion, but
when (M+28) and (M+41) ions are observed using methane, they are useful for
verifying the molecular weight.
The charge transfer reaction (D) produces a radical molecular ion (i.e., an ion
with an odd number of electrons) that dissociates quickly, giving EI-like spectra.
However, the energy deposited in the molecular ion and the resulting
fragmentation pattern does not depend on the electron energy of the ionizing
electrons. Common charge-transfer reagent gases are nitrogen and argon.

158

NOTE: Reagent ion formation can be a complex process. For example, for
proton transfer CI with methane used as the reagent gas, reagent gas ions are
formed as follows:
First, methane is ionized to form two primary ions:
CH
4
+ e- (CH
4

-
)
+
+ 2 e
-

CH
4
+ e- CH
3
+
+ e- + H
-
These primary ions then react very rapidly to form predominantly the secondary
ions,
CH
5
+
and C
2
H
5
+
:
(CH
4

-
)
+
+ CH
4
CH
5
+
+ CH
3

-

CH
3
+
+ CH
4
C
2
H
5
+
+ H
2

The CI Parameters

Reagent Gas

When you select a standard reagent gas (i.e., methane, isobutane, acetonitrile or
ammonia), the CI parameters for the selected gas are set automatically, and you
do not need to change the default values of the CI parameters. Be aware that if
you do change a CI parameter and set it incorrectly, you may not be able to
operate properly in CI. However, the CI parameters: Max. Ion Time, Max. React
Time, CI Storage Level Ejection Amplitude (v), and Background Mass can be
varied to optimize for sensitivity.
CI Storage level
CI Storage level is the value of the smallest mass stored in the ion trap during
the ionization of the reagent gas and the lowest mass stored during the reaction

159
period. The CI storage Level is typically set to a value that is lower than the
mass of the reagent ion of interest. The CI Storage Level can be set to any
value from 5 to 150 m/z. The optimum CI storage level will depend on the
molecular ion of the analyte. Generally, one should use higher CI storage levels
for higher molecular ions, without raising the storage level to cause ejection of CI
reagent ions. For example, the molecular ion of the analyte is 352 m/z. Using
acetonitrile, raising the rf storage level to 25 m/z may give better sensitivity than
the default of 19 m/z. If the CI storage level is raised, the Ejection amplitude will
have to be increased. For acetonitrile, raising the rf storage level from 19 to 25
m/z, requires an increase in the ejection amplitude from 15 to 25 volts. These
values are determined empirically.
Ejection Amplitude (v)
Ejection Amplitude (v) is a voltage that corresponds to a low mass ejection cutoff
that is slightly higher than the mass of the largest reagent ion produced by the
selected reagent gas. This voltage actively ejects unwanted ions (i.e., not
reagent ions) that are produced during ionization. All ions with masses equal to
or greater than the level established by this voltage will be ejected prior to the CI
reaction. When this value is set to 0, active ejection is disabled; otherwise,
increasing the voltage decreases the ejection cutoff mass. Generally, higher CI
storage values require higher ejection voltages. The voltage should not be set so
high as to cause the ejection of CI reagent ions.
Background mass
Background mass is a mass value that is greater than or equal to the mass of the
largest reagent ion produced by the selected reagent gas. All ions with masses
less than this mass value are ejected from the ion trap after the reaction between
the reagent ions and sample molecules. The background mass level can be set
to any value from 10 to 300 m/z. For methane, ammonia, and isobutane, the
reagent ion ejection levels are 45, 45, and 65 m/z, respectively.
Target TIC Value
In CI Auto mode, the target TIC value determines how many ions are allowed in
the ion trap. A maximum value of 30000 can be set.
Maximum ionization time
Maximum ionization time is the maximum time that energetic electrons, emitted
from the filament, are allowed to interact with reagent gas molecules to form
reagent ions. In CI, the maximum ionization time can be set to any value from 10
to 2500 usec. For methane, ammonia, and isobutane, the maximum ionization
time is usually set to 2000 usec.
Maximum reaction time
Maximum reaction time is the maximum time that reagent gas ions are allowed to
react with sample molecules to form ions. The maximum reaction time can be set
to any value from 1 to 128 milliseconds. For methane, isobutane, and ammonia,
the maximum reaction time is typically set to 60 milliseconds.

160
Prescan Ionization Time
Prescan Ionization Time parameter as used in MS/MS applications is set to 200
usec.
Default Parameters for Reagent Gases used in Chemical Ionization Mode
Reagent Gas Methane Isobutane Ammonia
Maximum Ionization Time
(usec)
2000 2000 2000
Maximum Reaction Time
(msec)
60 60 60
CI Storage Level (m/z) 13 19 13
CI Background Mass (m/z) 45 65 40
Ejection Amplitude (v) 9.0 15 9
Using Non-Standard CI Reagent Gases
Gases other than methane, ammonia, or isobutane can be used successfully
with the Saturn GC/MS. If you are using a non-standard CI reagent gas, you
need to select the Reagent Gas list item labeled "User Defined". Then you will
need to input the name of the gas and the values for the CI parameters; the
parameter values will not be set up automatically.
NOTE: When you install a new supply of a non-standard reagent gas, you must
adjust the reagent gas pressure. After the pressure has been adjusted properly,
you should check the pressure at least once every day if you plan to operate in
CI on a daily basis. For procedures to adjust and check the pressure of a non-
standard reagent gas, please contact a Customer Support Representative.
How to Optimize the CI Background Mass
The proper setting for the CI background mass eliminates reagent ions which are
left over after the reaction period.
With the CI reagent connected and properly adjusted, click the CI Gas control on
the System Control Manual Control page to open the CI gas valve solenoids.
Turn on the trap and observe the spectrum over the scan range specified in the
acquisition method, (dont use adjust CI Gas). Look for any ions at the low end of
the range. The figure below shows an acetonitrile spectrum with the CI
background mass set too low (=50 m/z). The 54 ion is clearly visible and has
caused a reduced ionization time. The next figure shows a proper background
mass setting for the same conditions (=65 m/z).

161

CI Background Mass Set Too Low.

CI Background Mass Properly Set.
How to Determine the Proper Ejection Amplitude
The proper setting for the Reagent Ion Eject Amplitude will remove EI generated
fragments but not affect the reagent ions.
With the CI reagent connected and properly adjusted, click the CI Gas control on
the Manual Control page in System Control to open the CI gas valve solenoids.
Turn on the trap and observe the spectrum over the scan range specified in the
acquisition method, (dont use Adjust CI Gas). Temporarily set the CI
background mass to a value below that of the highest mass reagent ion (record
the previous value so you can restore it when you finish with this procedure).
Adjust the Ejection Amplitude until the reagent ion starts to be diminished.
Restore the CI background mass and verify that no reagent ions remain.

162
Chemical Ionization Using Fixed Parameters

The reaction parameters that are normally set by the Auto Control can also be
set manually. For Chemical Ionization using fixed parameters, the instrument
uses the Ionization Time entered in the method editor. The reaction time that
will be used is determined as follows:
Time Ionization x
Time Ionization Maximum
Time Reaction Maximum
= Time Reaction Set
where the maximum reaction and ionization times are entered below the
Ionization Time.
Using Liquid CI Reagents
Introduction
Liquids may be used with the Saturn GC/MS as CI reagents in addition to the
standard CI reagent gases. The liquid is placed in a reservoir and connected in
place of the tank of CI gas. The vapor pressure of the liquid reagent is usually
sufficient to provide a constant, low flow to allow operation in the CI mode.
Hardware
The figure below shows a functional block diagram of the CI plumbing setup for
using liquid reagents.
Liquid
Reservoir
CI Shutoff
Valve
Restrictor Restrictor
CI Solenoid
To Manifold
CI Needle
Valve
To Roughing Pump

Functional Block Diagram of Liquid CI Plumbing

163
Choice of Liquid CI Reagents
Many liquids may be used as CI reagents. The general requirements are a
moderate vapor pressure and fairly low molecular weight. If the molecular weight
is too high, you may have problems seeing low molecular weight analytes
because they will be excluded as the reagent ions are ejected. If the vapor
pressure is too low, not enough reagent will enter the Saturn GC/MS for effective
CI operation. This may be remedied by passing a stream of helium through the
reagent vial. This strategy has been used successfully with water as the reagent.
The following have been used as liquid CI reagents on a Saturn GC/MS:
- Methanol
- Dimethyl ether
- Dimethylamine
- Acetonitrile
- Diethyl ether
- Carbon disulfide
- Water (with a helium stream)
Setting CI Parameters for Liquid Reagents
Set the CI Storage level sufficiently low to store the CI reagent ions.
Set the CI background mass to a level sufficiently high that reagent ions do not
appear in the CI spectrum.
Set the Reagent ion eject amplitude to a value between 7.4 and 12.5 volts. As a
starting point, use these values:
Mass Eject Amplitude
<20 7.5
21-50 9
>50 12.5
Adjust the value up or down as necessary to eject ions above the highest
reagent ion while not ejecting the ions from the reagent.
Suggested CI Parameters for Liquid CI Reagents
Reagent Liquid Acetonitrile d3-Acetonitrile Methanol
CI Storage Level (m/z) 19 19 19
Ejection Amplitude (v) 15 15 15
Background Mass (m/z) 65 65 55
Target TIC 5000 5000 5000
(sec)
2000 2000 2000
Maximum Reaction Time
(msec)
40 20 40
Prescan Ion Time (usec) 100 100 100

164

Setting the Reagent Pressure for Liquid CI Reagents
Connect a liquid reagent reservoir containing the chosen liquid to the liquid
reagent inlet block.
Open the CI needle valve 6-7 turns counterclockwise.
Open the CI gas valve solenoids by clicking on the CI Gas Control on the System
Control page and allow the vapor flow from the reservoir to equilibrate. If, after
several minutes, there is not enough CI gas entering the trap, further open the
needle valve (clockwise).
While observing the spectrum using Adjust CI Gas, turn the CI needle valve to
increase or decrease the amount of reagent entering the trap until the resolution
between M and M+1 just starts to degrade. For best results when using
acetonitrile, use a filament emission current of at least 20 uA and maintain at
least 50% valley between m/z 41 and m/z 42.

Properly Adjusted Acetonitrile Reagent Spectrum

Properly Adjusted Methanol Reagent Spectrum

165
Adjusting the CI Reagent Gas Pressure for Gases Other
Than Methane
When you install a new supply of reagent gas, you must adjust the pressure of
the CI reagent gas in the ion trap. After the reagent gas pressure has been
adjusted properly, we recommend that you check the pressure at least once
every day if you intend to perform CI analyses on a daily basis.
The reagent gas pressure is adjusted (or checked) by using the Adjust CI Gas in
System Control. See System control section.
Checking the CI Reagent Gas Pressure. In these procedures, in which methane
serves as the reagent gas, you observe the methane spectrum and adjust the
methane pressure so that: the ratio of the peak heights at mass 17 (CH
5
+) to
mass 16 (CH
4
+) is about 10:1; the ratio of the peak heights at mass 17 to 29
(C
2
H
5
+) is about 1:1; and mass 41 (C
3
H
5
+) is visible.
If you are using isobutane or ammonia as the reagent gas, you can use the same
procedures to adjust and check the reagent gas pressure, with the following
modifications:
Isobutane With isobutane as the reagent gas, observe the isobutane
spectrum and adjust the reagent gas pressure so that the ratio of the peak
heights at mass 57 [(CH
3
)
3
C
+
] to mass 43 [(CH
3
)
2
CH
+
] is about 1:1.
Ammonia With ammonia as the reagent gas, observe the ammonia
spectrum and adjust the gas pressure so that the ratio of the peak heights at
mass 18 [(NH
3
)H
+
] to mass 17 (NH
3
+
) is about 10:1.
In each case, by following these guidelines, the reagent gas pressure in the ion
trap will be approximately 1 x 10
-5
Torr to 2 x 10
-5
Torr (about 1.3 x 10
-3
to 2.6 x
10
-3
Pa).

Reagent Ion Spectrum for Isobutane

166

Reagent Ion Spectrum for Ammonia
Tuning for CI Operation
In CI, as in EI, the Saturn GC/MS is tuned to achieve the best combination of
maximum peak height (sensitivity), optimum resolution of peaks, and smooth
peak shape. In addition, as in EI, the key to proper CI tuning is to optimize the
number of ions in the ion trap: too few ions, sensitivity suffers; too many ions,
resolution and peak shape suffer.
In CI, the two main factors that affect the number of ions in the ion trap are the
ionization time and the reaction time. (The filament emission current is an
important third factor.)
To a first approximation, the number of reagent ions formed is directly
proportional to the ionization time, and the number of sample ions formed is
directly proportional to the reaction time.
To tune the Saturn GC/MS for CI operation, you simply tune and calibrate the
instrument from System Control Auto Tune section. You do not need to run a
different automatic setup, tuning, and calibration program for CI. The setup
parameters and mass calibration established for EI are also satisfactory for CI.
Low-Pressure CI vs. High Pressure CI
The conventional high pressure CI source in quadrupole or magnetic mass
spectrometers requires reagent gas pressures on the order of 1 Torr. Such high
pressures are necessary because the residence time of ions is very short, about
10
-5
seconds. Higher pressures result in the generation of the large number of
reagent ions that are necessary for successful chemical ionization in this short
time frame.
The Saturn GC/MS ion trap accumulates reagent ions and holds them for
reaction periods on the order of 1 to 128 milliseconds. In this longer time frame, a
lower reagent gas pressure (ca. 10
-5
Torr) produces a large population of sample
ions.

167
The practical advantages of low-pressure CI are:
No need for an expensive vacuum pumping system to handle the large
amounts of reagent gas
Low consumption of expensive high-purity reagent gas
Minimal contamination of the ion source
The potential of alternating EI and CI scans without the compromises in
spectral quality typically seen in high-pressure sources
Very good CI sensitivity in the full-scan mode
Liquid reagents are easily used
Recommended Reading
- For more information about the theory of chemical ionization and the
interpretation of CI mass spectra, refer to Chemical Ionization Mass
Spectrometry by Alex G. Harrison, CRC Press, Boca Raton, Florida, 1983.
- For a comparison of high-pressure and low-pressure CI in an ion trap, refer
to S.M. Boswell, R.E. Mather, and J.F.J. Todd, Chemical Ionization in the
Ion Trap: a Comparative Study, Int. J. Mass Spectrom. Ion. Proc. 99 (1990),
139-149.
- For examples of liquid CI reagents, refer to:
G.F. Bauerle, Jr., B.J. Hall, N.V. Tran, and J.S. Bradbelt, Ion-Molecule
Reactions of Oxygenated Chemical Ionization Reagents with Vincamine, J.
Am. Soc. Mass Spectrom. 7 (1996), 250-260.

G. Moneti, et.al, Acetonitrile as an Effective Reactant Species for Positive-
Ion Chemical Ionization of Hydrocarbons by Ion-Trap Mass Spectrometry,
Rapid. Commun. in Mass Spectrom., 10 (1996), 167-170.

168

169
2000 MS Method Command
Reference
Spreadsheet editing

Item Description
Add Duplicates MS parameters of the last segment and adds it to the
end of the current table.
Insert Inserts a row before the one currently selected with the parameter
values of the highlighted row.
Delete Deletes the currently selected row.
Default Will insert system default parameters.
Restore Inserts parameters that were present when the method was first
opened, or last saved.

170

Item Description
Segment Description Comment Line. 20 characters can be entered.
Start Time Start time of segment in minutes. 0.00 to 649.99 min.
End Time Time segment will be terminated. 0.10 to 650 min.
Low Mass Lower end of mass range to be acquired. 10 to 650 m/z.
High Mass Upper end of mass range to be acquired. 10 to 650 m/z.
Ionization Mode Method of ion formation in trap.
Ion Preparation Options applied after ionization to alter the ions stored in
the trap before analysis.
Special Applications To specify data acquisition in Profile mode (vs. Centroid)
or to specify a pre-acquisition flow sampling period.
The flow sampling segment

Item Description
Method Start Time The time to flush the system before sample collection
begins plus the actual sampling time. Time of -30 to 0
minutes may be entered.
Flow-Sampling Start Time/
End Time
The duration of the actual sampling, from -10.00 to 0
minutes. If time = 0, no flow sampling is done.
Sample Flow Rate Set from 1 to 100 mL/min. Must be equal to value set
on EMFC in manual mode. If EMFC is set to auto
mode, the sample flow rate specified will be
downloaded at the start of the injection

171
Ionization Mode

Item Description
EI-Fixed Ions formed by electrons for a time set in method.
EI-Auto Ions formed by electrons for time calculated from AGC function
CI-Fixed Ions formed by collisions with CI reagent ions for time set in method.
CI-Auto Ions formed by collisions with CI reagent ions for time calculated
from previous scan.
None Selected when hardware should be turned off (i.e. solvent peak
elution)
Ion Preparation

Item Description
SIS Selectively trap ions, range of ions or ejection of ions.
MS/MS Isolate and dissociate an ion or ions.
AMD Find optimum dissociation conditions for MS/MS for single parent
ion.
MS
n
Use two to five parent ions for sequential dissociation.
uSIS Unit mass isolation of 1 to 10 ions.

172
Segment Setpoints

Item Description
Scan Time The duration of each scan (in seconds). Values from 0.10
to 5.00 seconds per scan. Below is displayed the number
of micro scans per scan for the selected mass range and
scan time.
Multiplier Offset Multiplier offset (relative to 10
5
gain). Range 300 Volts.
Emission Current Emission current may be set from 5 to 100 A.
Count Threshold The minimum number of intensity counts per sampling
interval required before a signal is recorded. Values from 0
to 1000 counts; it is typically set to 0 or 1 count.
Mass Defect Mass defect is defined as the difference between the
nominal mass of an atom (or ion) and its exact mass.
Values from -300 mu per 100u to +300 mu per 100u can
be set.
Cal Gas Click on box if Calibration gas is used in the Method
segment.

173
Ionization Mode - EI Auto

Item Description
Mass Range
Segment Breaks
The EI scan is made up of between 1 and 6 scan
segments, each holding a contiguous mass-range
segment. Overall, the set covers the entire mass range of
10 to 650 m/z. Only the intermediate segment boundaries
can be changed by the user.
Ionization Storage
Level
The rf voltage used during the ionization period. Values
from 5 to 150 m/z.
Ionization Time
Factor
The Ionization Time Factor, given as a percent, is a
number that is multiplied by the calculated ionization time
(determined by the AGC pre-scan pulse) to give the actual
ionization time. Values from 1 to 999%.
Target TIC Value
Target TIC value determines how many ions AGC allows
into the ion trap during the calculated ionization time.
Range of values is 10 to 65000.
Maximum
Ionization Time
Sets the limit for the longest ionization time which AGC can
use. Values from 10 to 65000 usec.
Prescan
Ionization Time
This ionization time determines the number of ions formed
for the prescan. This value is then used to calculate the
ionization time for the analytical scan. Range 10 to 2500
usec.
Background Mass
The lowest mass used to determine the target TIC (total
ion current) value; all ions of lower mass are ejected from
the ion trap before the AGC prescan pulse. The
background mass can be set to any value from 10 m/z to
300 m/z; it is typically set to 45 m/z.
rf Dump Value
This value specifies the high m/z used for the prescan. It
should always be as high or higher than the analytical scan
range high mass.

174
Ionization Mode - EI Fixed

Item Description
Mass Range Segment
Breaks
The EI scan is made up of between 1 and 6 scan
segments, each holding a contiguous mass-range
segment. Overall, the set covers the entire mass range
of 10 to 650 m/z. Only the intermediate segment
boundaries can be changed by the user.
Ionization Storage
Level
The rf voltage used during the ionization period. Values
from 5 to 150 m/z.
Ionization Time
Factor
The Ionization Time Factor, given as a percent, is a
number that is multiplied by the calculated ionization
time (determined by the AGC pre-scan pulse) to give the
actual ionization time. Values from 1 to 999%.
Ionization Time
Sets the fixed ionization time. Values from 10 to 65000
usec.
Max Ionization Time
Sets the maximum ionization time used by the system.

175
The CI Parameters
CI Auto

Reagent Gas

Item Description
Reagent Gas
Select CI reagent for application. Select User-Defined for
gas not listed.
CI Storage level
Value of the smallest mass stored in the ion trap during the
ionization and reaction period of the reagent gas. Values
from 5 to 150 m/z.
Ejection
Amplitude (v)
This voltage actively ejects unwanted ions (i.e., not reagent
ions) that are produced during the ionization stage of the CI
scan function. When this value is set to 0, active ejection is
disabled.
Background mass
The mass value that is greater than or equal to the mass of
the largest reagent ion produced by the selected reagent
gas. Values from 10 to 300 m/z.
Target TIC Value
Target TIC value determines how many ions are allowed in
the ion trap. CI uses a portion of the ions detected during
the previous analytical scan to calculate the ionization and
reaction times for the next analytical scan. Values from 10
to 30000.
Maximum ionization
time
Maximum time that energetic electrons, emitted from the
filament, are allowed to interact with reagent gas molecules
to form reagent ions. In CI, the maximum ionization time can
be set to any value from 10 to 2500 usec.

176
Item Description
Maximum reaction
time
Maximum time that reagent gas ions are allowed to react
with sample molecules to form ions. The maximum reaction
time can be set to any value from 1 to 128 milliseconds.
Prescan Ionization
Time
Ionization time of the prescan uses in MS/MS. This is
normally set to 200 usec for CI.
CI Fixed Parameters

Item Description
Reagent Gas
Select CI reagent for application. Select User-Defined for
gas not listed.
CI Storage level
Value of the smallest mass stored in the ion trap during the
ionization and reaction period of the reagent gas. Values
from 5 to 150 m/z.
Ejection Amplitude
(v)
This voltage actively ejects unwanted ions (i.e., not reagent
ions) that are produced during the ionization stage of the CI
scan function. When this value is set to 0, active ejection is
disabled. Range 0 to 65.0 volts
Background mass
The mass value that is greater than or equal to the mass of
the largest reagent ion produced by the selected reagent
gas. Values from 10 to 300 m/z.
Ionization Time
Fixed time CI reagent ions are formed. Values from 10 to
2000 usec.
Maximum ionization
time
Maximum time that energetic electrons, emitted from the
filament, are allowed to interact with reagent gas molecules
to form reagent ions. In CI, the maximum ionization time can
be set to any value from 10 to 2500 usec.
Maximum reaction
time
Maximum time that reagent gas ions are allowed to react
with sample molecules to form ions. The maximum reaction
time can be set to any value from 1 to 128 milliseconds.

177
Ion Storage (SIS) Parameters

Item Description
Storage Mass
Ranges
Table to enter ion(s) or range of ions for selective storage.
Enter up to five mass ranges.
Low Mass Low m/z integer mass. Mass range from 25 m/z to 650 m/z.
High Mass High m/z integer mass. Mass range from 25 m/z to 650 m/z.
Ejection Masses Table to enter ion(s) for selective ejection. Enter up to five
ions.
Ion Mass Integer mass(es) of those ion(s) to be ejected. Use ADD
button to enter value.
Amplitude Range is 1% to 200% with a default of 100%.

Customize SIS

Item Description
Ionization Storage
Level
Minimum mass that can be stored and isolated. Range: 20
m/z s mass s 60 m/z. Default = 48 m/z.
Autoscale SIS waveform amplitude is automatically scaled as a function
of the frequency components and storage rf voltage selected.
By unchecking Autoscale, the user can enter a waveform
amplitude.

178

The MS/MS Ion Prep Method

Item Description
Isolation Mass to be isolated and window of isolation
Parent Ion Mass (m/z) Integer or exact mass. Parent ion mass range is
50 to 650 m/z.
Isolation Window (m/z) Integral and fractional mass isolation windows
are both accepted. Range is 1.0 to 7.0 m/z and
is mass dependent. The default value is 3.0 m/z.
Dissociation Waveform type and used for dissociation.
Waveform Type Nonresonant or resonant excitation.
Excitation Storage Level Rf storage level in m/z when the dissociation
waveform is applied following isolation. The
excitation storage level range depends on the
parent mass, but the storage level must lie more
than 2 mass units below the lowest product ion
value.
Excitation Amplitude Range for nonresonant excitation is 0 to 100
volts. For resonant excitation, the range is 0 to
60 volts. Default values for nonresonant
excitation is 20 volts and 0.2 volts for resonant
excitation.
The MS q Calculator

179
Item Description
MS q Calculator Use the q Calculator for suggested
excitation storage levels.
Desired Product Mass Enter product mass expected from
dissociation.
Desired q Value Empirically observed q value of 0.4
provides an optimum yield of product
ions.

Customize Non-resonant Method

Item Description
Ionization Storage
Level
The m/z value the rf is maintained during ionization and
the coarse isolation. Range 35 to 160 m/z (upper limit of
range depends on parent ion m/z), default = 48 m/z.
Ejection Amplitude Amplitude (v) of the ejection waveform during the coarse
isolation step. Range 0 to 60 volts, default=20.
Low Edge Offset Integer value step to optimize the ejection of the mass
just below the parent ion mass. Range is 0 to 20 steps.
The default value is 6.
High Edge Offset The integer value step to optimize the ejection of the
mass just above the parent ion mass. Range is -20 to 20
steps.
High Edge Amplitude Amplitude of broadband waveform use to eject masses
above the isolated parent ion. Default is 30 volts.

180
Item Description
Isolation Time The dwell time during which the rf field is held constant
in the high mass ejection step. Range 1 - 10 msec.
Excitation Time Time for collision-induced dissociation (CID) by ion
excitation. Range 0 to 1000 msec. The default is 20
msec.

Customize Resonant Method

Item Description
Ionization Storage Level The m/z value the rf is maintained during
ionization and the coarse isolation. Range 35
to 160 m/z (upper limit of range depends on
m/z of the parent ion), default = 48 m/z.
Ejection Amplitude Amplitude (v) of the ejection waveform during
the coarse isolation step. Range 0 to 60 volts,
default=20.
Low Edge Offset Integer value step to optimize the ejection of
the mass just below the parent ion mass.
Range is 0 to 20 steps. The default value is 6.
High Edge Offset The integer value step to optimize the ejection
of the mass just above the parent ion mass.
Range is -20 to 20 steps.
High Edge Amplitude Amplitude of broadband waveform use to eject
masses above the isolated parent ion. Default
is 30 volts.

181
Item Description
Isolation Time The dwell time during which the rf field is held
constant in the high mass ejection step.
Range 1 - 10 msec.
Excitation Time Time for collision-induced dissociation (CID)
by ion excitation. Range 0 to 1000 msec. The
default is 20 msec
Modulation Range Mass range over which the rf storage field is
modulated during resonant CID. The range is
0 to 12 steps, default is 2 steps. Value of 0
gives a fixed rf storage field, i.e., no
modulation.
Modulation Rate The number of microseconds that will be spent
at each step. The range is 29 usec to 5600
usec, default is 3000 usec/step.
Number of Frequencies Enter an odd integer in the range of 1 to 121.
A frequency number of one generates a single
supplementary frequency applied to the end
caps. An integer of 3, generates three
frequencies: the resonance frequency and
frequencies 500 Hz above and below that
frequency.
CID Frequency Offset To offset the dissociation frequency. The CID
frequency can be adjusted between 3000
Hz.
Automated Methods Development (AMD)

Item Description
Parent Ion Mass (m/z) Integer or exact mass. Parent ion mass range is 50 to
650 m/z.
Isolation Window (m/z) Integral and fractional mass isolation windows are both
accepted. Range is 1.0 to 14.0 m/z and is mass
dependent. The default value is 3.0 m/z.

182
Item Description
Excitation Storage
Level
Rf storage level in m/z when the dissociation waveform
is applied following isolation. The excitation storage level
range depends on the parent mass, but the storage level
must lie more than 2 mass units below the lowest
product ion value.
Excitation Amplitude Range for nonresonant excitation is 0 to 100 volts. For
resonant excitation, the range is 0 to 60 volts. Default
values for nonresonant excitation is 20 volts and 0.2
volts for resonant excitation.

Item Description
Ionization Storage Level The m/z value the rf is maintained at during
ionization and the coarse isolation. Range 35 to
160 m/z, default = 48 m/z.
Ejection Amplitude Amplitude (v) of the ejection waveform during
the coarse isolation step. Range 0 to 60 volts,
default=20.
Low Edge Offset Integer value step to optimize the ejection of
the mass just below the parent ion mass.
Range is 0 to 20 steps. The default value is 6 .
High Edge Offset The integer value step to optimize the ejection
of the mass just above the parent ion mass.
Range is -20 to 20 steps.

183
Item Description
High Edge Amplitude Amplitude of broadband waveform used to eject
masses above the isolated parent ion. Default
is 30 volts.
constant in the high mass ejection step. Range
1 - 10 msec.
Excitation Time Time for collision-induced dissociation (CID) by
ion excitation. Range 0 to 1000 msec. The
default is 20 msec.
modulated during resonant CID. The range is 0
to 10 steps, default is 2 steps. Value of 0 gives
a fixed rf storage field, i.e., no modulation.
Modulation Rate The number of microseconds that will be spent
at each step. The range is 29 usec to 5600
usec, default is 3000 usec/step.
Number of Frequencies Enter an odd integer in the range of 1 to 121. A
frequency number of one generates a single
supplementary frequency applied to the end
caps. An integer of 3, generates three
frequencies: the resonance frequency and
frequencies 500 Hz above and below that
frequency.
frequency can be adjusted between 3000 Hz.
Ion Preparation MS/MS
Set up Multiple Reation Monitoring by adding lines to a MS/MS run with different
parent ion masses and different dissociation parameters.

Item Description
Parent Ion Mass (m/z) Integer or exact mass. Parent ion mass range is 50
to 650 m/z.
Isolation Window (m/z) Integral and fractional mass isolation windows are
both accepted. Range is 1.0 to 14.0 m/z and is
mass dependent. The default value is 3.0 m/z.

184
excitation storage level range depends on the parent
mass, but the storage level must lie more than 2
mass units below the lowest product ion value.
Excitation Amplitude Range for nonresonant excitation is 0 to 100 volts.
For resonant excitation, the range is 0 to 60 volts.
Default values for nonresonant excitation is 20 volts
and 0.2 volts for resonant excitation.
Ionization Storage Level The m/z value the rf is maintained at during
ionization and the coarse isolation. Range 35 to 160
m/z, default = 48 m/z.

Item Description
Ejection Amplitude Amplitude (v) of the ejection waveform during the
coarse isolation step. Range 0 to 60 volts,
default=20.
Low Edge Offset Integer value step to optimize the ejection of the
mass just below the parent ion mass. Range is 0 to
20 steps. The default value is 6.
High Edge Offset The integer value step to optimize the ejection of the
mass just above the parent ion mass. Range is -20 to
20 steps.
High Edge Amplitude Amplitude of broadband waveform use to eject
masses above the isolated parent ion. Default is 30
volts.
constant in the high mass ejection step. Range 1 - 10
msec.
excitation. Range 0 to 1000 msec. The default is 20
msec.
modulated during resonant CID. The range is 0 to 10
steps, default is 2 steps. Value of 0 gives a fixed rf
storage field, i.e., no modulation.
Modulation Rate The number of microseconds that will be spent at
each step. The range is 29 usec to 5600 usec,
default is 3000 usec/step.
Number of Frequencies Enter an odd integer in the range of 1 to 121. A
frequency number of one generates a single
supplementary frequency applied to the end caps. An
integer of 3, generates three frequencies: the
resonance frequency and frequencies 500 Hz above
and below that frequency.
frequency can be adjusted between 3000 Hz.

185

MS
n

MS
n
uses two parent ions for sequential dissociation. The additional dissociation
step can be used to increase selectivity of analyte versus background or for
additional structure information.

First, work out optimized conditions for MS/MS of the first parent ion. AMD will
make this process go faster.
Then optimize the conditions for dissociation of that product ion (entered under
parent ion 2). You may need to make sequential injections using the MS
n

method. If the second generation product ion is in the original EI or CI spectrum,
then you can use AMD to find the optimum conditions.

Item Description
Parent Ion Mass (m/z) Integer or exact mass. Parent ion 1 mass range
is 50 to 650 m/z. Parent ion 2 mass range is
from 50 to (parent ion-1)m/z, and so on.
Isolation Window (m/z) Integral and fractional mass isolation windows
are both accepted. Range is 1.0 to 14.0 m/z
and is mass dependent. The default value is
3.0 m/z.

186
Item Description
excitation storage level range depends on the
parent mass, but the storage level must lie
more than 2 mass units below the lowest
product ion value.
Excitation Amplitude Range for nonresonant excitation is 0 to 100
volts. For resonant excitation, the range is 0 to
60 volts. Default values for nonresonant
excitation is 20 volts and 0.2 volts for resonant
excitation.

Item Description
Ionization Storage
Level
The m/z value the rf is maintained at during ionization and
the coarse isolation. Range 35 to 160 m/z, default = 48
m/z.
Ejection Amplitude Amplitude (v) of the ejection waveform during the coarse
isolation step. Range 0 to 60 volts, default=20.
Low Edge Offset Integer value step to optimize the ejection of the mass just
below the parent ion mass. Range is 0 to 20 steps. The
default value is 6 .
High Edge Offset The integer value step to optimize the ejection of the mass
just above the parent ion mass. Range is -20 to 20 steps.
High Edge Amplitude Amplitude of broadband waveform use to eject masses
Isolation Time The dwell time during which the rf field is held constant in
the high mass ejection step. Range 1 - 10 msec.

187
Item Description
excitation. Range 0 to 1000 msec. The default is 20 msec.
Modulation Range Mass range over which the rf storage field is modulated
during resonant CID. The range is 0 to 10 steps, default is
2 steps. Value of 0 gives a fixed rf storage field, i.e., no
modulation.
Modulation Rate The number of microseconds that will be spent at each
step. The range 29 usec to 5600 usec, default is 3000
usec/step.
Number of
Frequencies
Enter an odd integer in range of 1 to 121. A frequency
number of one generates a single supplementary
frequency applied to the end caps. An integer of 3,
generates three frequencies: the resonance frequency and
frequencies 500 Hz above and below that frequency.
CID Frequency Offset To offset the dissociation frequency. The CID frequency
can be adjusted between 3000 Hz.

188

189
2000 MS Method Electron
Ionization
The Electron Ionization Scan Function with Automatic
Gain Control (AGC)
The ion trap has a maximum storage capacity, beyond which mass resolution
and spectral quality deteriorate. The number of ions created is proportional to the
ionization time, with more ions being produced the longer the ionization time.
Automatic Gain Control (AGC) controls the ionization time in order to maintain
the number of ions in the trap at the optimum level.
The AGC scan function consists of a prescan and up to six scan segments. The
prescan is done using resonance ion ejection and the number of ions detected in
the prescan is used to calculate the ionization time for the six scan segments.
The figure below illustrates four scan segments correspond to the following four
portions of the mass range (default values): 10 to 99 m/z, 100 to 249 m/z, 250 to
399 m/z, and 400 to 650 m/z. One scan involves one complete ramping of the rf
voltage over the mass range selected by the user. The rf voltage is ramped at a
constant rate of approximately 5600 m/z per sec. One complete scan at this fixed
rate produces a microscan.

The AGC Scan Function
The AGC software automatically selects an ionization time from 10 sec to 65
msec for each of the six scan segments of the microscan, depending on the
amount of analyte in the ion trap and the tuning parameters. An estimate of the
number of ions formed in the ion trap is provided by a short prescan that consists
of a 0.1 millisecond ionization period. For low levels (e.g., for baseline or small

190
GC peaks) the maximum ionization time of 65 milliseconds is selected, which
offers maximum sensitivity. As the amount of analyte increases, the ionization
time is decreased automatically in order to prevent saturating the ion trap with
ions.
The ion signals in each microscan are scaled automatically to correct for the
variation in ionization time. Microscans are averaged to improve the spectral
quality.
Ion Formation
In the EI mode electrons are passed through the ion trap cavity during the
ionization period. These electrons collide with the neutral sample molecules
present and transfer some of their energy to the molecules. These energetic
molecules decompose through a series of reactions producing ions and neutral
fragments. This set of fragment ions, characteristic of the sample molecule,
makes up the mass spectrum. The degree of fragmentation is a function of the
internal energy of the molecules, which is a function of the energy imparted by
the electrons, as well as the ion trap temperature and the axial modulation
voltage amplitude.
The ionization time is the time (between 10 s and 65 milliseconds) during which
the electron gate voltage is positive, and the electron beam from the filament is
permitted to enter the ion trap. The electron beam generates ions by colliding
with sample and/or background molecules which are present within the ion trap.
The AGC software provides control of the ionization time so that the quantity of
ions can be maintained at the optimum level.
The number of ions formed in the trap is also a function of the intensity of the
electron beam. In general, increasing the filament emission current increases the
quantity of ions produced. The relationship between the filament emission
current and the measured TIC (i.e., the number of ions generated in the ion trap)
is not a strictly linear one. In particular, the emission current and the measured
TIC do not vary linearly for emission current values above 40 uA and at high
sample concentration.
Keep in mind that both the ionization time and the intensity of the electron beam
directly control the number of ions formed, and that the ion trap performs best
(producing the highest quality spectra with good resolution) when an optimum
quantity of ions (or charge) exists within its chamber.
AGC Prescan
The 0.1 millisecond ionization is followed by a ramping of the rf voltage to eject
the permanent background from 35 m/z to an upper mass limit selected by the
user. This upper mass limit is defined as the background mass. The default value
for the upper mass limit is 45 m/z; as a result, all masses below the background
mass (i.e., those masses corresponding to the chemical background) are ejected
from the trap.
The rf voltage is then ramped to its maximum value, and all ions with masses
above the background mass (i.e., those masses corresponding to sample ions)
are ejected from the ion trap and are detected by the electron multiplier. The
electron multiplier produces a signal proportional to the number of ions detected.

191
The ion current measured during the AGC prescan is known as the AGC peak
area. The AGC peak area is proportional to the number of ions formed during the
prescan ionization. The AGC software uses the measured ion current as a
reference to optimize the ionization time for each scan as a function of analyte
concentration.
Scan Segment Setup Period
The prescan is followed by the first segment of the six scan segments. Each
segment can be divided into two parts: a setup period and a scanning period.
Each setup period can be subdivided into the following four stages:
First stage: The rf voltage is set to near 0V for 2 milliseconds. This setting
allows the rf voltage generator circuit to stabilize while clearing the trap cavity of
all ions.
Second stage: The rf voltage is set to, and stabilizes at, the storage voltage,
selected to store, or trap, all ions of interest in the ion trap cavity.
Third stage: First, the electron gate is turned ON. Energetic electrons from the
heated filament are accelerated into the ion trap, where they interact with sample
molecules and sample ions are formed. After the ionization period, the electron
gate is turned OFF, and additional electrons are prevented from entering the ion
trap.
The newly formed sample ions are then permitted to stabilize in their orbits at the
storage voltage. This stabilization period is referred to as the cool time. The
length of this period is fixed.
Fourth stage: The electron multiplier is made ready, and the rf voltage is
ramped quickly from the storage voltage to a value appropriate to begin the mass
scanning of the segment.
Mass Scanning
During mass analysis, the rf voltage is ramped from a low voltage to a higher
voltage.
The ion trap operates in the resonance ejection mode. In this mode, at low rf
voltage (for example, at the storage voltage) most ions have stable oscillations in
the ion trap cavity. However, as the rf voltage is increased, ions of progressively
greater mass-to-charge ratios become unstable and are ejected from the cavity.
The voltage at which an ion is ejected from the ion trap cavity is defined as its
resonance voltage. At a voltage below its resonance voltage, an ion travels in a
stable orbit, oscillating along all three axes. At or above its resonance voltage,
the trajectory of the ion becomes unstable. As the rf voltage increases above the
resonance voltage, the amplitude of the oscillation of the ion increases most
rapidly in the axial direction. As a result, when ions are no longer stable in the ion
trap cavity, they are ejected from the cavity in a tightly collimated beam upward
and downward. The ejection of ions of each mass-to-charge ratio occurs over a
very short time period. One half of the ions go up; these ions strike the top
endcap and are neutralized. The other half of the ions go down and pass through
the holes in the bottom endcap; many of these ions strike the electron multiplier
and are detected.
The rf voltage is ramped at a constant rate of approximately 5600 m/z per sec.
One complete scan at this fixed rate produces a microscan. Depending upon the

192
mass range and scan time, more than one microscan may be obtained during
each scan. (The number of microscans per scan for each set of mass-
range/scan-time conditions selected is displayed on the data system monitor
after these conditions are specified.) If two or more microscans are obtained,
they are averaged by the SAP Board and then stored as one mass spectrum by
the data system. This averaging of microscans provides improved spectral
quality.
At the completion of the scanning period, the rf voltage is again set to near 0V,
and the electron multiplier put into STANDBY. The entire process (setup and
scanning) is repeated up to six times per microscan, once for each of the six
segments.
Basic Equation of the AGC Software
The AGC software sets the ionization time to maintain the optimum quantity of
ions for each of the segments according to the following equation:
a
m
t
p a SF x
TIC
TIC
x IT IT =
where:
IT
a
is the actual ionization time to be used for segment a in a six segment
microscan;
IT
p
is the ionization time of the prescan (default value of 0.1 millisecond);
TIC
m
is the area in counts of the total ion AGC peak from the prescan
measurement;
TIC
t
is the tunable target TIC value used as a reference for the prescan
measurement calculations; and
SF
a
is the scale factor for segment a. It is a percentage of the actual ionization
time (IT
a
) that permits individual adjustment of the response and resolution of
each segment.
Increasing the target TIC increases the ionization time for all the segments;
decreasing it will decrease the ionization time. The target TIC is used as a
general resolution adjustment for the entire mass range (all six segments
together).
From the equation above, it is apparent that when the measured TIC increases
because the ion trap is generating more ions (usually due to an increase in
sample or background pressure), then the AGC software will reduce the
ionization time automatically, and vice versa. Also, if the target TIC is increased,
the ionization time for any given pressure will increase. This causes the ion trap
to create more ions. Likewise, reducing the target TIC value will decrease the
number of ions in the trap.

193
Software Parameters
Segment Setpoints

Scan Time
The duration of each scan (in seconds). The scan time can be set to any value
from 0.100 to 5.000 seconds per scan. Below the scan time input box is
displayed the number of microscans per scan for the selected mass range and
scan time. The number of microscans per scan is computed automatically; it
cannot be set directly. It is displayed for information only. The minimum duration
for the scan time is determined by the selected mass range.
Multiplier Offset
To improve detection limits, the multiplier voltage may be increased or decreased
by 300 volts of the Electron Multiplier 10
5
gain. The same multiplier gain must be
used for determining the calibration curve and analyzing unknown samples.
Emission Current
The number of ions formed in the trap is a function of both the ionization time
and the intensity of the electron beam. In general, increasing the filament
emission current increases the quantity of ions produced. The relationship
between the filament emission current and the measured TIC (i.e., the number of
ions generated in the ion trap) is not a strictly linear one. In particular, the
emission current and the measured TIC do not vary linearly for emission current
values above 40 A and at high sample concentration.
In certain cases, a high emission current can be used to increase the sensitivity.
One of these is EI/MS/MS where the MS/MS isolation step eliminates the higher
background that would normally arise from a high emission current. The
emission current may be set from 5 to 100 A.
Count Threshold
The minimum number of intensity counts per sampling interval required before a
signal is recorded. (The maximum number of counts per sampling interval is
4095.) The peak threshold can be set to any value from 0 to 1000 counts; it is
typically set to 0 or 1 count.

194
Mass Defect
Mass defect is defined as the difference between the nominal mass of an atom
(or ion) and its exact mass. Its importance arises from the fact that the Saturn
GC/MS reports molecular weights to the nearest integer mass unit only. The
software must decide which mass to assign the measured intensity to. If the
exact mass of an ion happens to fall close to the dividing line between integer
masses, it may be assigned to the wrong mass. This is more likely for molecules
with higher molecular weights, since the mass defects for several atoms may add
together to produce a sizable mass defect. The mass defect parameter may be
set to any value from -300 mu per 100u to +300 mu per 100u. The formula for
calculating the mass defect parameter is:
u mu x
Mass Integer
Mass Integer Mass Actual
Defect Mass 100 / 10
5
=
For example, hexachlorobenzene (C
6
CI
6
) with an exact mass (for the base peak)
of:
8104 . 283 ) 9659 . 36 1 ( 9689 . 34 5 ( ) 0000 . 12 6 ( = + + x x x
has a mass defect of:
u mu x 100 / 76 . 66 10 284 / ) 284 8104 . 283 (
5
=
Similarly, dodecane (C
12
H
26
) has an exact mass of:
2028 . 170 ) 0078 . 1 26 ( ) 0000 . 12 12 ( = + x x
and a mass defect of:
u mu x 100 / 29 . 119 10 170 / ) 170 2028 . 170 (
5
+
Obviously, if a sample contains both of these compounds, the mass defect
parameter cannot be optimized for both in a single segment. For most analyses
the mass defect should be set to 0 in order to avoid mass misassignments, or
carefully program it with multiple segments.
Cal Gas
The calibration gas may be turned on during an acquisition by clicking on the Cal
Gas checkbox.
Ionization Mode - EI Auto

195
Mass Range Segment Breaks
Each EI scan is divided by default into four mass segments: 10 to 99 m/z, 100 to
249 m/z, 250 to 399 m/z and 400 to 650 m/z. For certain applications, the mass
ranges in these segments can be adjusted. Additional segments (maximum of 6
segments) can be added by clicking on the Insert button.
Ionization Storage Level
Each segment has its own ionization storage level. This corresponds to an rf
voltage that is used to hold ions in the trap during the ionization period. It affects
ion storage in two ways the storage efficiency of higher mass ions increases
as the level increases, while lower mass ions are not stored if their mass falls
below the cutoff. With AGC on, the default storage level is set to 35 m/z, causing
all ions above 35 m/z to be stored. This value gives good storage efficiency for
ions up to 650 m/z, while not storing the 18 and 19 m/z ions resulting from water
vapor.
For certain analyses, the storage voltage may be increased to prevent the
storage of ions produced from the solvent. For example, to exclude ions
produced from methanol (mass 32 and below), the storage voltage may be set to
38 m/z for all segments. Keep the EI Background mass greater than or equal to
the segment ionization storage voltage.
Ionization Time Factor
The Ionization Time Factor is a secondary factor that determines how well the
Saturn GC/MS is tuned. The Ionization Time Factor, given as a percent, is a
number that is multiplied by the calculated ionization time (determined by the
AGC pre-scan pulse) to give the actual ionization time. The default value of the
time factor is 100%. Ionization Time Factor determines the actual ionization time
for each segment; thus, it determines the number of ions in the ion trap for that
segment
The calculated ionization time, determined by the AGC pre-scan pulse, is
generally the optimum value for segment 2. At lower masses (segment 1),
however, an actual ionization time of as low as 75% (and never lower than 50%)
of the calculated ionization time will sometimes provide a better tune. And for
higher masses (segments 3 and 4), an actual ionization time of up to 125% (and
never higher than 200%) of the calculated value sometimes provides better
results.
As the ionization time factor is increased (actual ionization time increased), the
peak height increases. However, the resolution of adjacent mass peaks may
decrease and the peak shape might distort.
Target TIC Value
In EI mode with AGC on, the target TIC value determines how many ions AGC
allows into the ion trap during the calculated ionization time. While increasing the
target TIC value will increase peak heights, increasing it too far will result in a
loss of mass resolution. This would be observed as mass misassignments and/or
incorrect isotope abundance ratios. For full-scan EI operation, a target TIC of
20,000 is a good starting point. Under special circumstances, e.g., MS/MS, a
much lower target TIC is required. As the m/z distribution of the stored ions
becomes smaller, fewer ions can be trapped without a loss of resolution.

196
This sets the limit for the longest ionization time which AGC can use. For
maximum sensitivity, start with the default value of 25,000 sec. In certain
special cases a smaller value may be used, e.g., to reduce unwanted ion-
molecule reactions. The highest Maximum Ionization Time can be set is 65,000
sec.
Prescan Ionization Time (sec)
This ionization time determines the number of ions formed for the prescan. This
value is then used to calculate the ionization time for the analytical scan. The
preset value of 100 sec works for EI operation. For cases where few ions might
be formed in the prescan (e.g., EI-MS/MS) use a large value such as 1500 sec.
Care must be exercised, however, since a large value could produce so many
ions in the EI mode that the prescan becomes saturated and AGC no longer
functions properly.
Background Mass
The lowest mass used to determine the target TIC (total ion current) value; all
ions of lower mass are ejected from the ion trap before the AGC prescan pulse.
The background mass can be set to any value from 10 m/z to 300 m/z; it is
typically set to 45 m/z. The background mass should always be set at least two
m/z higher than the Ionization Storage Level.
rf Dump Value (m/z)
This value specifies the high m/z used for the prescan. It should always be as
high or higher than the analytical scan range high mass. In most cases, leave at
the default value of m/z=650. In certain circumstances, operating at 400 or 450
(matching the analytical scan) may allow operation in spite of high mass noise.

197
Ionization Mode - EI Fixed
When AGC is off, a fixed ionization time scan function is used to coordinate the
processes that occur in the ion trap. This scan function consists by default of four
segments that compare qualitatively to those of the Auto scan function. It may
contain up to six segments. However, the fixed ionization time scan function
contains no prescan. Thus, the ionization times for each segment do not vary as
a function of sample concentration. The Ionization Time can be set from 10 to
65,000 sec.
Manual tuning in Fixed mode is performed by altering the Ionization Storage
Levels and Ionization Times for each segment of the microscan.

198

199
2000 MS Method Ion Preparation
The Ion Preparation Method
The two fundamental processes in mass spectrometry are ion creation and ion
analysis. For some applications, the ability to manipulate the ion population
following ion creation but prior to ion analysis through such techniques as
selective storage or dissociation may be advantageous. Although this may
require additional instrumentation when using other mass spectrometers, the ion
trap can accomplish it by means of an ion preparation method (IPM), which
modifies the scan function. Advantages associated with IPMs are similar to those
of other sample preparation methods, e.g., reduction of noise, increased
selectivity, etc.
Intermediate Scan Segments (ISS)
The use of the Ion Preparation technique introduces intermediate scan segments
(ISSs) into the basic rf scan function. These allow you to customize the prescan
and analytical scan(s) for both electron- and chemical-ionization modes of
analysis.
In the case of electron ionization (EI), ISS insertion takes place between creation
of the ions (ionization) and ion analysis. Electron ionization uses the automatic
gain control (AGC) scan function, which consists of a prescan and up to four
analytical scans. As seen in the figure, the prescan and analytical scans include
ionization periods, ISSs, and six rf voltage ramps (only two ramps shown) over a
user-defined range.

Automatic gain control scan function showing location of intermediate scan segments
With chemical ionization (CI), there are two steps in ion creation (ionization and
reaction). The ion preparation method is capable of inserting ISSs following

200
either or both segments of the scan function. Chemical ionization uses the
previous scan for ion control.
As shown below, the analytical scan includes an ionization period, a reaction
period, ISSs, and an rf voltage ramp for mass analysis.

CI scan function showing location of intermediate scan segments
Each intermediate scan segment is defined by the following parameters:
- Duration (in time) of the segment
- Beginning rf storage level
- Ending rf storage level
- DC voltage
- Waveform applied to the end cap electrodes
- Amplitude of the waveform
- States of two auxiliary outputs (ON or OFF)
- State of axial modulation signal (ON or OFF)
- State of the electron multiplier (ON or OFF)
The ionization portion of the scan function can also be modified to include
application of a waveform and rf modulation. The reaction period can also be
modified to include application of a waveform.

201
Specifying the Ion Preparation Parameters

The Ion Preparation Parameters control how the basic EI or CI scan functions
are modified to prepare the ions for scanning. You have control over which ions
are ejected, which are retained, and which will undergo dissociation (CID). Your
input and the Ion Preparation technique you are using determine how the scan
function is constructed and what custom waveforms are created to complete the
analysis.
Theory of Operation of the SIS Option
Using the Selected Ion Storage (SIS) option, you may selectively accumulate or
store specific ions in the ion trap. Success with this technique requires that there
be no excessive space-charge build up. Optimum mass resolution is achieved by
controlling the number of ions in the trap. When the concentration of background
matrix or co-eluting compound is large compared to the target compound,
Automatic Gain Control (AGC) maintains the correct number of ions in the trap
by reducing the ionization time. However, this also reduces the number of target
compound ions available for analysis.
SIS eliminates unwanted ions by ejecting them from the trap. Given the optimum
number of ions that can be stored in the trap, SIS enriches the sample ions
relative to the unwanted matrix ions by ejecting the latter throughout ionization.
The unwanted ions are ejected from the trap by a technique known as resonant
ion ejection.
Trapped ions exhibit a characteristic, or secular, frequency of oscillation. This
frequency depends on the mass of the ion and the amplitude of the fundamental
storage rf field. An ion's secular frequency increases with increasing storage rf
voltage, and decreases with increasing mass.
Normally, mass scanning results from the application of a single supplemental
dipole field to the end caps of the ion trap, and the application of a linear
frequency increase of rf voltage. As the rf voltage is increased, the ion's secular
frequency increases until it matches the frequency of the applied supplemental
field. At that point, resonance occurs and the ion absorbs energy from the
external field. The amplitude of the ion motion increases, and continues to
increase until the ion is ejected from the trap and the ion is detected.
Resonant ion ejection may also be used to eject multiple ions in a fixed rf storage
field. This is accomplished by applying multiple frequencies to the end caps of
the ion trap. One convenient method of applying multiple frequencies is to use a
broadband multifrequency waveform. The multifrequency waveforms used in SIS
include those frequencies required to eject the unwanted ions from the trap
without affecting the ions to be stored.

202
Initially, you specify the mass window of ions to be stored. Because each mass
has a unique secular frequency at a given storage rf voltage, it is possible to
construct a waveform that does not include frequencies near the secular
frequencies of the ions to be stored. The resulting waveform consists of a
distribution of discrete frequencies with missing frequencies, called notches,
corresponding to the frequencies of the stored ions.
Modulation (the periodic increase, then decrease) of the storage rf increases and
decreases the secular frequencies of the ions in the trap. Thus, the unwanted
ions may be brought in and out of resonance with frequencies in the applied
supplemental waveform, so that unwanted ions are ejected and ions of interest
are selectively accumulated.
The figure below is a timing diagram of the SIS scan function. Ionization begins
when the electron gate is turned on and electrons enter the trap. At the same
time, the supplemental waveform (WF) is turned on, and ion ejection begins.
With the electron gate and waveform both turned on, the amplitude of the rf
trapping field is modulated to vary the secular frequencies. Application of the
waveform and rf field modulation continues for another cycle after the electron
gate is turned off. This ensures that all remaining unwanted ions are ejected.

SIS Scan-Function Timing Diagram
Selected Ion Storage (SIS) Parameters
NOTE: The Ion Trap must be calibrated for optimum performance. Do SIS
Calibration in the Tutorial Section before running any SIS methods.
Click on the Ion Preparation-SIS tab

203

Under Storage Mass Ranges, enter the low m/z integer mass and the high m/z
integer mass for each of the mass windows to be selectively stored. Delete any
mass range not needed. You may enter up to five mass ranges. The default
parameters permit any mass range from 53 m/z to 650 m/z to be stored, given a
storage rf of 48 m/z.
Under Ejection Masses click on Ion Mass press the Add button, and enter the
integer mass(es) of those ion(s) to be ejected, along with the corresponding
amplitude(s) as percentages of the amplitudes that would normally be used in a
SIS ejection waveform. Enter up to five masses to eject. The Amplitude range is
10% to 200% with a default of 100%.
Customize SIS
The minimum allowable mass is determined by the storage rf level, which may
be accessed by clicking on Customize.

Ionization Storage Level
Using the default storage rf level of 48 m/z, the minimum low mass that can be
entered is 53 m/z (48 + 5 m/z).
Allowable Storage Mass Range: (storage rf + 5) < mass < 650 m/z.
Default = 48 m/z.
The lowest storage rf level that can be entered is 20 m/z, which allows a
minimum low mass of 25 m/z to be acquired.
The figure below shows the relationship between the minimum mass window that
can be stored and the isolated mass. Note that unit mass isolation can only take
place at low mass; at higher masses, a range of ions is stored even when a
single mass is entered.

204

As shown below, the window of ions ejected also depends on mass. A single
mass can only be ejected at low mass values. If a single high mass value is
entered in the table, a range of ions will be ejected.

Autoscale Waveform
Under default operation (Autoscale = ON), the SIS waveform amplitude is
automatically scaled as a function of the frequency components and storage rf
voltage selected.
NOTE: The amplitude of the waveform should be optimized for each Saturn
GC/MS system. The method described in Tutorials, How to Calibrate SIS, has
been found to be adequate for tuning the amplitude in most Saturn GC/MS
systems. However, you may also manually increase or decrease the waveform
amplitude if you prefer.

To manually specify the waveform amplitude, deselect (uncheck) Autoscale. The
field for Waveform Amplitude appears active.
Enter the desired Waveform Amplitude in volts.
Range: 0 < amplitude < 60.00 volts. Default = 15.00 volts.

205
Tips for Using SIS
Observe these recommendations for best results when using the SIS application.
- When selectively storing ions that are easily fragmented by collision-induced
dissociation (CID), use wide mass isolation ranges and low amplitude
waveforms.
- As the frequency notches become increasingly narrow and the voltage of the
frequency components increases, the ions that you wish to store acquire
sufficient energy to dissociate or be ejected. As a result, a small fraction of
these ions may be lost due to dissociation or ejection.
- Target TIC values less than 10,000 are recommended when using SIS
applications, especially with a narrow mass window. Values in excess of
10,000 may cause space charge build-up, which can decrease the linear
range for quantitation and result in loss of resolution.
The MS q Calculator
For convenience, The MS q Calculator is available in all Ion Preparation Options.

Storage rf values are often reported in terms of the Mathieu q parameter in the
scientific literature. The value of the q parameter determines the stability of the
parent ion trajectory. More stable trajectories allow higher excitation voltages to
be applied before ions are ejected from the trap. It has been empirically observed
that a q value of 0.4 provides an optimum yield of product ions. This calculator
utility determines the corresponding CID storage rf value (m/z) following user
entry of an ion mass (m/z) and desired q.

206

207
2000 MS Method MS/MS Option:
Theory of Operation
Overview
This section describes the four basic operations in Saturn Ion Trap Tandem
Mass Spectrometry (MS/MS) for electron ionization (EI):
- Ion formation and matrix ion ejection
- Parent ion isolation
- Product ion formation
- Product ion mass scanning.
Chemical ionization (CI) MS/MS uses a subset of these operations.
Note that the utility of the MS/MS technique derives from the following:
- optimally filling an ion trap with the selected parent ion;
- obtaining qualitative structural information about the sample by forming the
product ion spectrum; and
- increasing the signal-to-noise ratio by eliminating interfering matrix ions in
the product ion spectrum during isolation.
Ion Formation and Matrix Ion Ejection
Ionization of the sample and any co-eluting matrix occurs by electron ionization.
During ionization, a broadband multifrequency waveform is applied to the end
caps of the ion trap to resonantly eject ions below the specified parent ion mass.
This removes unwanted low-mass ions whose space charge would otherwise
affect the storage efficiency of the parent ion. Removal of most of the space
charge from the trap improves mass resolution in subsequent MS/MS steps.
Following ionization, a second broadband waveform is applied to the trap to eject
those ions whose masses lie above the specified parent ion mass. This removes
most of the remaining unwanted ions from the trap. There now remains in the
trap the optimum number of parent ions having the desired m/z value, along with
a few ions with values of m/z slightly above and below it.
The advantage of this two-step approach is that it only requires one calculation of
the waveforms. If subsequent adjustments are needed to accommodate changes
in mass calibration, they can be made automatically by software that
independently modulates the rf fields in each ion-ejection step.

208

MS/MS Scan Function
Parent Ion Isolation
The parent ions can be completely isolated from any remaining matrix ions in
another two-step process.
The first step ejects the ions with masses below the parent ion mass by ramping
the rf field amplitude with axial modulation applied to the end cap electrodes.
This step resonantly ejects all ions having masses up to, and including, the mass
just below the parent ion mass. Axial modulation is then turned off.
In the second step, a broadband multifrequency waveform (WF2) is applied to
the trap to simultaneously eject all masses above the parent ion mass. Isolation
occurs at elevated rf levels where mass resolution is optimal. Thus, it is possible
to achieve unit mass isolation over the entire mass range of the ion trap.
Achieving unit isolation is useful in isolating a single mass in an isotopic cluster,
or in separating the parent ion from interfering matrix ions. This high resolution
isolation method is further advantageous in that it is calibrated using standard
mass calibration information, and uses the same broadband waveform for all
masses. Thus, if the system is recalibrated, or if a new parent ion mass is
selected, recalculation of the waveform is not required.
Product Ion Formation
Product ions are formed from the parent ions by collision-induced dissociation
(CID). The parent ions constantly undergo collisions with helium gas in the ion
trap. Normally these collisions involve relatively small energies, but if the
translational energy of the parent ion is increased, the collisions may convert the
translational kinetic energy to internal vibrational energy.
If the parent ion acquires enough vibrational energy, one or more chemical
bonds in the ion may be broken, forming ions of lower m/z than the original

209
(parent ion) m/z. The m/z distribution that results from the CID process depends
on the characteristics of the parent ion and the amount of energy that has been
converted into internal vibrational energy.
The translational kinetic energy of the parent ion can be increased using either of
two methods. Each method requires application of a waveform to the trap. The
waveform amplitude is called the CID excitation amplitude, and the length of time
that the waveform is applied is called the excitation time.
The first method involves nonresonant excitation. In this case, a low frequency
supplemental dipole field is applied to the end caps of the trap, resulting in an
instantaneous change in the potential energy of the ion in the trapping field.
1

The restoring force of the trapping field converts the newly increased potential
energy of the ion into increased translational kinetic energy. A portion of this
kinetic energy is then converted into internal vibrational energy upon subsequent
collisions. This process is repeated during each oscillation cycle of the low
frequency dipole field.
The second method for increasing the parent ion kinetic energy involves
resonant excitation. This method requires application of a high frequency
supplemental dipole field to the end caps of the ion trap. The frequency must
match the oscillation frequency of the trapped ion. The resonant frequency of the
trapped ion depends on ion mass, space charge, rf trapping field amplitude, and
other instrumental factors. Thus, it is difficult to precisely calculate its value. The
amplitude of the rf trapping field is therefore modulated over a specified range.
As the resonant frequency of the trapped ion depends on the magnitude of the rf
field, modulating the rf field amplitude results in a modulation of the resonant
frequency of the ion. Modulation of this frequency causes the frequency of the
ion to periodically match that of the applied supplemental dipole field. Thus, the
energy coupled to ion motion is maximized, and the effects of shifts in the ion
resonant frequency are minimized. The effectiveness of the resonant excitation
method depends on the mass range over which the rf field is modulated, and the
total time spent in resonance.
An advantage of using nonresonant excitation is that it is not critical to match the
applied dipole frequency to that of the ion. Consequently, the method is affected
neither by electronic drifts, space charge effects, nor sample concentration. This
results in reproducible product ion spectra that are unaffected by changes in the
trapping conditions and sample concentration. This method is often useful with
parent ions that fragment by the breakage of a single weak chemical bond to
form highly stable ions containing functional groups that do not undergo
significant rearrangements. A disadvantage of the method is that it is not
selective with respect to excitation of ions in the trap . Therefore, the method
cannot be selectively tuned to excite only ions having a particular m/z. The
method is also less useful with parent ions in which multiple chemical bonds are
broken and with parent ions that undergo complex rearrangements following
collision-induced dissociation.
The resonant excitation method is selective to the mass range that is excited. It
permits coupling of energy to the motion of an ion having a particular m/z value
in a very controlled way. Consequently, the rate that the amplitude of the ion
motion increases is just balanced by the rate that energy is removed by
collisions. The ion is not ejected and energy can be deposited as internal energy
by increasing the number of collisions. This is done by increasing the excitation
time. Thus, it is possible to fragment parent ions that require the breakage of

1
The dipole field is simply an electric field oriented along the axis of the trap.

210
multiple chemical bonds or that undergo significant rearrangements. Periodic
modulation through ion resonance results in an averaging of the energy coupled
into the ion motion and provides a reproducible product ion spectrum, even with
changes in concentration. A disadvantage of this method is that two parameters
in addition to the excitation time and CID excitation amplitude need to be
optimized; these are the modulation range and CID bandwidth.
Changing the CID bandwidth permits simultaneous excitation of ions within a
range of masses. As CID bandwidth increases, the corresponding mass range
also increases. At a given CID bandwidth, mass range increases with increasing
ion mass, and decreases with increasing excitation rf storage level.
Excitation rf Storage Level (m/z): 48
CID Bandwidth
( )
Mass
Range
0
10
20
30
40
50
60
0 2 4 6 8 10 12 14 16 18 20
m/z=500 m/z=400 m/z=300 m/z=200 m/z=100

Mass range vs. CID bandwidth for an excitation rf storage level of 48 m/z
Excitation rf Storage Level (m/z): 143
CID Bandwidth
Mass
Range
0
5
10
15
20
25
30
0 2 4 6 8 10 12 14 16 18 20
m/z=500 m/z=400 m/z=300 m/z=200

Mass range vs. CID bandwidth for an excitation rf storage level of 143 m/z

211
Note that at a storage level of 48 m/z and a CID bandwidth of 4 kHz, the mass
range increases from 3 to 40 m/z when the parent ion mass increases from 100
to 400 m/z. Given a parent ion mass of 400 m/z and a CID bandwidth of 4 kHz,
the mass range decreases from 40 m/z for a storage level of 48 m/z to a range of
12 m/z for a storage level of 143 m/z.
The amount of energy that is converted to internal energy in the parent ion
depends on the number of collisions (excitation time), the relative energy of the
collisions (CID excitation amplitude), and the rate that the internal energy is
removed by collisional deactivation (excitation method). Collision-induced
dissociation in the ion trap is always in competition with ion ejection. If the CID
excitation amplitude selected is too large, the parent ion will be ejected to the
trap electrodes before it can collide with background helium atoms. If the CID
excitation amplitude selected is too small, the energy of the parent ion will not
exceed the internal energy threshold required to break the chemical bonds and
form product ions. This is because energy is constantly being removed by low
energy collisional deactivation. Therefore, the CID excitation amplitude and the
excitation time are both used to optimize the CID process in conjunction with an
appropriate choice of excitation method.
Product Ion Mass Scanning
Following formation of the product ions by collision-induced dissociation, a single
rf ramp is used along with the axial modulation field to resonantly scan ions from
the trap into the electron multiplier. This process generates the product ion
spectrum.
Chemical Ionization
Chemical ionization (CI) may also be used to selectively fill the ion trap. In this
case, the ion formation and matrix ion ejection steps described above are
modified. Insertion of the three subsequent MS/MS operations, i.e., parent ion
isolation, product ion formation, and product ion mass scanning, into the basic CI
scan function (following the ionization and reaction steps) creates the CI-MS/MS
scan function.
EI/MS/MS and CI/MS/MS Automatic Space Charge
Control
Space charge control for EI/MS/MS and CI/MS/MS occurs by forming the ions
during a fixed ionization period. Ion formation occurs in the same manner as for
EI or CI. After ion formation, all ions outside of the isolation window specified by
the user are removed from the trap. The ions are subsequently scanned from the
trap at the normal scan rate.
Summary
The four operations described above, i.e., ionization, parent ion isolation, product
ion formation, and product ion mass scanning, are used in the analytical scan.
When automatic space charge control is used the number of parent ions in the
isolation window are used to determine the ionization time required to maintain
the optimum number of ions in the trap. Thus, the total ion space charge level is
held constant as the sample and matrix levels change. Maintaining a constant

212
level of parent or product ions in the analytical scan results in consistent,
reproducible product ion spectra.
Lower target values may be required with the MS/MS option to prevent space
charging effects. Based on the isolated parent ion, the following target values are
recommended.

Parent Ion Target
60 < m/z < 150 10000
150 < m/z < 500 5000
500 < m/z < 650 2000
Additionally, the EI-Auto PreScan ionization time must be changed from the
default value. This is done automatically when the user selects MS/MS ion prep.
The PreScan ionization time is changed to 1500 sec.

The MS/MS Ion Prep Method
MS/MS Software Parameters

Under the Isolation header, enter the Parent Ion Mass (m/z). The parent ion
mass range is 50 to 650 m/z.
NOTE: Integer mass values may be used if the mass isolation window (next
step) is greater than 1.5 m/z. If the window size is less than 1.5 m/z, or if the
mass defect of the parent ion is greater than approximately 0.3 m/z, use the
exact fractional mass.

213
Under the Isolation header, enter the Isolation Window (m/z).
The full mass isolation window range is 1.0 to 14.0 m/z; the actual range is mass
dependent. The default value is 3.0 m/z. Integral and fractional mass isolation
windows are both accepted. If mass isolation windows smaller than 1.5 m/z are
used, the exact mass of the parent ion should be entered in Parent Ion Mass.
NOTE: When first developing a method, you may wish to start with a mass
isolation window of 3 m/z to ensure that the ion is centered in the window, e.g.,
given a parent ion mass of 502 m/z and a mass isolation window of 3 m/z, ions of
masses 501, 502, and 503 m/z would be isolated. If there is a need to reduce the
window because of interfering ions, this should be done in a later step because
the customized parameters may require optimization.

Some ions are more easily dissociated during the isolation step. Therefore,
increasing the window will reduce the ion loss by dissociation at the expense of
selectivity.
Under the Dissociation header, select the Waveform Type by clicking on
nonresonant or resonant excitation.

The nonresonant method is usually used first because it is easier.
Excitation Storage Level (resonant or nonresonant excitation)
Definition: the rf storage level in m/z when the dissociation waveform is applied
following isolation.
The excitation storage level range depends on the parent mass, but the storage
level must lie more than 2 mass units below the lowest product ion value. The
default value is 48 m/z for both resonant or nonresonant modes.
Use the "q" Calculator for suggested excitation storage levels.
NOTE: Set the excitation storage level to avoid ejection of the lowest mass
product ion. If, for example, a parent ion of 403 m/z dissociated to product ions
with m/z values of 350, 200, and 131, you would not want to use a storage level
value above 126 m/z.
Excitation Amplitude in volts.
The amplitude range for nonresonant excitation is 0 to 100 volts. For resonant
excitation, the range is 0 to 60 volts. The default values are 20 volts for the
nonresonant excitation method and 0.2 volts for the resonant excitation method.

214
NOTE: If the excitation amplitude used is too large, the parent ion and product
ion spectra will be absent because both ions will be ejected from the trap. If the
value is too small, the parent ion spectrum will be dominant and the product ion
spectrum will be weak or missing.
The MS q Calculator
For convenience, The MS q Calculator is available in all Ion Preparation Options.

Storage rf values are often reported in terms of the Mathieu q parameter in the
scientific literature. The value of the q parameter determines the stability of the
parent ion trajectory. More stable trajectories allow higher excitation voltages to
be applied before ions are ejected from the trap. It has been empirically observed
that a q value of 0.4 provides an optimum yield of product ions. This calculator
utility determines the corresponding CID storage rf value (m/z) following user
entry of an ion mass (m/z) and desired q.
NOTE: Right click of the mouse on the q calculator button provides a q to |
calculator.

Customize Non-resonant Method
The parameters in the MS/MS Ion Prep Method Editor window are the basic
ones needed to create a MS/MS Ion Prep Method file. For the vast majority of
applications, no other information is required. However, some applications may
require further customization.
NOTE: Be sure that you have specified the parent ion mass before opening the
Customize Parameters window.

215

Customize Parameters window is separated into three sections. Ionization,
Isolation and Dissociation.
Ionization
Ionization Storage Level: The m/z value at which the rf is maintained during
ionization and the coarse isolation step. The range is 35 to 160 m/z, with a
default value of 48 m/z.
Ejection Amplitude: the amplitude (in volts) of the ejection waveform during the
coarse isolation step. The default value will work for most ions. For certain ions
that are less stable, this value may need to be reduced in order to minimize the
amount of energy imparted to the parent ion during isolation. The range of the
ejection amplitude is from 0 to 60 volts, with a default value of 20 volts.
Isolation
Low Edge Offset: The integer value step to optimize the ejection of the mass
just below the parent ion mass. The low edge offset range is 0 to 20 steps. The
default value is 6 .
Low Edge Offset affects the isolation window on the low mass side of the parent
ion. Increasing the value in the positive direction (increasing the default from 6 to
7 steps) opens the isolation window on the low mass side of the parent ion.
Decreasing the offset (decreasing from the default 6 to 5 steps) decreases the
window on the low mass side. The offset should be adjusted to minimize the
amplitude of the adjacent masses below the parent ion. Initially, adjust in 2 step
increments. Typically, a 2 step adjustment will eliminate the mass below the
parent ion.

216
High Edge Offset: The integer value step to optimize the ejection of the mass
just above the parent ion mass. The High Edge Offset range is -20 to 20 steps.
The default value is 2.
High Edge Offset affects the isolation window on the high mass side of the
parent ion. Increasing the offset (from 4 to 5 steps) increases the window;
decreasing the offset (from 4 to 3 steps) decreases the window. The offset
should be adjusted to minimize the amplitude of adjacent masses above the
parent ion.
High Edge Amplitude: Amplitude of broadband waveform use to eject masses
Isolation Time: The dwell time during which the rf field is held constant in the
high mass ejection step.
A B

The isolation time range is 1 to 10 msec. The default time is 5 msec.
A decrease in the Isolation Time may be required to isolate unstable ions. This
depends on the amount of parent ion intensity that is lost when adjusting the high
offset. Adjustment of the isolation time reflects a compromise between the
requirements of long times to efficiently eject the next highest mass during
isolation, and minimization of CID-based parent ion losses during isolation.
Unstable ions can often be recognized by asymmetric tailing of the mass peak
towards the low side of the spectrum during normal mass scanning. In the case
of the mass at m/z = 219 from the calibration gas PFTBA, the parent ion intensity
is frequently reduced to the CID intensity of the parent ion by the broadband
waveform used to eject the high mass ions above the parent ion.
Some of the frequency components in the waveform will fall close to the resonant
frequency of the parent ion and may couple energy into the ion motion. Unstable
ions can undergo CID at very low energies. By decreasing the isolation time, the
parent ion spends less time in the trap with the waveform present. Stable ions
from PFTBA that can be used to adjust the isolation parameters are m/z = 69,
131, 264, 464, 502, and 614. Column bleed from polysiloxane phases produces
stable clusters of ions starting at m/z = 181, 207, 281, and 429.

217
Dissociation
Excitation Time: The excitation time is the time required for collision-induced
dissociation (CID) by ion excitation. The excitation time range is 0 to 1000 msec.
The default excitation time is 20 msec for both resonant and nonresonant
excitation.
Customize Resonant Method
NOTE: Be sure that you have specified the parent ion mass before opening the
Customize Parameters window.

Customize Parameters window is separated into three sections. Ionization,
Isolation and Dissociation.
Ionization
Ionization Storage Level: The m/z value at which the rf is maintained during
ionization and the coarse isolation step. The range is 35 to 160 m/z, with a
default value of 48 m/z.
Ejection Amplitude: the amplitude (in volts) of the ejection waveform during the
coarse isolation step. The default value will work for most ions. For certain ions
that are less stable, this value may need to be reduced in order to minimize the
amount of energy imparted to the parent ion during isolation. The range of the
ejection amplitude is from 0 to 60 volts, with a default value of 20 volts.
Isolation
Low Edge Offset: This parameter provides a fine adjustment for the isolation
window to optimize the ejection of the mass just below the parent ion mass. The
low edge offset range is 0 to 20 steps. The default value is 6.
Large positive values widen the isolation window towards low masses.

218
High Edge Offset: This parameter provides a fine adjustment for the isolation
window to optimize the ejection of the mass just above the parent ion mass. The
High Edge Offset range is -20 to 20 steps. The default value is a function of the
parent ion mass.
Large positive values widen the isolation window towards high masses.
High Edge Amplitude: Amplitude of broadband waveform used in the two-step
isolation to eject masses above the isolated parent ion. The default value works
well for stable ions, but may need to be reduced for unstable ions. The range of
values is 0 to 60 volts with a default value of 30 volts.
Isolation Time: The dwell time that the broadband waveform is applied during
the high mass elimination step. The default value works well for stable ions, but
may need to be reduced for unstable ions. The range of values is 1 to 10 msec
with a default value of 5 msec.
A B

NOTE: In the case of unstable ions, the isolation efficiency can be improved by
decreasing the isolation time.
Dissociation
Excitation Time: The excitation time is the time required for collision-induced
dissociation (CID) by ion excitation. The excitation time range is 0 to 1000 msec.
The default excitation time is 20 msec for both resonant and nonresonant
excitation.
Modulation Range: The step range over which the rf storage field is modulated
during resonant CID. This modulation greatly reduces any effect of changing
secular frequency with concentration. The default is sufficient for exciting a single
ion. When trying to excite an isotopic cluster, increase this value and/or increase
the CID bandwidth. The range is 0 to 12 steps. The default value is 2 steps.

219
NOTE: This value is not used if the nonresonant CID method is selected. A
value of 0 gives a fixed rf storage field, i.e., no modulation
Modulation Rate:
The number of microseconds that will be spent at each step. The range is 29
usec to 5600 usec, with the default value of 3000 usec/step. The default value is
adequate for nearly all applications.
Number of Frequencies: Enter an odd integer in the range of 1 to 121 for the
number of frequencies. A frequency number of one generates a single
supplementary frequency applied to the end caps. An integer of 3, generates
three frequencies: the resonance frequency and frequencies 500 Hz above and
below that frequency
CID Frequency Offset : For certain applications it maybe desirable to offset the
dissociation frequency. The CID frequency can be adjusted between 3000 Hz
Tandem Mass Spectrometry (MS/MS)
How to Customize Parent Ion Isolation
If you wish to further optimize parent ion isolation by reducing the isolation
window, first build a method with a mass isolation window of 3 m/z, an excitation
time of 0 msec, and a CID (excitation) amplitude of 0 volts. This permits you to
observe only the isolation of the parent ion without the influence of CID. The
exact fractional mass of the ion should be used for the parent ion mass.
Use a fixed sample source, such as perfluorotributylamine (PFTBA) calibration
gas, or the column bleed obtained by raising the gas chromatograph oven
temperature to 300C. Adjust the isolation parameters to isolate a single ion.
How to Select an Excitation Technique
The compound and matrix you are using determine which excitation technique
you should use. Nonresonant excitation works well with most compounds, but
resonant excitation has been found to work better with some. You are advised to
begin your analysis with nonresonant excitation because it requires optimization
of fewer parameters. If the results desired cannot be obtained using nonresonant
excitation, switch to resonant excitation.
How to Optimize the Nonresonant CID Parameters
Follow these steps to optimize the nonresonant or resonant excitation CID
parameters. Determine whether the CID (excitation) amplitude used was too
large or too small.
NOTE: If the CID (excitation) amplitude used was too large, the parent ion and
product ion spectra will be absent because both ions will have been ejected from
the trap. If the value was too small, the parent ion spectrum will be dominant and
the product ion spectrum will be weak or missing.

220
Increase or decrease the CID (excitation) amplitude until a change in the spectra
is observed. In the case of nonresonant CID, use 10 volt steps; for resonant CID,
use 0.2 volt steps. Continue to increase or decrease the CID (excitation)
amplitude, but in smaller increments until suitable ion spectra are obtained.
Adjust the excitation time in 10-ms steps to optimize the spectra.
NOTE: If the parent ion is ejected instead of forming a product ion, increase the
excitation rf level from 48 to 55 m/z and adjust the CID (excitation) amplitude. In
general, increasing the rf storage level necessitates the use of a higher
amplitude to dissociate the ions. Do not, however, raise the excitation rf level
above the storage level of the product ions.
How to Customize the Resonant Excitation Method
Using a fixed sample source such as perfluorotributylamine (PFTBA) calibration
gas or the column bleed obtained by raising the gas chromatograph oven
temperature to 300C, follow these steps to customize the resonant excitation
method.

Reduce the modulation range to 0 steps. The modulation rate will now have no
effect on the spectra, i.e., the rf storage level is fixed. Iteratively adjust the CID
(excitation) amplitude and excitation time to optimize parent-to-product ion
conversion.
NOTE: If the amplitude used is sufficiently large, the parent ion should be
ejected. Parent ion ejection indicates that the CID frequency applied to the end
caps is properly resonant and that the trap function has been correctly calibrated.
Increase the modulation range to 2 steps.
Alternatively, increase the CID bandwidth by increasing the Number of
Frequencies from 1 to 3 frequencies. This increases the mass range around the
parent ion that is excited. Several frequencies may be used with or without
modulation, and may be useful when exciting isotopic clusters.

221
Automated Methods Development
Automated Method Development (AMD) is used to optimize CID conditions for
product ion formation in a MS/MS method. AMD uses up to 10 different sets of
conditions for the same parent ion.
- When using Automated Method Development (AMD) option, set the Saturn
method for 1 microscan per analytical scan by adjusting the Scan Time
(Segments Setpoints). The easiest way to do this is to use the down-scroll
button in the Scan Time edit control to reduce the time to its lower limit. The
software calculates the minimum scan time allowed based on the duration of
one microscan for the current method parameters. This will ensure that the
maximum number of cycles through the different voltages (scan segments)
across each peak is performed.
- A strategy for using AMD to determine the optimum excitation storage level
and excitation voltage:
1. Determine the parent ion and retention time for each compound from an
injection using normal EI mode. Build a multi-segment acquisition
method, with one segment per compound.
2. Use the default conditions with Automatic Methods Development to
determine the mass of the product ion(s). AMD allows the CID voltage to
be incremented on a scan-by-scan basis (25v, 30v, 35v) for up to 10
scans and then the cycle repeats.
3. Once the m/z value of the product ion is determined, make the following
calculation. Product ion m/z divided by 1.4 = the highest CID rf excitation
level. For example, if the product ion is m/z 140, then the rf excitation
level must be no higher than 100. This will ensure good trapping
efficiency of the product ion. The value of 1.4 is a ratio of the q ejection
value (.908) and the q value at Beta(1/3) of 0.63.
4. Once the rf excitation level is set, the only variable to optimize is the CID
voltage. This can be done with two injections using AMD. The first
injection can use voltage increments of 10 volts (Nonresonant) or 0.2
volts (Resonant). Once you get close with this first injection, lower the
voltage increment and optimize the voltage with the second injection.
Determining the Optimum Voltage for Nonresonant
Excitation Using Automated Methods Development
(AMD)
Follow these steps to determine the optimum voltage for nonresonant excitation
by using AMD while injecting the parent compound.

222

It is a good idea to verify that the parent ion is isolated without a large loss in
intensity. This can be done by setting the excitation amplitude for scan segment
1=0 volts. Inject the sample and examine the spectra across the peak
Set the excitation rf equal to the lowest mass product ion expected divided by
1.4. If the product ions are not yet known, start with the excitation rf=48 m/z and
an excitation time of 20 ms. Set up the AMD method to cycle through excitation
voltages using increments of 5 or 10 volts.
NOTE : If you require a more accurate value for this voltage, you may inject the
sample and increase the CID (excitation) amplitude by 2 or 3 volts for each group
in the vicinity of the best values found with the 10-volt increments.
NOTE: If the rf level has been raised to trap the lowest product ion and a
satisfactory number of product ions still has not been obtained, either try another
parent ion or switch to resonant excitation. Some ions are sufficiently stable that
they are ejected from the trap before they can acquire enough energy to
dissociate. You may also try increasing the excitation time.
Determine the optimum voltage by plotting the product ion intensity data as a
function of CID (excitation) amplitude as shown below.

Nonresonant Excitation of a Typical Ion
Excitation amplitude (volts)
I
0
200
400
600
800
1000
1200
0 10 20 30 40 50 60 70 80 90 100
Parent ion
Product ion 1
Product ion 2

223
Determine the optimum rf level by plotting the product ion intensity data as a
function of CID (excitation) amplitude for different rf levels as shown below.

Product Ion Formation vs. Excitation RF for a Typical Ion
Using Nonresonant Excitation
P
0
100
200
300
400
500
600
700
800
900
1000
0 10 20 30 40 50 60 70 80 90 100
RF=48 m/z RF=63 m/z RF=95 m/z

NOTE: The maximum yield of product ions shifts to higher CID (excitation)
amplitudes as the rf level is increased.
Determining the Optimum Voltage for Resonant
Excitation Using Automated Methods Development
(AMD)
Follow these steps to determine the optimum voltage for resonant excitation
using AMD while injecting the parent compound.
Set the excitation rf equal to the lowest mass product ion expected divided by
1.4. If the product ions are not yet known, start with the excitation rf=48 m/z and
an excitation time of 20 ms. Set up the AMD method to cycle through excitation
voltages using increments of .2 or .5 volts.
Determine the optimum voltage by plotting the product ion intensity data as a
function of CID (excitation) amplitude as shown below.

Resonant Excitation of a Typical Ion
I
0
200
400
600
800
1000
1200
0 1 2 3 4 5 6 7
Parent ion
Product ion 1
Product ion 2

This figure shows a typical breakdown curve for resonant excitation using default
modulation parameters.

224
MS/MS
You can do multiple reaction monitoring by adding lines of different parent ions
masses and different dissociation parameters. The limit is nine.

Unit Resolution Selected Ion Storage
Unit Resolution Selected Ion Storage (uSIS) is capable of isolating up to 9 ions with unit mass
isolation. This method is useful for those cases where the standard SIS window is too large.

Use uSIS when narrow mass ranges are required by your application. Allowed
storage windows vary up to 3u at m/z less than 80 and up to 14u at m/z 420 and
above. If larger ranges are needed, use the SIS option.
MS/MS/MS
MS
3
uses two parent ions for sequential dissociation. The additional dissociation
step can be used to increase selectivity of analyte versus background or for
additional structure information.

225

First, work out optimized conditions for MS/MS of the first parent ion. AMD will
make this process go faster.
Then optimize the conditions for dissociation of that product ion (entered under
parent Ion 2). You may need to make sequential injections using the MS
3

method. If the second generation product ion is in the original EI or CI spectrum,
then you can use AMD to find the optimum conditions.

226

227
2000 MS Method Section
Overview
In the 2000 MS Configuration section, you configured your hardware for a 2000
and opened the System Control Window for instrument control and acquisition.
At this point, you could simply inject a sample and acquire mass spectra.
However, it is not likely that the startup Method will have the method settings that
are appropriate for your analysis. Therefore, the startup Method will need to be
edited to enter the settings appropriate for your analysis. Method Builder is used
to view and edit methods. It can be accessed from MS Workstation Toolbar
under the icon that is labeled that View/Edit Methods or the startup.mth button.
The method can also be accessed from the System Control bar by clicking on
the Startup1.mth button.

Using Star Assistant to Create a New Method
If you click on the Method Builder button on the MS Workstation Toolbar, you will
get this dialog box.

If you choose Create a New Method File, the Star Assistant Wizard will guide you
in building this new method.

228

You will first be asked to select the instrument configuration for which you want
to create a method.

Select Instrument 1 for the 2000 module and click on Next.

229

You will be asked to select the channels on which post-run processing will be
performed.

When you have selected the data channels and type(s) of post-run processing to
be run for each detector, the Star Assistant will create a Method containing all of
the sections that are needed to control the hardware, collect data and do the
post-run processing specified. These Method sections will contain default values
for all of the parameters. These parameters will need to be edited to match your
analysis.

230
The Method Builder Window
As you step down through the Method tree, the parameters associated with each
section of the Method are displayed for editing.

Detailed information about the menu items and Toolbar buttons can be found in
the online help.
Method Notes

The first item in the Method is the Method Notes section. Method Notes is a free
form text field where information about the Method or the application can be
entered. Method Notes are displayed in the File Open dialog boxes used
whenever you select a Method.
Method Notes can help explain to the operator when a Method should be used.
They can also be used to convey sample preparation information and reminders
to refer to specific items in the labs Standard Operating Procedures.

231
The 2000 MS Method Windows
Under the Method Directory item 2000 Mass Spec Control, click on the item MS
Method Editor. The display on the right will now show the MS method. Note that
you may click on the splitter bar separating the Method Directory from the
Method Display and adjust the position so that the entire Method is visible on the
screen. Alternatively you may click on the display button on the far left of
the Method View toolbar to hide the Method Directory.

Spreadsheet editing
Method windows contain spreadsheet tables for time, mass ranges, ionization
mode, or Ion Preparation parameters. All spreadsheets behave similarly.

Highlight rows by clicking on the row numbers on the left side of the spread
sheet. Clicking on the Add button will duplicate MS parameters of the last
segment (except for the segment description) and add a row to the end of the
current table. Clicking on the Insert button will insert a row before the currently
selected row with the same parameter values. The Delete button will delete the
currently selected row. The Default button will insert system default parameters
to the current segment. The Restore button will insert current segment
parameters that were present when the method was first opened or last saved. A
method can contain a maximum of 250 segments.

232
Generally, Method Segment 1 is a Filament/Multiplier Delay. This segment will
be acquired with the filament and multiplier turned off to protect the instrument
until after the elution of the solvent peak. The delay time can be set to 650
minutes, although 150 minutes is the recommended maximum. The Ionization
Mode is None. If a Filament/Delay segment is not needed, Delete the row.
Select the Method Segment 2 Segment Description to enter purpose of
segment. Click or tab to Start Time (min.) and enter time to start segment and
tab to End Time to enter end time. The segment time may be set to any value
from 0.10 to 650.00 minutes.
Click or tab to Low Mass to enter low mass for acquisition and tab to High Mass
to enter high mass value. The mass range can be set to any value from 10 to
650 m/z.
Tab to Ionization Mode. Click on the arrow and select the type of ionization to
be done in this segment. Details of each ionization mode are given in the Method
Editor.

Tab to Ion Preparation. Click on the arrow and select the option to be used in
the segment. The None selection will acquire regular EI or CI spectra. Details of
each option are given in the Method Editor

Multisegment Chromatogram Time Gaps
In a single acquisition it is possible to acquire data in different Ion Modes (EI/CI -
Auto/Fixed) and/or using different Ion Preparation techniques. When multiple
segments have been acquired, MultiChro displays each segment independently
in the Chromatogram display. There will be no connection between the last point
in one segment and the first point of the next segment. There is a small time gap
between segments. This gap is usually 1.0 0.2 seconds for all acquisition
modes except Automated Method Development (AMD) for MS/MS method
development. Using 10-segment AMD, the break between segments is about 1.5
seconds.

233
Click on the Special Application button.

From within the Special Application dialog, one may specify that data should be
acquired in Profile Mode (as opposed to Centroid).
NOTE: Data Handling cannot process a data file collected in profile mode.
Also from within the Special Application dialog, one may specify a pre-
acquisition flow-sampling period.
The Flow Sampling Segment
The flow sampling segment was designed for air monitoring systems, but can be
used for other applications as well. Using the optional hardware to connect the
Electronic Mass Flow Controller (EMFC) readout to the Saturn GC/MS allows the
actual flow rate to be monitored over the sampling interval and recorded in the
data file. The data, sampled at a rate of once per second, is used to determine
the actual sampled volume and is saved as the flow profile. The Method Start
Time includes the time to flush the system, as well as the actual sampling time.
The actual sample volume to be concentrated is determined by the specified
sample flow rate and the sampling duration (start time - end time). The
theoretical and actual sample volume can be viewed in the log file section of the
data file. The flow sampling segment is always performed before the other
segments in the acquisition method, unless its duration is set to zero. Having the
flow sampling segment as a separate segment performed before the rest of the
acquisition makes the chromatographic retention time independent of the
sampling duration: the data system clock is reset when the sampling is
completed. Note that the GC run time is not reset at the end of the sampling
segment.
The flow sampling segment is accessed via the Special Application button. The
flow sampling segment has the following:
- Method Start Time: The time to flush the system before sample collection
begins plus the actual sampling time. Times of -30 to 0 minutes may be
entered.
- Start Time/ End Time: The duration of the actual sampling, from -10.00 to 0
minutes. If the duration of the segment is set to 0, no flow sampling is done.
- Sample Flow Rate: (from 1 to 100 mL/min) If the EMFC is in manual mode,
the sample flow rate must equal the rate set on the EMFC. If the EMFC is set
to auto mode, the sample flow rate specified will be downloaded at the start
of the injection.

234
You now see additional tab dialogs for Segment Setpoints and Ionization Mode.
Examine the parameters, which may be adjusted in the Segment Setpoints
dialog. Click the tab "Ionization Mode - EI Auto" to see those parameters. Details
about these parameters is in the Main Editor Window.

235
2000 MS Method System Control
The Startup Method
When you enter System Control and display the Saturn System Control Window,
the Startup1.mth (first time) or the last active Method for Saturn is activated.
The Startup method is a copy of the Default method and can be used to build
new Saturn control methods. The Default method is placed in the file
directory to ensure the existence of a skeletal valid method for the operator
to build on. Please use caution not to alter this method when developing
new methods. Change the Startup method if a customize set of base
parameters are to be used to build methods.
NOTE: In building new methods, clicking on the Defaults button will place
instrument valid default values in the section being build, regardless of the values
placed in the Default.mth.
To change Methods, simply click on the Activate a Method button on the System
Control Toolbar or choose Activate Method from the File menu.

236
Editing Methods from the Saturn Status and Control
Window
The Saturn System Control or Acquisition Window contains a "Method:" button
that allows you to directly edit the active Method.

When you click on this button, Method Builder is opened with the active Method
loaded. You can then edit that section or any other section of the Method as
described previously.
Once you have edited the Method and closed the Method Builder window, you
are prompted to reactivate the Method. Reactivating the Method downloads the
changes to the Saturn system.

NOTE: If you access the active method from the method editor via the Star Bar,
when the method editor is closed or the file saved, the method must be
reactivated in system control. To reactivated the current method, click on the
button from the System Control toolbar.

Changing Method End Time from the Saturn Control and
Status Window
During a Saturn acquisition, the end time of the acquisition can be changed from
the Control and Status window.

237
Click on the Endtime button.

Enter the new end time and click on OK.
Importing Method Sections
You may wish to copy sections from one Saturn Method file to another. This can
be done by opening the Method file that you want to edit in Method Builder. Then
from the Method Builder File menu, select Import Section

The Import command prompts you to select the file containing the sections you
wish to import. Once you have selected the file, a dialog box of sections
contained in the Method file is displayed. Highlight the sections that you wish to
import by clicking on them. If you click on one section and then hold down the
shift key while clicking on another section, all of the sections in between will be
selected. Holding down the control key while clicking on a section will add that
selection to those files already selected. Clicking on a highlighted section while
holding down the control key will remove that section from the list of selected
files.

238

When the desired sections have been highlighted, click on the Import button to
import them into the Method being edited. If the Method already has sections
with the same module address and channel ID, you will be prompted to reassign
a new module address and channel number to the imported section or overwrite
the existing section in the current method.
Deleting Method Sections
To remove sections from a 2000 MS Method, open the Method containing the
sections you wish to remove in Method Builder. Click on the Delete Section
button on the Method Builder Toolbar or select Delete Section from the File
menu.

A dialog box of sections contained in the Method file is displayed. Highlight the
sections that you wish to delete by clicking on them. If you click on one section
and then hold down the shift key while clicking on another section, all of the
sections in between will be selected. Holding down the control key while clicking
on a section will add that selection to those files already selected. Clicking on a
highlighted section while holding down the control key will remove that section
from the list of selected files.

239

When the desired sections have been highlighted, click on the Delete button to
delete them from the Method being edited. You will prompted to confirm that you
want to delete each section before it is deleted.
Printing the Method
To print a method from Method Builder, click on the Print button on the Toolbar
and select the Method section or sections to be printed. The active Method can
also be printed from the System Control Toolbar and the MS Workstation
Toolbar. Click on the Active Method Options button on the System Control
Toolbar or on the Method Operations button on the MS Workstation Toolbar and
select Print Method.
Password Protecting a Method
A Method can be password protected from changes by clicking on the Set
Password button on the Method Builder Toolbar or selecting Set Password from
the File menu.

Enter the password and then re-enter it to verify that it was not mistyped.

240

After a Method has been password protected, the password will be required to
save changes to the Method.
Once a Method is password protected, it can be activated and used for
instrument control and data acquisition. It can also be viewed from Method
Builder. Only the saving of changes to the Method will be inhibited unless the
correct password is entered.

241
3800 GC Method Command
Reference
3800 GC AutoSampler

When the 8400 AutoSampler or 8410 AutoInjector is selected, the AutoSampler
window may contain up to five sections. The topmost section is common to all
modes of operation. The entries in this section are described below.
In addition, all modes of operation also include a Default Clean section and a
Clean Mode section. When Viscous, Volatile, or User Defined modes are
selected, the Internal Standard section is displayed. In User Defined mode, the
More User Defined button is displayed to provide access to the dialog box to
set the User Defined parameter. The Default Settings for Predefined
AutoSampler Modes contains a table showing the parameters that are used by
the 8400/8410 for each of the predefined modes of operation.

242

Item Description
AutoSampler Type 8400, 8410, or None

Specifies whether or not an 8400 AutoSampler or 8410
AutoInjector is installed on the 3800 GC. If an 8400 or 8410
is not installed on the GC or is turned off, select None. When
8400 or 8410 is selected, the following items are displayed
for editing.
Syringe Size (uL) 5 uL or 10 uL
Selects the size of the syringe that is installed on the
8400/8410 for use with this method. A 5 microliter or a 10
microliter syringe may be used with the 8400/8410.
Injection Mode Std Split/Splitless, Std On Column, Neat, Viscous, Volatile, or
User Defined
Sets the 8400/8410 parameters for the predefined modes of
operation.
Sample Depth (%) 0 to 100 %
Specifies how far the syringe needle is to go down into the
sample vial. 100% is the bottom of the vial. 0% is the bottom
of the vial septum.

Solvent Depth (%) 0 to 100 %
Specifies how far the syringe needle is to go down into the
solvent vial. 100% is the bottom of the vial. 0% is the bottom
of the vial septum.

Default Clean Section

Default Cleaning occurs when the Stop button on the front panel of the 3800 GC,
the Reset button on the 3800 Status Window in Star Workstation System
Control, or the Stop Automation menu item in the Star Workstation System
Control Automation menu is pressed after the 8400/8410 has started its run and
before it has finished its sampling and post-injection washing operations. Default
Cleaning also occurs when the 3800 GC has a fatal automation fault after the
8400/8410 has started its run and before it has finished its sampling and post-
injection washing operations.

243

Item Description
Vial I, II, or III
Specifies which of the three solvent vials will be used by the
Default Cleaning
Volume (uL) 0 to 10.0 microliters with 10 uL syringe
0 to 5.0 microliters with 5 uL syringe
Specifies the amount of cleaning solvent that will be drawn up
with each syringe cleaning stroke.
Strokes 0 to 10
Specifies the number of times the cleaning solvent will be drawn
up into the syringe and expelled into the waste cup.
Speed (uL/sec) 0.1 to 50.0 L per second with 10 L syringe
0.1 to 25.0 L per second with 5 L syringe
Specifies the speed at which the cleaning solvent will be drawn
up into the syringe and the speed at which it is expelled into the
waste cup.
Clean Mode Section

Item Description
Pre-Inj Solvent
Flushes
0 to 99
Specifies the number of times each selected cleaning
solvent will be drawn up into the syringe and expelled into
the waste cup before flushing with next cleaning solvent (if
more than one cleaning solvent source is specified) or the
sample.
Pre-Inj Sample
Flushes
0 to 99
Specifies the number of times the sample will be drawn up
into the syringe and expelled into the waste cup before the
syringe is loaded for injection.
Post-Inj Solvent
Flushes
0 to 99
Specifies the number of times each selected cleaning
solvent will be drawn up into the syringe and expelled into
the waste cup before flushing with next cleaning solvent (if
more than one cleaning solvent source is specified).
Clean Solvent Source I, II, III, I & II, I & III, II & III, or I & II & III
Selects which solvent vial or sequence of solvent vials will
be used to flush the syringe before and after injection.

244
Internal Standard Section

Item Description
Use

Yes or No
If Yes, an internal standard addition will be used. When
internal standard addition is used, the internal standard
solution will be drawn up into the syringe from the specified
solvent vial before the sample is drawn up.
Vial I, II, or III
Selects which solvent vial contains the internal standard.
Volume (uL) 0 to 9.0 L with 10 uL syringe
0 to 4.9 L with 5 uL syringe
Specifies the amount of internal standard to be drawn into
the syringe before the sample.
Drawup Speed
(uL/sec)
Specifies the speed at which the internal standard will be
drawn up into the syringe.
Pause Time (sec) 0 to 9.9 seconds
Specifies how long the syringe is to remain in the internal
standard vial after drawing up the internal standard.
Air Gap Yes or No
If Yes, 1 L of room air will be drawn into the syringe to
create an air gap between the internal standard and the
sample.

245
More User Defined Settings Dialog Box

This dialog box is accessed from More User Defined button that is displayed
when the User Defined mode is selected.
Solvent Plug Settings

Item Description
Vial I, II, or III
Selects which solvent vial to use for the solvent plug.
Volume (uL) 0 to 10.0 L with 10 L syringe
0 to 5.0 L with 5 L syringe
Specifies the amount of solvent to be drawn into the
syringe before the sample or internal standard.
Drawup Speed
(uL/sec)
Specifies the speed at which the solvent will be drawn up
into the syringe.
Specifies how long the syringe is to remain in the solvent
vial after drawing up the solvent.
Air Gap Yes or No
If Yes, 1 L of room air will be drawn into the syringe to
create an air gap before the solvent plug.

246
User Defined Settings

Item Description
Fill Volume (uL) 0 to 10.0 L with 10 L syringe
Specifies the sample volume that will be used for each fill stroke.

Fill Strokes 0 to 99
Specifies the number of the times the sample will be pumped in
and out of the syringe before loading the sample volume into the
syringe.

Sample Air Gap Yes or No
If Yes, 1 L of room air will be drawn into the syringe to create
an air gap before the sample plug.

Air Plug after
Sample
Specifies the volume of room air that will be drawn into the
syringe after it is loaded with sample.

Viscosity Settings

Item Description
Viscosity Delay (sec) 0 to 9.9 seconds
Specifies how long the syringe is to remain in the sample
vial after drawing up the sample.
Fill Speed (uL/sec) 0.1 to 50.0 L per second with 10 L syringe
Specifies the speed at which the sample will be drawn up
into the syringe.

247
Item Description
Inject Speed (uL/sec) 0.1 to 50.0 L per second with 10 L syringe
Specifies the speed at which the contents of the syringe
will be expelled into the injector.
Pre-Inj Delay (sec) 0 to 99.9 seconds
Specifies the length of time the syringe needle resides in
the injector before expelling the syringe contents.
Post-Inj Delay (sec) 0 to 99.9 seconds
Specifies the length of time the syringe needle remains in
the injector after expelling the syringe contents.
Default Settings for Predefined AutoSampler Modes
The following table lists the parameter settings used for each of the Predefined
8400/8410 modes using a 10 L syringe. If the predefined modes do not work
acceptably for your samples, use the User Defined mode to enter settings that
will work better with your samples. The values listed in this table provide a
starting point for setting the various parameters.

Parameter
Std
Split/
Splitless
Std On-
Column

Neat

Volatile

Viscous
Solvent Plug
Settings:
Solvent plug is not used with predefined modes. If you wish to use
solvent plug injections, you must use User Defined mode.
PreDefined
Settings:

Fill Volume 7.5 L 7.5 L Not used Not used Not used
Fill Strokes 5 5 0
0 0
Sample Air Gap No No No No No
Air Plug after
Sample
1 L 1 L 1 L 1 L 1 L
Viscosity
Settings:

Viscosity Delay 0 sec 0 sec 0 sec 6 sec 9.9 sec
Fill Speed 2 L/sec 2 L/sec 2 L/sec 1 L/sec 1 L/sec
Inject Speed 50 L/sec 2 L/sec 50 L/sec 1 L/sec 5 L/sec
Pre-Inj Delay 0 sec 0 sec 0 sec 0 sec 0 sec
Post-Inj Delay 0 sec 6 sec 0 sec 0 sec 12 sec
Instead of fill strokes Neat mode fills the syringe with sample at 2 L/sec then
expels it into the waste cup at 50 L/sec. It does this a total of six times. Then it
fills the syringe with sample at 2 L/sec and expels it back into the sample vial at
50 L/sec. This pumping action is done three times. After this is completed, the
sample is loaded into the syringe and injected using the parameters in the table.

248
3800 GC Sample Delivery

Item Description
Front Valve Oven
Middle Valve Oven
Rear Valve Oven
The 3800 GC can have up to three valve ovens installed
(front, middle, and rear). The tabs at the top of the window
select the valve oven position.
Valve Oven
Installed
Indicate whether or not the Valve Oven at each position is
installed by clicking on the Yes or No radio buttons.
Valve Oven on/off Indicate whether or not you will use the installed Valve Oven
by clicking on the ON or Off radio buttons.
Temperature (C) Specifies the isothermal temperature of each Valve Oven.
Time Time settings to program how each valve is used initially and
at the indicated time.
Valve 1-7 Use the first row to indicate how each valve is used. Click on
the arrow in the top of each Valve column, and select from the
choices displayed in the combo box. The second row contains
the initial setting for each Valve when the Method is activated.
The following rows contain the time-programmed settings for
each of the seven Valves.
Add Adds a line to the spreadsheet.
Insert Inserts a line above the currently selected row in the
spreadsheet.
Delete Deletes the currently selected row(s) in the spreadsheet.
Sort Sorts the spreadsheet rows by time.

249
3800 GC Injector

Item Description
Front Injector
Middle Injector
Rear Injector
The 3800 GC can have up to three injectors
installed (front, middle, and rear). The tabs at
the top of the window select the injector
position.
Injector Type 1041, 1061, 1079, SPT.
Specifies the type of injector installed in the
selected position. Select None if no injector
is installed at that position.
Injector Oven On or off.
Turns the injector oven in the selected
position on or off.
Click on the following injector types for a description of the parameters that
appear when the injector is selected.
1041 Injector

Item Description
Injector Oven On or off
Turns the 1041 injector oven in the selected position on or off.
Temperature (C) 50-450 C.
Specifies the oven temperature.

250
1061 Injector

Item Description
Injector Oven On or off
Turns the 1041 injector oven in the selected position on or off.
Temperature (C) 50-450 C
1079 Injector

Item Description
Injector Coolant On or Off
Turns the coolant valve on when the injector is cooling
down. The Coolant valve will not be used if the Off
position is selected.
Enable Coolant at (C) 30-450 C
Specifies the temperature for the coolant valve to turns
on.
Coolant Timeout (min) 0.01-999.99 min
Provides a safety measure to save coolant after the
specified time, if either the injector fails to reach its set
temperature or the GC does not go into run.
Split Ratio If the appropriate EFC type has been configured, displays
the Split Ratio dialog box.
Temp (C) -99-450 C

251
Item Description
Rate (C/min) 1-200 C /min
The Rate in the first row is always blank and cannot be
edited.
Hold (min) 0.01-999.99 min
Total (min) 0.01-999.99 min
Cannot be edited.
spreadsheet.

Spilt Ratio Dialog Box
This dialog is displayed from the 3800 GC Injector window when a 1079 injector
is configured with type 1 EFC.

Item Description
Time 0.00-999.99 min
Split State On/Off
If the split state is ON, then the sample is split according to the split
ratio specified. If the split state is OFF, then all the sample enters
the column.
Split Ratio Off, 1 to 10,000
Use a split ratio of 100 after injection to vent the injector. Use a
very low split ratio after flushing to conserve carrier gas.
Insert Inserts a line above the currently selected row in the spreadsheet.

252
SPT

Item Description
Injector
Coolant
On or Off
Turns the coolant valve on when the SPT injection device is cooling
down. The cryogenic will not be used if the Off position is selected.
Enable
Coolant at (C)
30-450 C
Specifies the temperature for the coolant valve to turns on.
Coolant
Timeout (min)
0.01-999.99 min
Safety measure to save coolant after the specified time if either the
SPT fails to reach its set temperature or the GC does not go into run.
Temp (C) -185-450 C
Hold (min) 0.01-999.99 min
Cannot be edited.
Insert Inserts a line above the currently selected row in the spreadsheet.

253
3800 GC Flow/Pressure

Item Description
Front EFC
Middle EFC
Rear EFC
The 3800 GC can have up to three injector EFC modules
installed (front, middle, and rear). The tabs at the top of the
window select the EFC position.
EFC Type None, Type 1 (for 1079 injectors), Type 3 (for 1041/1061
injectors), Type 4 (for valved systems).
Specifies the type of EFC installed in the selected position.

Click on the following EFC types for a description of the parameters that appear
when the EFC type is selected.
Type 1 (for 1079 injectors)

254

Item Description
Pressure (psi) 0.1-100.0 psi
Rate (psi/min) 0.01- 400.00 psi/min
The Rate in the first row is always blank and
cannot be edited.
Hold (min) 0.01- 999.99 min.
Cannot be edited.
Constant Flow On or off
Click on Constant flow to disable the
spreadsheet and reveals the constant flow rate
value.
Column Flow (ml/min) Specifies the desired constant Column Flow.
Insert Inserts a line above the currently selected row
in the spreadsheet.
Delete Deletes the currently selected row(s) in the
spreadsheet.
Type 3 (for 1041/1061 injectors)

Item Description
Flow (ml/min) 0.1- 100.0 ml/min
Rate
(ml/min/min)
10.0 ml/min/min
The Rate in the first row is always blank and cannot be edited.
Hold (min) 0.01-999.99 min
Cannot be edited.
spreadsheet.

255
Type 4 (for valved systems)

Item Description
Pressure (psi) Pressure spreadsheet
100.0 psi
Rate (psi/min) 0.1-100.0 psi/min
The Rate in the first row is always blank and cannot be edited.
Hold (min) 999.99 min
Time Flow spreadsheet
Initial - 999.99 min
Total Flow (ml/min) 1-1000 ml/min.
Add Adds a line to the spreadsheet. This button appears next to
both the top and bottom spreadsheet.
spreadsheet. This button appears next to both the top and
bottom spreadsheet.
Delete Deletes the currently selected row(s) in the spreadsheet. This
button appears next to both the top and bottom spreadsheet.
Sort Sorts the spreadsheet rows by time. This button appears next
to the bottom spreadsheet.

256
3800 GC Column Oven

Item Description
Column Oven Coolant On or Off.
Specifies whether or not the column coolant will be used.
Enable Coolant at (C) 30- 450 C
Specifies the temperature at which to enable the coolant.
Coolant Timeout (min) 0.01-999.99 min
Provides a safety measure to save coolant after the
specified time, if either the injector fails to reach its set
temperature or the GC does not go into run.
Stabilization Time (min) 10.0 min
Specifies the column Stabilization Time.
Temp (C) -99 - 450 C
Rate (C/min) 0.01- 100.0 C/min
edited.
Hold (min) 0.01-999.99 min
Cannot be edited. Column Oven End Time (Total) is
displayed in all time-programmed windows of the Method.
spreadsheet.

257
3800 GC Detector

Item Description
Front Detector
Middle Detector
Rear Detector
The 3800 GC can have up to three detectors installed
(front, middle, and rear). The tabs at the top of the
window select the detector position.
Detector Type None, FID, TCD, TSD, ECD, PFPD
Specifies the type of detector installed in the selected
position.
Detector Oven On or off.
Turns the detector oven in the selected position on or
off.
Electronics On or off.
Temperature (C) 50- 450 C
Methanizer Displays the Methanizer dialog box for the selected
position.

Click on the following detector types for a description of the parameters that
appear when the detector is selected.

258
FID Detector

Item Description
Turns the detector oven on or off.
Electronics On or Off.
Indicates whether the installed FID will be used or not.
Temperature (C) 50- 450 C.
Time Initial - 999.99 min.
Range 9, 10, 11, 12.
Autozero Yes or No.
Set to yes at initial time means that the FID Autozero is on
continuous before the run starts.
spreadsheet.
Time Constant Slow or Fast.
EFC Type None or Type 11 for the FID detector.
Make up Flow (ml/min) 0-50 ml/min.
H2 Flow (ml/min) 0-50 ml/min.
Air Flow (ml/min) 0-500 ml/min.
Methanizer Installed Yes or No.
Methanizer Oven On or Off.

259
TCD Detector

Item Description
Turns the TCD oven on or off.
Indicates whether the installed TDC will be used or not.
Specifies the TCD Temperature.
Filament Temp (C) 0-390 C.
Specifies the Filament Temperature.
Range 0.5 and 5.0 mV.
Whenever possible, operate the TCD at the lowest practical
filament current.
Autozero Yes or No.
Set to yes at initial time means that the FID Autozero is on
continuous before the run starts. Autozero is automatically
disabled once the run starts.
Polarity Positive or Negative.
Converts the polarity to reverse the peaks that appear in the
negative direction.
spreadsheet.

260
Item Description
Carrier Gas He or N2/Argon.
Filament Temp Limit (C) 390 or 490 C.
EFC Type None, Type 13, Type 14 , Type 16.
Specifies the installed type.
Ref/Makeup Flow
(ml/min)
0-100 l/min.
Temperature (C) 450 C.
TSD Detector

Item Description
Turns the detector oven on or off.
Specifies the TSD temperature.
Bead Current (A) 2.4 - 3.8 A.
Range 9, 10, 11, 12.

261
Item Description
Autozero Yes or No.
Set to yes at initial time means that the TSD Autozero is
on continuous before the run starts. Autozero is
automatically disabled once the run starts.
Bead Power On or Off.
spreadsheet.
spreadsheet.
EFC Type None or Type 12 for the TSD detector.
H2 Flow (ml/min) 0-6.0 ml/min.
Air Flow (ml/min) 0- 200 ml/min.

262
ECD Detector

Item Description
Turns the TCD oven on or off.
Indicates whether the installed ECD will be
used or not.
Range 1 or 10.
Autozero Yes or No.
Set to yes at initial time means that the
ECD Autozero is on continuous before the
run starts. Autozero is automatically
disabled once the run starts.
Insert Inserts a line above the currently selected
row in the spreadsheet.
spreadsheet.
Cell Current N2 High, N2 Std, CAP, Ar-CH4, Zero.
Contact Potential (mV) 0- 800 mV.
EFC Type None, Type 13 for the ECD.

263
Item Description
PFPD Detector

Item Description
Turns the PFPD oven on or off.
Indicates whether the installed PFPD will be used or
not.
Specifies the PFPD Temperature.
Square Root Mode On or Off.
Range 8, 9, 10.
Autozero Yes or No.
Set to yes at initial time means that the PFPD Autozero
is on continuous before the run starts. Autozero is
automatically disabled once the run starts.
spreadsheet.
spreadsheet.

264
Item Description
Photomultiplier Voltage
(V)
300- 900 V.
Gate Delay (msec) 20 msec.
Gate Width (msec) 20 msec.
Trigger Level (mV) 10- 2000 mV.
EFC Type None or Type 15 for the PFPD detector.
Air 1 Flow (ml/min) 0- 50 ml/min.
H2 Flow (ml/min) 0- 30 ml/min.
Air 2 Flow (ml/min) 0- 30 ml/min.
Methanizer Dialog Box
This dialog box is displayed by clicking on the Methanizer button at the bottom of
the detector window.

Item Description

265
3800 GC Output

Item Description
Port A
Port B
Port C
The 3800 GC can have up to three output ports installed
(A, B, and C). The tabs at the top of the window select
the output port position.
Port Installed? Yes or No.
Indicates whether or not the Port at each position is
installed. For the installed Port, the Output time program
is used to program the detector signal source and
attenuation.
Signal Source Front, Middle Rear.
Attenuation Powers of 2 from 1- Infinite.
spreadsheet.
spreadsheet.

266
3800 GC Data Acquisition

Item Description
Detector Bunch Rate Powers of 2 from 1 to 128 points.
Sets the detector bunch rate in numbers of points;
shows the resulting frequency in Hz. With increased
bunch rates, less disk space is required for storing the
data. With decreased rates, more data is collected.
Bunch rate should be set appropriately for the
narrowest peak of interest in your chromatogram.
Monitor Length 16 to 128 bunched points.
Sets the number of points collected during the
monitoring period, shows the resulting time in seconds.
Used to set the number of data points used to calculate
the baseline noise. Generally, a larger value entered
here will yield a lower noise calculation.
FID/TSD Detector Full
Scale
(Font, Middle, Rear)
1V, 10V, 100V, 1000V.
Specifies the maximum detector value that will be
processed by the Varian MS Workstation. The dynamic
range of the FID and TSD detectors are equivalent to
1000V full scale, but if your peaks of interest fall
significantly below this value, you may wish to limit the
full scale value here. Since the attenuation setting used
by the Standard Report application to scale the
chromatogram printout is based on the detector's full
scale value, a lower full scale value will allow you to
scale smaller peaks with greater resolution.

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3800 GC Method Section
Overview
In the 3800 GC Configuration section, you configured your hardware for an
instrument and opened the System Control Window for the instrument. At this
point, you could simply inject a sample, as described in the following sections.
However, it is not likely that the default Method will have the method settings that
are appropriate for your analysis. Therefore, the default Method will need to be
to view and edit methods. It can be accessed from:

This button on the MS Workstation Toolbar opens
Method Builder and prompts you to create a new
method or open and existing one.

This button on the System Control Toolbar allows
you to view and edit the method file shown on the
button.

This button on the MS Workstation Toolbar allows
button.


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to create a method.

Select Custom to create a Method for an instrument that is not attached to the Varian
MS Workstation.
Select the Instrument for which this method will be used.

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Select the detectors for post-run processing.

For each detector in the Method, you will be asked to select the channels on
which post-run processing will be performed.

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analysis.

Title Bar
Menu Bar
Toolbar
This navigation window shows the overall structure of the Method, its sections and
subsections. The branches can be expanded by clicking on the plus sign or
contracted by clicking on the minus sign to show the desired level of detail.

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The parameters window shows the parameters for the highlighted item in the
navigation window. Method parameters are viewed and edited in this window.
the online help.
Method Notes

The 3800 GC Method Windows
The 3800 GC entry specifies the Varian MS Workstation module address of the
GC that the Method uses. The module Address in the parameter window can be
changed so that a Method developed for an instrument using one module
address can be easily modified for use on another instrument at a different
module address.

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The 3800 Method section contains seven Method windows: Sample Delivery,
Injector, Flow/Pressure, Column Oven, Detector, Output, and Detector
Information. These windows contain all parameters that control the operation of
the 3800 GC during a chromatographic run.
Spreadsheet editing
Certain Method windows contain spreadsheet tables for time, temperature or
flow programming. All spreadsheets behave similarly.

Add a row at the bottom of the spreadsheet.
Insert a row before the currently selected row.
Delete currently selected rows.
Sort rows by time (available in time program spreadsheets).

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Select rows by clicking and dragging on the row numbers on the left side of the
spreadsheet.

One or more rows can be selected by clicking and dragging on this column.
Spreadsheets that specify time programs can display duplicate times, but all
duplicates must be eliminated before you can save your work.
Checking Method End times
All editing windows other than the column oven window and detector info window
show the current end time of the column oven program above the Save and
Cancel buttons.

The column oven endtime is shown.
If you enter program end times for components other than the column oven that
exceed the column oven end time, the following warning is displayed.

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When the Method is downloaded to the 3800 GC, component program end times
that exceed the column oven end time will be truncated.
Sample Delivery Window
The Sample Delivery window contains the Valve Table Program and up to three
Valve Oven Programs (Front, Middle, Rear).

Use these tabs to select which Valve Oven Program you wish to edit.
Indicate whether or not the Valve Oven at each position is installed by clicking on the
Yes or No radio buttons.
If you indicate that a Valve Oven is installed, a Valve Oven switch and a
Temperature setting will appear.

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Indicate whether or not you will use the installed Valve Oven by clicking on the On
or Off radio buttons.
Use the spreadsheet to build a time program to turn the programmable valves on and
off.
Specify the isothermal temperature of each Valve Oven.
The first two rows of the spreadsheet are added automatically. Use the first row
to indicate how each Valve is used, by clicking on the arrow in the top cell of
each Valve column. Select from the choices displayed in the combo box.
Configure each Valve to match the setup on the 3800 GC that will be running the
method.
The second row of the spreadsheet contains the Initial setting for each of the
seven Valves. Each Valve will be switched to this setting when the method is
activated, and restored to this setting when each chromatographic run is
completed.
Rows after the second row of the spreadsheet contain the time-programmed
settings for each of the seven Valves. Each Valve will be switched to the setting
in each row at the indicated time.

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Injector Window
The Injector window contains up to three Injector Programs (Front, Middle, Rear).
Use the Injector Programs to specify the temperature setpoints of the isothermal
1041, 1061 and 1177 Injectors, and to specify the temperature ramp and split
ratio of the programmable 1079 Injector.

Use the tabs to select which Injector Program you wish to edit.
Select the type of injector (1041, 1061, or 1079) at each position, or select None if
no injector is installed at that position.
1079 Injector
If you indicate that a 1079 Injector is installed, an Oven Power switch and a
Coolant switch will appear.

Indicate whether or not you will use the installed 1079 injector by clicking on the On

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If you indicate that Coolant is turned on, specify the desired Enable Coolant at
temperature and Coolant Timeout.
Use the spreadsheet to build a temperature ramp program to heat and/or cool the
1079 injector.
The first row of the spreadsheet contains the Initial temperature and hold time for
the 1079 injector. The 1079 will equilibrate to this setting when the method is
activated, and will be restored to this setting when each chromatographic run is
completed.
Rows after the first row of the spreadsheet contain the programmed settings for
each of the ramp segments. Each segment will ramp to the specified
temperature at the specified rate (assuming the rate is achievable), and then
hold the temperature for the specified time. (Note that the Rate in the first row is
always blank and cannot be edited. Also note that the entire Total column cannot
be edited.)
1079 Split Ratio

If the 1079 Injector is connected to a Type 1 EFC, press the Split Ratio button to
build the Split Ratio Time Program.
NOTE: You must have already configured the Type 1 EFC in the corresponding
position in the Flow/Pressure Section before you can program the split ratio.
Specifically, to build a 1079 Split Ratio Program, a Front 1079 must have a
corresponding Front Type 1 EFC, a Middle 1079 must have a corresponding
Middle Type 1 EFC, and a Rear 1079 must have a corresponding Rear Type 1
EFC.
Use the Split Ratio spreadsheet to build a split ratio time program to control the
1079 injector / Type 1 EFC combination.

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You can use a spit ratio of 100 after injection to vent the injector of any residual
solvent.
Use a very low split ratio after flushing to conserve carrier gas.
The first row of the spreadsheet contains the Initial Split State and Split Ratio for
completed.
Rows after the first row of the spreadsheet contain the time-programmed settings
for the 1079 Split Ratio. The Split Valve will be switched to the ratio in each row
1177 Injector
If you indicate that a 1177 Injector is installed, an Oven Power switch, a
Temperature setting and a Split Ratio button will appear.
Indicate whether or not you will use the
installed 1177 injector by clicking on
the On or Off radio buttons.
Set the desired
Temperature.
If the 1177 Injector is connected to a Type 1
EFC, press the Split Ratio button to build the
Split Ratio Time Program.

Specifically, to build a 1177 Split Ratio Program, a Front 1177 must have a
corresponding Front Type 1 EFC, a Middle 1177 must have a corresponding
Middle Type 1 EFC, and a Rear 1177 must have a corresponding Rear Type 1
EFC.

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You can use a split ratio of 100 after injection to vent the injector of any residual
solvent.
completed.
1041 Injector

Indicate whether or not you will use the installed 1041 Injector by clicking on the On
or Off radio buttons.If you indicate that a 1041 Injector is to be turned on, select the
desired Temperature setting.
1061 Injector

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Indicate whether or not you will use the installed 1061 Injector by clicking on the On
If you indicate that a 1061 Injector is to be turned on, select the desired Temperature
setting.
SPT Injection Device
If you indicate that a Sample Preconcentration Trap (SPT) is installed, an Oven
Power switch and a Coolant switch will appear.

Indicate whether or not you will use the installed SPT by clicking on the On or Off
radio buttons.
If you indicate that Coolant is turned on, specify the desired Enable Coolant at
temperature and Coolant Timeout.
Use the spreadsheet to build a temperature program to heat and/or cool the SPT.

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Flow/Pressure Window
The Flow/Pressure window contains up to three EFC Programs (Front, Middle,
Rear). Use the EFC Programs to specify the pressure ramp of the Type 1 EFC,
the pressure ramp and total flow time program of the Type 4 EFC, and the flow
ramp of the Type 3 EFC.

Use the tabs to select which EFC Program you wish to edit.
Select the type of EFC (Type 1, Type 3, or Type 4) at each position, or select None
if no EFC is installed at that position.
Type 1 EFC (for 1079/1177 Injectors)
If you indicate that a Type 1 EFC is installed, a pressure ramp spreadsheet will
appear.

Use the spreadsheet to build a pressure ramp program to control the Type 1 EFC.

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The first row of the spreadsheet contains the Initial pressure and hold time for the
Type 1 EFC. The EFC will equilibrate to this setting when the method is
completed.
each of the ramp segments. Each segment will ramp to the specified pressure at
the specified rate (assuming the rate is achievable), and then hold the pressure
for the specified time. (Note that the Rate in the first row is always blank and
cannot be edited. Also note that the entire Total column cannot be edited.)

Constant Column Flow for Type 1 EFC
Constant Column Flow mode for Type 1 EFC is enabled in the Flow/Pressure
window.

Click on the Radio Button to turn on the Constant Column Flow Mode. This mode
disables the spreadsheet and reveals the constant flow rate value.
Enter the desired Column Flow.
When the method is activated in System Control, the Varian MS Workstation will
generate and download the appropriate pressure program corresponding to the
Column Temperature program, the Column Setup Length and Diameter, the
Carrier Gas, and the ambient Barometric Pressure. These parameters are
specified at the 3800 GC front panel, and the Barometric Pressure is measured
by the 3800 at the time the Method is downloaded. The 3800 will run the
pressure program to hold the Column Flow at the specified value as the Column
Temperature is ramped during each run.

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Type 3 EFC (for 1041/1061 Injectors)
If you indicate that a Type 3 EFC is installed, a flow ramp spreadsheet will
appear.

The first row of the spreadsheet contains the Initial flow and hold time for the
completed.
each of the ramp segments. Each segment will ramp to the specified flow at the
specified rate (assuming the rate is achievable), and then hold the flow for the
specified time. (Note that the Rate in the first row is always blank and cannot be
edited. Also note that the entire Total column cannot be edited.)

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Type 4 EFC (for Valved Systems)
If you indicate that a Type 4 EFC is installed, a pressure ramp spreadsheet and a
flow time program spreadsheet will appear.

Pressure spreadsheet.
Flow spreadsheet.
The first row of the pressure spreadsheet contains the Initial pressure and hold
time for the Type 4 EFC. The EFC will equilibrate to this setting when the method
is activated, and will be restored to this setting when each chromatographic run
is completed.
Rows after the first row of the pressure spreadsheet contain the programmed
settings for each of the ramp segments. Each segment will ramp to the specified
pressure at the specified rate (assuming the rate is achievable), and then hold
the pressure for the specified time. (Note that the Rate in the first row is always
blank and cannot be edited. Also note that the entire Total column cannot be
edited.)
Use the flow spreadsheet to build a flow time program to control the Type 4 EFC
total flow. The first row of the flow spreadsheet contains the Initial Total Flow for
the Type 4 EFC. The EFC will equilibrate to this setting when the method is
completed.
Rows after the first row of the flow spreadsheet contain the time-programmed
settings for the Total Flow. The Total Flow will be switched to the value in each
row at the indicated time.

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Column Oven Window
The Column Oven window contains the Column Oven Program. Use the Column
Oven Program to specify the Coolant Parameters and Stabilization Time of the
Column Oven, and to specify its programmable temperature ramp.

Indicate whether or not you will use the Coolant by clicking on the On or Off
radio buttons.
Use the spreadsheet to build a temperature ramp program to heat and/or cool
the Column Oven.
Specify the desired temperature at which to enable the coolant.
Specify the desired Coolant Timeout.
Specify the desired Stabilization Time.
the Column Oven. The Column Oven will equilibrate to this setting, and stabilize
for the specified Stabilization Time, when the method is activated, and will be
restored to this setting when each chromatographic run is completed.
be edited.)

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Detector Window
The Detector window contains up to three Detector Programs (Front, Middle,
Rear). Use the Detector Programs to specify the operating temperatures, gas
flow rates and parameters of the detectors.

Use the tabs to select which Detector Program you wish to edit.
Select the type of Detector (FID, TSD, TCD, ECD, or PFPD) at each position, or
select None if no Detector is installed at that position.
Detector EFC modules
The detector Electronic Flow Control modules (EFC), if installed on your 3800
GC, are detector-specific and can be programmed from the Detector window.
Select the type of Detector EFC at each position, or select None if no Detector
EFC is installed at that position. Use the detector EFC program in each detector
window (Front, Middle, Rear) to specify the gas flow rates for each module.
Note that selecting the make-up gas and the auto-calibration of the module can
be performed from the Detector EFC Setup and configuration screens on the
3800 GC.
FID Detector
If you indicate that an FID Detector is installed, an Oven Power switch, an
Electronics switch, a Temperature setting and a Time Constant setting will
appear.

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Indicate whether or not you will use the installed FID Detector by clicking on the
On or Off radio buttons.
If you indicate that an FID Detector is to be turned on and heated, select the
Time-program the detector range and autozero in the spreadsheet.
Select the desired FID Time Constant by clicking on the Slow or Fast radio
buttons.
Select the desired gas flow rates for the detector EFC.
The first row of the spreadsheet contains the Initial Range and Autozero for the
FID Detector. The FID will switch to this setting when the method is activated,
and will be restored to this setting when each chromatographic run is completed.
for the Range and Autozero. They will be switched to the value in each row at the
indicated time.
Methanizer
The Methanizer is programmed from the Detector window. Note that the Front
Methanizer is programmed from the Front Detector tab, the Middle Methanizer
from the Middle Detector tab, and the Rear Methanizer from the Rear Detector
tab.

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Program the Methanizer in the position corresponding to the tab in the Detector
window by clicking on the Methanizer button.
The Methanizer Program dialog box will appear.

Indicate that a Methanizer is installed by selecting the Yes radio button.
Indicate whether or not you will heat the installed Methanizer by clicking on the
If you indicate that a Methanizer is to be heated, select the desired Temperature
setting.
TCD Detector
If you indicate that a TCD Detector is installed, an Oven Power switch, an
Electronics switch, a Temperature setting, and a Filament Temperature setting
will appear in the top portion of the window, and additional detector adjustments
will appear below the spreadsheet.

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If you indicate that an TCD Detector is to be turned on and heated, select the
desired Temperature and Filament Temperature setting.
Indicate whether or not you will use the installed TCD Detector by clicking on the
You can time-program the detector range, autozero, and polarity in the
spreadsheet.
Select the desired TCD Time Constant by clicking on the Slow or Fast radio
buttons.
Select the desired Carrier Gas and Filament Temperature Limit from the
available choices.
Three EFC types are available for the TCD detector. Select the type that is
installed on your 3800 GC.
Select the desired gas flow rates for the sample side and the reference side of
the TCD.
The first row of the spreadsheet contains the Initial Range, Autozero, and
Polarity for the TCD Detector. The TCD will switch to this setting when the
method is activated, and will be restored to this setting when each
chromatographic run is completed.
for the Range, Autozero, and Polarity. They will be switched to the value in each

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Micro-TCD Detector
If you indicate that a Micro-TCD Detector is installed, an Oven Power switch and
an Electronics switch will appear in the top portion of the window, and additional
detector adjustments will appear below the spreadsheet.
NOTE: The Micro-TCD cell temperature is set to 110 C and is not adjustable.

Indicate that a Micro-TCD Detector is installed
Indicate whether or not you will use the installed Micro-TCD Detector by clicking
on the On or Off radio buttons.

You can time-program the detector range, autozero, and polarity in the
spreadsheet.

Select the desired TCD Time Constant by clicking on the Slow or Fast radio
buttons.
Select the desired Carrier Gas from the available choices.
The first row of the spreadsheet contains the Initial Range, Autozero, and
Polarity for the Micro-TCD Detector. The Micro-TCD will switch to this setting
when the method is activated, and will be restored to this setting when each
for the Range, Autozero, and Polarity. They will be switched to the value in each

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TSD Detector
If you indicate that a TSD Detector is installed, an Oven Power switch, an
Electronics switch, a Temperature setting, a Bead Current setting and a Time
Constant setting will appear.

If you indicate that an TSD Detector is to be turned on and heated, select the
desired Temperature and Bead Current setting.
Indicate whether or not you will use the installed TSD Detector by clicking on the
You can time-program the detector range, autozero, and bead power in the
spreadsheet.
Select the desired TSD Time Constant by clicking on the Slow or Fast radio
buttons.
Select the desired gas flow rates for the detector EFC.
The first row of the spreadsheet contains the Initial Range, Autozero, and Bead
Power settings for the TSD Detector. The TSD will switch to this setting when the
method is activated, and will be restored to this setting when each
for the Range, Autozero, and Bead Power. They will be switched to the value in
each row at the indicated time.

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ECD Detector
If you indicate that an ECD Detector is installed, an Oven Power switch, an
Electronics switch, and a Temperature setting will appear in the top portion of the
window, and additional detector adjustments will appear below the spreadsheet.

If you indicate that an ECD Detector is to be turned on and heated, select the
Indicate whether you will use the installed Detector Oven and Electronics by
clicking on the On or Off radio buttons.
You can time-program the detector range and autozero in the spreadsheet.
Select the desired ECD Time Constant by clicking on the Slow or Fast radio
buttons.
Select the desired Make up gas flow rate.
Select the desired Cell Current and Contact Potential from the available choices.
ECD Detector. The ECD will switch to this setting when the method is activated,
and will be restored to this setting when each chromatographic run is completed.
indicated time.

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PFPD Detector
If you indicate that a PFPD Detector is installed, an Oven Power switch, an
Electronics switch, Square Root Mode switch, and a Temperature setting will
appear in the top portion of the window, and additional detector adjustments will
appear below the spreadsheet.

If you indicate that an PFPD Detector is to be turned on and heated, select the
Indicate whether you will use the installed Detector Oven and Electronics by
clicking on the On or Off radio buttons.
Enable or disable Square Root Mode.
You can time-program the detector range and autozero in the spreadsheet.
Select the desired PFPD Photomultiplier Voltage, Gate Delay, Gate Width, and
Trigger Level from the available choices.
Select the desired gas flow rates.
PFPD Detector. The PFPD will switch to this setting when the method is
completed.
indicated time.

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Output Window
The Output window contains up to three Output Port Programs (Port A, Port B,
Port C). Use the Output Port Programs to time program the detector signal
source and attenuation at each port.

Use the tabs to select which Output Port Program you wish to edit.
Indicate whether or not the Port at each position is installed by clicking on the
Yes or No radio buttons.
Time-program detector signal source and attenuation in the spreadsheet.
The first row of the spreadsheet contains the Initial Signal Source and
Attenuation for the Port. The Port will switch to this setting when the method is
completed.
for the Signal Source and Attenuation. They will be switched to the value in each

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Data Acquisition Window
The Data Acquisition window contains instructions for collecting a baseline noise
sample (Noise Monitor) and for selecting the full scale for the FID and TSD
detectors. The Varian MS Workstation will sample the baseline noise on the first
derivative of the detector signal before each run. This sample is used to estimate
the baseline noise. The estimate is more accurate as the sample size is
increased, but the sample takes longer to acquire.
The Varian MS Workstation will set the full scale for the detector signal as
specified here. The dynamic range of the FID and TSD detectors are equivalent
to 1000V full scale, but if your peaks of interest fall significantly below this value,
you may wish to limit the full scale value here.
Since the attenuation setting used by the Standard Report application to scale
the chromatogram printout is based on the detector's full scale value, a lower full
scale value will allow you to scale smaller peaks with greater resolution.

The 3800s 40 Hz data rate can be reduced by bunching. Enter the bunch size
here. The resulting bunched data rate is shown to the right.
Enter the size of the noise sample as the number of bunched data points.
Select the full scale signal setting for the FID and TSD detectors.

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Autosampler Window
The Autosampler window contains sampling parameters for the 8400/8410
Autosampler when attached to the 3800 GC. The parameters include selection of
the sampling syringe size, the penetration depth for sample and solvent wash
vials, the default clean and clean modes, and the injection modes.

Default clean steps are used in the case that automation is stopped or a serious
fault is detected.
Select Pre and Post injection syringe clean modes.
Injection Mode

The Injection Mode selection consists of five predefined injection modes:
Standard Split/Splitless, Standard On-Column, Neat, Viscous and Volatile. If any
of these modes cannot satisfy your injection needs, a sixth User Defined mode is
available. Selecting User Defined mode allows you access to all 8400
autosampler parameters to fine-tune your injection.
Consult the Online Help for a detailed description of all Injection Mode
parameters.

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Auto-Configuring the Method to Match the 3800 GC
Hardware
When you edit a 3800 GC Method while the corresponding GC is online in
System Control, you are warned if the Method configuration does not match the
hardware on the GC.

Click on Yes to change the Method to match the GC.
Click on No to accept the Method as is.
If you choose to auto-configure the Method, the following dialog is displayed.

Uploading the Method from the 3800 GC
You can get the Method from the GC and save it in the Varian MS Workstation.
This allows you to do local Method editing on the 3800 GC front panel and then
save this Method for later use on the Workstation.

To upload the Method from the 3800 GC to System Control, select Upload
Active Method from Modules from the File menu.

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You are then prompted for the name of the file under which to save the Method.
The active Method in System Control is updated to reflect the parameters
obtained from the 3800 GC.
The Startup Method
When you start System Control and display an Instrument Window, the last
active Method for that instrument is activated. When System Control is started, it
will return to the initial settings in the Method that was last used on the
instrument.

Editing Methods from the 3800 Status and Control Window
The 3800 GC Status and Control Window contains a Method button that allows
you to directly edit the active Method corresponding to that GC.

Method button
When you click on this button Method Builder is opened with active Method
loaded and the corresponding Instrument Module selected. You can then edit
that section or any other section of the Method as described previously.

299
changes to the Module.

You may wish to copy sections from one 3800 Method file to another. This can

import by clicking on them. If you click on one section and the hold down the shift
key while clicking on another section, all of the sections in between will be
files.

300


To remove sections from a 3800 Method open the Method containing the
menu.

and the hold down the shift key while clicking on another section, all of the

301

Printing the Method

the File menu.


302


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3800 GC System Control
Command Reference

The 3800 Status and Control window is divided into five display areas. These are
the 3800 Operation display, the Temp. Zones Status display, the Component
Status display, the 8400/8410 Carrousel display, and the Chromatogram display.
The left-most display area is the 3800 Operation display, which contains
information about the current run and the overall state of the GC.
The next display area to the right is the Temp. Zones Status display, which
shows the setpoint and current actual temperature of each heated zone in the
GC.
Next is the Component Status display. You select the component for which you
wish to see more detailed status information, including ready and fault status for
the selected component. You can change the component being displayed using
the selection box below the display area, or by clicking on the corresponding
temperature zone entry in the temperature zone status display.
3800 GCs that have an 8400 AutoSampler or 8410 AutoInjector installed will
have another display area, the 8400/8410 Carrousel display, that shows a

304
graphical representation of the 8400 or 8410 Carrousel. This display graphically
shows which vials are to be sampled, which vials have been sampled, which vial
is currently being sampled.
Below these display areas is the Chromatogram display. A selection box above
the chromatogram allows you to select the channels for which you want to view
the realtime chromatogram.
3800 Operation Display
The 3800 Operation display is in the left portion of the 3800 Status and Control window.

Item Description
Runtime Shows the elapsed time in minutes since the beginning
of the run. The maximum run time is 999.99 minutes.
Endtime Shows the time at which the run will end.
State Ready, Running, Stabilizing, Equilibrating, Computing,
Needs Monitor, Monitoring, Sampling, Connecting, or
Not Ready
Shows the state of the GC. The light appears green if
the GC is Ready or Running. Otherwise, the light is red.
Fault/No Fault indicator No Fault (green light) or Fault (red light).
When a hazardous or disabling fault occurs, any run in
progress will halt and the affected component will shut
down. If the fault is recoverable, then the run is not
terminated.
Valves Displays the 3800 GC valve status. A plus sign (+)
precedes the valve number if its state is energized. A
minus sign (-) precedes the valve number if the valve is
in the default state or if the valve is unused.
Start If the system is Ready, starts the GC Method and sends
a start signal to the GC. Equivalent to pressing Start on
the front panel of the GC. The Start button is disabled
unless the 3800 GC is in the Ready state.
Reset Resets the GC, advancing it to the next state. If it is
RUNNING, the GC aborts the current run, goes to the
READY state, and continues with the next injection in
the Sequence. Equivalent to pressing Stop on the front
panel of the GC.
Method Opens the Method Builder application for editing the
active 3800 GC method.

305
Temp Zones Status Display

The temperature zones status display is in the middle portion of the 3800 Status and Control window.
The display includes the setpoints and actual temperatures of the column oven, the three coolable
zones, and the three heatable-only zones of the 3800 GC. The display is Fault if a fault occurs in the
zone component or Off if the zone oven is off. If the zone has not been configured by the 3800 GC,
then N/A is displayed for the setpoints and actual temperature. Clicking on one of the temperature
zone entries will display the corresponding component status in the Component Status Display.
The LEDs indicate the status of each temperature zone. If the zone is not configured or the zone oven
is off, the LED is gray. If the temperature zone is Not Ready or there is a fault, then the LED is red.
Otherwise, the LED is green.
Component Status Display

The Component Status display is in the right portion of the 3800 Status and
Control window. Select the component status to view with the drop down list box
below the display area.

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Column Oven Status:
Item Description
Ready Yes or No.
The column oven is Ready (Yes) if the setpoints have been
achieved and stabilized. The column oven is Not Ready (No) if
readiness to start a run has not been achieved or if, during a
run, the oven becomes not ready or goes out of tolerance.
Some reasons the GC may go Not Ready during a run are: the
temperature program is too aggressive, the oven door is
opened, the coolant runs out, the power line voltage drops, etc.
Fault Yes or No.
Displays if a fault in the column oven component has occurred.
Oven Power On or Off.
Displays if the column oven component is turned off or on at
the 3800 GC.
Coolant On or Off.
Displays if the column oven coolant is enabled in the active
method.
Setpoint -99 to 450 C
Displays the column oven programmed temperature setting in
the active method.
Actual -99 to 450 C
Displays the actual temperature of the column oven at the 3800
GC.
Stabilization
Time
0.00 to 10.00 min
Shows the 3800 GC column oven stabilization time in minutes.
The stabilization time counts down from the programmed
method value and then displays 0.00 minutes when the
stabilization period is over.
Enable Column
Oven Coolant at
30 C to 450 C
Displays the programmed column oven temperature at which
the column oven coolant is enabled.
Timeout 0.01 min to 999.99 min
Displays the programmed coolant time-out value in the active
method for the column oven.
Timed Out Yes or No.
Displays Yes if the coolant time-out period has elapsed for the
column oven.

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AutoSampler Status:
This option is only shown on 3800 GCs that have an 8400 AutoSampler or 8410
AutoInjector connected to them.

Item Description
8400/8410 State Ready or Running
Current Vial 0 through 99 for 8400 AutoSampler
1 through 21 for 8410 AutoInjector
Plunger Strokes Displays the number of times that the syringe plunger has
been stroked up and down. This can be used to help monitor
syringe wear and plan for syringe replacements.
Injection Mode Shows the injection mode specified in the active 3800 GC
method.
Injection number: x
of y
where x and y are any number between 1 and 9.
Shows the number of the injection that is currently being run
and the total number of injections scheduled for that sample.
Injectors used Pos 1
Pos 2
Pos 1 then 2
Pos 2 then 1

Shows the injector positions that the 8400/8410 will use for
current run.
2nd Injection

Duplicate or Advance
This field is only displayed when the 8400/8410 is in Dual
Mode or Duplicate Mode.

Tray Orientation
(8410 AutoInjector
Only)
Vials 1 through 10,
Vials 11 through 16, or
Vials 17 through 21
Shows the range of vials accessible from the current 8410
carrousel location.

308
Sample Delivery Status:
Item Description
Valve 1 through
Valve 7
If the valves are configured in the 3800 GC, displays the
assigned valve name and current state at the 3800 GC. The
possible valve names, default state of the valve, and the
energized state of the valve are listed below.

Name Default State Energized
State
Unused
Front Split
Middle Split
Rear Split
Gas Sampling
Liquid
Sampling
Sample
Internal Std
Surrogate Std
Series Bypass
Backflush to
Det
Backflush to
vent
Column
Selection
Injection to
detector
Injection to
vent
Alternate
injection
Simultaneous
Injection
Methanizer
Bypass
Sample
Preconcentration

External Event A
External Event B
External Event C
External Event D

Off
On (split)
On (split)
On (split)
Fill

Fill
Off
Off
Off
Series
Forward

Forward

Column 1

Backflush

Backflush

Column 1

Fill

Series

SPT Trap

Off

Off

Off

Off

On
Off (s/less)
Off (s/less)
Off (s/less)
Inject

Inject
On
On
On
Bypass
Backflush

Backflush

Column 2

Inject

Inject

Column 2

Inject

Bypass

SPT Desorb

On

On

On

On

309
1177 Injector Status:
Item Description
Ready Yes or No.
The 1177 injector oven is Ready (Yes) if the setpoints have
been achieved and stabilized. The 1177 injector oven is Not
Ready (No) if readiness to start a run has not been achieved or
if, during a run, the oven becomes not ready or goes out of
tolerance.
Fault Yes or No.
Displays if a fault in the 1177 injector component has occurred.
1177 Oven On or Off.
Displays if the 1177 injector oven component is turned off or on
at the 3800 GC. The 1177 injector is an isothermal injector.
Setpoint 50 to 450 C
Displays the 1177 injector oven programmed temperature
setting in the active method.
Actual 50 to 450 C
Displays the actual temperature of the 1177 injector oven at
the 3800 GC.
Split State On or Off.
Displays the current split state of the 1177 injector method.

1079 Injector Status:
Item Description
Ready Yes or No.
The 1079 injector oven is Ready (Yes) if the setpoints have
been achieved and stabilized. The 1079 injector oven is Not
Ready (No) if readiness to start a run has not been achieved
or if, during a run, the oven becomes not ready or goes out
of tolerance. Some reasons the GC may go Not Ready
during a run are: the temperature program is too aggressive,
the oven door is opened, the coolant runs out, the power line
voltage drops, etc.
Fault Yes or No.
Displays if a fault in the 1079 injector component has
occurred.
1079 Oven On or Off.
Displays if the 1079 injector oven component is turned off or
on at the 3800 GC.
Coolant On or Off.
Displays if the 1079 injector oven coolant is enabled in the
active method.
Setpoint -99 to 450 C
Displays the 1079 injector oven programmed temperature
Actual -99 to 450 C

310
Item Description
Displays the actual temperature of the 1079 injector oven at
the 3800 GC.
Split Ratio 1 to 10000 or Off
Displays the current split ratio of the 1079 injector method.
The split ratio is defined as the Column Flow + the Split Flow
/ the Column Flow.
Enable 1079
Injector Coolant at
30 C to 450 C
Displays the programmed injector oven temperature at which
the 1079 injector oven coolant is enabled.
Timeout 0.01 min to 999.99 min
method for the 1079 injector oven.
Displays Yes if the coolant time-out period has elapsed for
the 1079 injector oven.
1041/1061 Injector Status:
Item Description
Ready Yes or No.
The 1041/1061 injector oven is Ready (Yes) if the setpoints have
been achieved and stabilized. The 1041/1061 injector oven is Not
Ready (No) if readiness to start a run has not been achieved or if,
during a run, the oven becomes not ready or goes out of
tolerance.

Fault Yes or No.
Displays if a fault in the 1041/1061 injector component has
occurred.

1041/1061
Oven
On or Off.
Displays if the 1041/1061 injector oven component is turned off or
on at the 3800 GC. The 1041 and 1061 injectors are isothermal
injectors.
Setpoint 50 to 450 C
Displays the 1041/1061 injector oven programmed temperature
Actual 50 to 450 C
Displays the actual temperature of the 1041/1061 injector oven at
the 3800 GC.

311
SPT Injector Status:
Item Description
Ready

Yes or No.
The SPT injector oven is Ready (Yes) if the setpoints have
been achieved and stabilized. The SPT injector oven is Not
or if, during a run, the oven becomes not ready or goes out
of tolerance. Some reasons the GC may go Not Ready
during a run are: the temperature program is too aggressive,
the oven door is opened, the coolant runs out, the power line
voltage drops, etc.
Fault

Yes or No.
Displays if a fault in the SPT injector component has
occurred.
SPT Oven

On or Off.
Displays if the SPT injector oven component is turned off or
on at the 3800 GC.
Coolant On or Off.
Displays if the SPT injector oven coolant is enabled in the
active method.
Setpoint

-99 to 450 C
Displays the SPT injector oven programmed temperature
Actual

-99 to 450 C
Displays the actual temperature of the SPT injector oven at
the 3800 GC.
Enable SPT Coolant
at

30 C to 450 C
Displays the programmed injector oven temperature at which
the SPT injector oven coolant is enabled.
Timeout

0.01 min to 999.99 min
method for the SPT injector oven.
Displays Yes if the coolant time-out period has elapsed for
the SPT injector oven.

Type 1 Injector EFC Flow/Pressure Status:
Item Description
Ready Yes or No.
The Type 1 Injector EFC component is Ready (Yes) if the
setpoints have been achieved and stabilized. The Type 1 Injector
EFC component is Not Ready (No) if readiness to start a run has
not been achieved or if, during a run, the EFC becomes not ready
or goes out of tolerance. Some reasons the GC may go Not
Ready during a run are: the temperature program is too
aggressive, the oven door is opened, the coolant runs out, the
power line voltage drops, etc.
Fault Yes or No.

312
Item Description
Displays if a fault in the Type 1 EFC component has occurred.
Type 1
Pressure
Setpoint
0.1 to 100 psi
Displays the programmed column head pressure setting in the
active method.
Actual Pressure 0.1 to 100 psi
Displays the actual column head pressure at the 3800 GC.
Column Flow Displays, in ml/min, the column flow rate calculated from the
column head pressure, column temperature, and column
parameters (carrier gas, column length, and internal diameter).
Linear Velocity Displays, in cm/sec, the column linear velocity calculated from the
parameters (carrier gas, column length, and internal diameter).
Total Flow Displays, in ml/min, the total flow rate through the system.
Displays the current split state of the 1079/1177 injector method.
Split Ratio 1 to 10000
Displays the current split ratio of the 1079/1177 injector method.
The split ratio is defined as the Column Flow + the Split Flow / the
Column Flow.
Item Description
Ready Yes or No.
setpoints have been achieved and stabilized. The Type 3
Injector EFC component is Not Ready (No) if readiness to
start a run has not been achieved or if, during a run, the
EFC becomes not ready or goes out of tolerance. Some
reasons the GC may go Not Ready during a run are: the
opened, the coolant runs out, the power line voltage drops,
etc.
Fault Yes or No.
Displays if a fault in the Type 3 EFC component has
occurred.
Type 3 Flow
Setpoint
0.1 to 100 ml/min
Displays the programmed column flow rate setting in the
active method.
Actual Flow 0.1 to 100 ml/min
Displays the actual column flow rate calculated from the
measured head pressure and column parameters (carrier
gas, column length, and internal diameter).
Pressure Displays, in psi, the measured column head pressure.
Linear Velocity Displays, in cm/sec, the column linear velocity calculated
from the column head pressure, column temperature, and
column parameters (carrier gas, column length, and internal
diameter).

313

Item Description
Ready Yes or No.
start a run has not been achieved or if, during a run, the EFC
becomes not ready or goes out of tolerance. Some reasons
the GC may go Not Ready during a run are: the temperature
program is too aggressive, the oven door is opened, the
coolant runs out, the power line voltage drops, etc.
Fault Yes or No.
Displays if a fault in the Type 4 EFC component has
occurred.
Type 4 Pressure
Setpoint
0.1 to 100 psi
Displays the programmed column head pressure setting in
the active method.
Actual Pressure

0.1 to 100 psi
Column Flow

Displays, in ml/min, the column flow rate calculated from the
parameters (carrier gas, column length, and internal
diameter).
This value is not displayed if the column length has not been
set in the 3800 GC column parameters setup.
Total Flow

1 to 1000 ml/min
Displays the programmed total flow rate in the active method.
Linear Velocity

Displays, in cm/sec, the column linear velocity calculated
column parameters (carrier gas, column length, and internal
diameter).
TCD Status:
Item Description
Ready

Yes or No.
The TCD detector is Ready (Yes) if the setpoints have been
achieved and stabilized. The TCD detector is Not Ready (No) if
readiness to start a run has not been achieved or if, during a run,
the TCD detector becomes not ready or goes out of tolerance.
temperature program is too aggressive, the oven door is opened,
the coolant runs out, the power line voltage drops, etc.
Fault

Yes or No.
Displays if a fault in the TCD detector component has occurred.
TCD Electronics

On or Off
Displays the TCD Electronics setting in the active method.
Range 0.05, 0.5, or 5.0

314
Item Description
Displays the TCD Range initial condition setting or the time-
programmed setting in the active method.
Time Const

Fast (50 msec) or Slow (200 msec)
Displays the electrometer time constant setting from the TCD
Adjustments in the active method.
Filament Temp

0 to 490 C
Displays the TCD Filament Temperature setting in the active
method.
Current Displays, in mA, the actual TCD current.
Balance Pct

Displays, in %, the TCD bridge balance. On the 3800 GC, the
bridge is balanced automatically and should normally set around
0%. A large offset in bridge balance (+ or -) could indicate a
potential problem.
Polarity

positive or negative
Displays the TCD Polarity initial condition setting or time-
Detector Signal Displays, in mV, the actual TCD detector signal at the 3800 GC.
Bunch Size Displays the data acquisition bunch size.
Freq Displays the data acquisition bunch rate, in Hz.
MicroTCD Status:
NOTE: The microTCD detector temperature is set to 110C and is not user
adjustable.

Item Description
Ready

Yes or No.
The microTCD detector is Ready (Yes) if the setpoints have
been achieved and stabilized. The microTCD detector is Not
or if, during a run, the microTCD detector becomes not ready
or goes out of tolerance. Some reasons the GC may go Not
aggressive, the oven door is opened, the coolant runs out,
the power line voltage drops, etc.
Fault

Yes or No.
Displays if a fault in the microTCD detector component has
occurred.
microTCD
Electronics

On or Off
Displays the microTCD Electronics setting in the active
method.
Range

0.05, 0.5, or 5.0
Displays the microTCD Range initial condition setting or the
time-programmed setting in the active method.
Time Const

Fast (50 msec) or Slow (200 msec)
Displays the electrometer time constant setting from the

315
Item Description
microTCD Adjustments in the active method.
Current Displays, in mA, the actual microTCD current.
Balance Pct

Displays, in %, the microTCD bridge balance. On the 3800
GC, the bridge is balanced automatically and should normally
set around 0%. A large offset in bridge balance (+ or -) could
indicate a potential problem.

Polarity

positive or negative
Displays the microTCD Polarity initial condition setting or

Detector Signal Displays, in mV, the actual microTCD detector signal at the
3800 GC.



FID Status:
Item Description
Ready Yes or No.
The FID detector is Ready (Yes) if the setpoints have been
achieved and stabilized. The FID detector is Not Ready
(No) if readiness to start a run has not been achieved or if,
during a run, the FID detector becomes not ready or goes
out of tolerance. Some reasons the GC may go Not

Fault Yes or No.
Displays if a fault in the FID detector component has
occurred.
FID Electronics On or Off
Displays the FID Electronics setting in the active method.

Range 9, 10, 11, or 12
Displays the FID Range initial condition setting or the time-

Time Const Fast (50 msec) or Slow (200 msec)
FID Adjustments in the active method.

Detector Signal Displays, in mV, the actual FID detector signal at the 3800

316
GC.



317
ECD Status:
Item Description
Ready Yes or No.
The ECD detector is Ready (Yes) if the setpoints have been
achieved and stabilized. The ECD detector is Not Ready (No) if
readiness to start a run has not been achieved or if, during a run,
the ECD detector becomes not ready or goes out of tolerance.
temperature program is too aggressive, the oven door is opened,
the coolant runs out, the power line voltage drops, etc.

Fault Yes or No.
Displays if a fault in the ECD detector component has occurred.

ECD
Electronics
On or Off
Displays the ECD Electronics setting in the active method.

Range 1 or 10
Displays the ECD Range initial condition setting or the time-

Displays the electrometer time constant setting from the ECD
Adjustments in the active method.

Detector
Signal
Displays, in mV, the actual ECD detector signal at the 3800 GC.



TSD Status:
Item Description
Ready Yes or No.
The TSD detector is Ready (Yes) if the setpoints have been
achieved and stabilized. The TSD detector is Not Ready
(No) if readiness to start a run has not been achieved or if,
during a run, the TSD detector becomes not ready or goes
out of tolerance. Some reasons the GC may go Not Ready
during a run are: the temperature program is too
Fault Yes or No.
Displays if a fault in the TSD detector component has
occurred.

318
Item Description
TSD Bead Power On or Off
Displays the TSD Bead Power initial condition setting or the

Range 9, 10, 11, or 12
Displays the TSD Range initial condition setting or the time-

TSD Adjustments in the active method.

Bead Current

2.4 to 3.8 A or Off
Displays the TSD Bead Current setting in the active method
or Off if the Bead Power is off.

Detector Signal Displays, in mV, the actual TSD detector signal at the 3800
GC.



PFPD Status:
Item Description
Ready

Yes or No.
The PFPD detector is Ready (Yes) if the setpoints have
been achieved and stabilized. The PFPD detector is Not
or if, during a run, the PFPD detector becomes not ready or
goes out of tolerance. Some reasons the GC may go Not
Fault

Yes or No.
Displays if a fault in the PFPD detector component has
occurred.
PFPD Electronics

On or Off
Displays the PFPD Electronics setting in the active method.
Range

8, 9, or 10
Displays the PFPD Range initial condition setting or the

319
Type 11 Detector EFC Status:
Item Description
Type 11
Displays the Detector EFC type. Detector EFC Type 11
has 3 channels and is used for FID detector gas control.
Ready Yes or No.
The Detector EFC is Ready (Yes) if the setpoints have
been achieved and stabilized. The Detector EFC is Not
Ready (No) if readiness to start a run has not been
achieved or if, during a run, the Detector EFC becomes not
ready or goes out of tolerance. Some reasons the GC
may go Not Ready during a run are: the temperature
program is too aggressive, the oven door is opened, the
coolant runs out, the power line voltage drops, etc.
Fault Yes or No.
Displays if a fault in the Detector EFC component has
occurred
Ch 1 (Make up) Set,
Actual
Displays, in ml/min, the programmed and actual channel 1
flow rate.
Ch 2 (H2) Set, Actual Displays, in ml/min, the programmed and actual channel 2
flow rate.
Ch 3 (Air) Set, Actual Displays, in ml/min, the programmed and actual channel 3
flow rate.
Item Description
Type 12
has 3 channels and is used for TSD detector gas control.
Ready Yes or No.
Fault Yes or No.
Ch 1 (Makeup) Set,
Actual
flow rate.
flow rate.
Ch 2 (Air) Set, Actual Displays, in ml/min, the programmed and actual channel 3
flow rate.

320
Item Description
Type 13
Displays the Detector EFC type. Detector EFC Type 13 has
1 channel and is used for either ECD or TCD detector gas
control.

Ready Yes or No.

Fault Yes or No.

Ch 1 (Makeup) Set,
Actual

flow rate for TCD detector gas control.

Ch 1 (Reference) Set,
Actual

flow rate for ECD detector gas control.

Item Description
Type 14
has 2 channels and is used for TCD detector gas control.

Ready Yes or No.

Fault Yes or No.

Ch 1 (Make up) Set,
Actual
flow rate.

Actual
flow rate if the channel 2 gas type is a Helium, Nitrogen, or
Argon reference.

Ch 2 (Make up) Set,
Actual
flow rate if the channel 2 gas type is a Helium, Nitrogen, or
Argon make-up.

321
Item Description
Type 15
has 3 channels and is used for PFPD detector gas control.

Ready Yes or No.

Fault Yes or No.

Ch 1 (Air 1) Set,
Actual
flow rate.

flow rate.

Ch 3 (Air 2) Set,
Actual
flow rate.

Item Description
Type 16
Displays the Detector EFC type. Detector EFC Type 16 has
2 channels and is used for TCD detector gas control.

Ready Yes or No.

Fault Yes or No.

Ch 1 (Make up) Set,
Actual
flow rate.

Actual
flow rate if the channel 2 gas type is a Hydrogen reference.

Ch 3 (Make up) Set,
Actual
flow rate if the channel 2 gas type is a Hydrogen make-up.

322
8400/8410 Carrousel Display
When an 8400 AutoSampler or 8410 AutoInjector is connected to your 3800, the
Carrousel display will be visible in the 3800 GC Status and Control window.

8400 AutoSampler Carrousel 8410 AutoInjector Carrousel
Item Description
Red fill Indicates vials listed in the active SampleList that have not
yet been sampled or are missing.

Green fill Indicates the vial (vials in Dual Mode) currently being
sampled.
Blue fill Indicates the vials in the active SampleList that have been
sampled.

Action Description
Click on a
vial position
Displays the vial number for that position for 5 seconds

Double-
click on a
vial position
Opens the Inject Single Sample dialog box to inject a single sample.

323
Chromatogram Display Toolbar

Shows or hides the toolbar.

Full Scale: zooms all traces to their full scale values. This button is the
same as double clicking in the chromatogram display window.

Vertical Full Scale: the chromatogram is zoomed such that all of the
trace is visible within the given time range. This command only affects
the displayed amplitude range, the time range is unaffected. This
button is the same as double clicking in the Y axis of the
chromatogram display window.

Horizontal Full Scale: the chromatogram is zoomed such that the
entire time range is visible. This command only affects the displayed
time range, the amplitude range is unaffected. This button is the same
as double clicking in the X axis of the chromatogram display window.

Previous Scaling: zooms to the previous time and amplitude range.
Each time you scale the chromatogram, the new scaling rectangle is
added to the end of a list of scaling rectangles. Previous scaling
zooms the display to the value stored in the previous position on the
list. This item is disabled when at the start of the list.

Next Scaling: zooms to the next time and amplitude range. Each time
you scale the chromatogram, the new scaling rectangle is added to
the end of a list of scaling rectangles. Next scaling zooms the display
to the value stored in the next position on the list. Since new scaling
rectangles are added to the end of the list, it implies that Next Scaling
is only available when you had formerly hit the Previous Scaling
button. That is, this item is disabled when at the end of the list.

Autoscaling: when depressed, the vertical axis is autoscaled
continuously. If the chromatogram trace exceeds the current vertical
scaling, the Y axis is automatically adjusted to keep the trace in view.

Cursor Display: turns the cursor on or off. The cursor follows the
chromatogram trace and displays the time and amplitude of its current
position in an info-panel.
Hold the control key down to allow the cursor to move anywhere on
the screen without following the active trace.

324
Chromatogram Zooming and Scrolling
The following mouse actions are possible for the chromatogram display window:

Action Effect of Action
Left mouse button click
and drag a selection.
Expands selected section of chromatogram to fill the
entire window.

Left mouse button
double click.
Zooms to full scale.

Left mouse click and
hold
Zooms isometrically from the mouse position, or, if you
are holding the control key down, zooms out from that
point. Once PowerZooming begins, you can move the
mouse around while the mouse button is still down to
change the point at which you are zooming

You can view other sections of the chromatogram while maintaining the same
zoom level by scrolling. Scroll bars are shown only if the time or amplitude range
of your zoomed view is less than the maximum time or amplitude range of the
chromatogram. Scrolling horizontally lets you see sections of the chromatogram
earlier or later than the current section. Scrolling vertically lets you see sections
of higher or lower amplitude.
You can scale vertically using the Attenuation Control to the right of the
chromatogram display window. This adjusts the amplitude range on a logarithmic
scale. When using the attenuation control, the lowest point of the active trace is
fixed, and the amplitude range is adjusted to a smaller range as you slide the
position indicator up and to a larger range as you slide it down.
You can zoom in the amplitude and time axes in the same way as you do in the
chromatogram display window. You can select a rectangular section of the axis,
PowerZoom, and double click in the axis. These actions zoom just like they
would in the chromatogram display window, except that only the amplitude
scaling is affected when zooming in the amplitude axis and only the time scaling
is affected when zooming in the time axis.
3800 Setup Dialog Box
This dialog box shows the hardware configuration reported by the 3800 GC. This
configuration is compared to and must match the configuration in the Method
when it is activated.

325

8400/8410 Dual Mode Setup Dialog Box

When the 8400 AutoSampler or 8410 AutoInjector is used in Dual Mode, this
dialog box is used to assign the detector channels to the datafile for the
corresponding sample. In Dual Mode operation, two datafiles are created; one for
the first sample injected, the other for the second sample injected. The samples
that are injected are identified by their 8400/8410 Injection Position as either
Position 1 or Position 2. The table in this dialog box allows the user to specify
which detector information to associate with each 8400/8410 Injection Position.
If the user enters the correct 8400/8410 Mounting Position, Front or Rear, then
the Injector that corresponds to each 8400/8410 Injection Position will be
correctly identified. The 8400/8410 Mounting Position specified in this Dialog box
has no effect on the actual operation of the AutoSampler. It is for informational
purposes only.

326

Field Description
8400/8410 Mounting
Position
(Informational entry
only)
Front or Rear
When set to match the physical mounting location of the
8400/8410, the Injector column in the table will show the
3800 injector that corresponds to the 8400/8410 Injection
Positions. The 8400/8410 Mounting Position specified in
this Dialog box has no effect on the actual operation of
the 8400/8410 AutoSampler.
8400/8410 Injection
Position
(not user modifiable)

Pos 1 and Pos 2
Specifies the 8400/8410 Injection Position for the other
entries in the row.

Injector
(not user modifiable)

When the 8400/8410 Mounting Position is set to match
the physical mounting location of the 8400/8410, this
column will show the 3800 injector that corresponds to
each of the 8400/8410 Injection Positions. This column is
for informational use only and does not affect the
operation of the 8400/8410 AutoSampler or Star WS.

Front XXXX Detector
where XXXX is the
abbreviation for the
type of detector

Yes or No
When yes is selected, the chromatographic data from this
detector channel will be added to the datafile created for
the sample injected in the 8400/8410 Injection Position
specified on the same line in the first column of the row.

Mid XXXX Detector
where XXXX is the
type of detector

Yes or No

Rear XXXX Detector
where XXXX is the
type of detector

Yes or No

327
Setup Ethernet Ports Dialog Box
This dialog box is displayed the first time that the Star Assistant guides you
through the setup of your 3800 in System Control. This dialog box is also
accessed from the Instrument/Setup Ethernet Communications menu item of
System Control.

Field Description
Address

44, 45, 46, or 47
Click the Address button to attach to a 3800 GC on the
Ethernet network. If you are running on a company network,
only GCs on the same local subnet appear in the Select
Available Modules dialog box that is displayed after clicking
the Address button.
Module Type

None or 3800
This field is set if you select a 3800 GC using the Address
button. If you specify an IP Address or Domain Name
explicitly, then select 3800 from this combobox.
IP Address or
Domain Name

This field is set if you select a 3800 GC using the Address
button. To connect to a GC in a different subnet, type its IP
Address directly into the IP Address or Domain Name field.
Status

Available, Online, In Use By <client>, Not Responding, or
No Address
Displays the connection status of the 3800 GC.
Status Meaning
Available
Online
In Use By <client>
Not Responding
No Address
Not in use by anyone
In use by this
Workstation
In use by another
Workstation
Not responding to
Workstation queries
No IP Address or
name specified
Actual IP Displays the actual IP address of the connected 3800 GC.

328

Setup...

Click to setup IP address management (BOOTP Server).
The Setup BOOTP Server Dialog Box is displayed.

Select the
Workststion IP
Address...

Allows you to select from one of the IP addresses
configured for this computer.
Setup BOOTP Server Dialog Box
the 3800 GCs must be added to the list of devices requiring IP addresses. IP
addresses must be assigned to GCs using a BOOTP Server. A BOOTP Server
lists Ethernet addresses (which are unique to each communication card installed
in each 3800 GC) along with the IP addresses that are to be assigned to the
corresponding device. You may obtain the Ethernet address for each GC from
the GCs front panel. Turn on the 3800 GC and press any key to allow it to start
in local mode.

Field Description
Manage IP addresses
from this Workstation

Checked or not checked
When IP addresses are managed from a central
location by a Network Administrator, the BOOTP
Server on your Workstation must be disabled (not
checked).
Require password entry
for this dialog box
Check this box to restrict access to the BOOTP Server

329
Field Description

dialog box to avoid inadvertent or unauthorized
changes to IP address assignments. If this item is
checked, the next time you enter the BOOTP Server
dialog box, you will be prompted for a password. The
initial password is blank (no password). To set your
password initially, enter the desired password in the
Enter new password and Re-enter new password
fields. Subsequent entry into the BOOTP Server will
require this password.
Ethernet Address

Displays the Ethernet address of any 3800 GCs
already connected to the network and powered on.
You may also manually enter an Ethernet address for
a 3800 GC (available from the 3800 GC front panel
display).
IP Address

Displays the IP address of any 3800 GCs already
connected to the network and powered on. You may
also manually enter an IP address for a 3800 GC. Use
the manual entry of IP addresses and Host Names
when individual IP addresses have been reserved for
use by each 3800 GC but IP Address and Host Name
management is not performed by a Network
Administrator.
Host Name

You must enter a name for each 3800 GC. The IP
address will not be assigned to the GC until a name is
entered.
Assign IP addresses
manually

Selected or not selected
Select this entry if you manually enter IP addresses
and Host Name entries in the table.
Assign IP addresses
starting from

Select this entry to consecutively assign IP addresses
beginning from a particular address. Enter the number
of IP addresses to assign automatically and the
starting IP address. As 3800 GCs are powered on, IP
addresses are automatically assigned from the
specified address.
Subnet Mask

Displays the subnet mask assigned to the Workstation.
This parameter is assigned in the TCP/IP network
setup in the Control Panel application.
Gateway

Displays the Gateway assigned to the Workstation.
This parameter is assigned in the TCP/IP network
setup in the Control Panel application.
Domain

Displays the Domain name assigned to the
Workstation. This parameter is assigned in the TCP/IP
network setup in the Control Panel application.
Advanced

Click for specialized IP address management entries.
The Advanced BOOTP Dialog Box is displayed.

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Advanced BOOTP Settings Dialog Box

Item Description
Assign Private Class A
addresses to Hosts Manually

Determines whether IP addresses must be
entered in the Setup BOOTP Server dialog box
(checked) or if they are generated (unchecked).
Use Subnet Mask

Enter the subnet mask here. This is only used
when the Manage IP addresses from this
Workstation checkbox is checked in the Setup
BOOTP Server dialog box.
Use Gateway

Enter the gateway address here. This is only
used when the Manage IP addresses from this
Use Domain

Enter the domain name here. This is only used
when the Manage IP addresses from this
8400/8410 SampleList Window Extensions

When a 3800 GC controls an 8400 AutoSampler or 8410 AutoInjector, the
SampleList for that instrument contains the following device-dependent fields.
Many of these SampleList fields are only shown and available for editing when
the 8400 AutoSampler or 8410 AutoInjector is used in Duplicate Mode or Dual
Mode. Refer to the help on the generic SampleList Window for a description of
the fields not listed below.

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Field Description
2nd Sample Name
(Dual Mode operation only)
Up to 19 characters
Sets the name of the second sample injected. This
column is only displayed when the 2
nd
Injection is
Advance or Clean & Adv.
2nd Inject Notes
(Dual Mode operation only)
up to 180 characters
Opens the Notes window for the selected second
sample to edit or create a note about the sample.
This column is only displayed when the 2
nd
Injection
is Advance or Clean & Adv.
Vial 0 through 99 for 8400 AutoSampler
1 through 21 for 8410 AutoInjector
Sets the AutoSampler vial number of each sample in
the SampleList. When the 2nd Injection is Advance
or Clean & Adv, two sequentially numbered vials
will be shown. The first vial will be injected on the first
injection and the next vial location will be sampled for
the second injection.
Injection Volume

0.1 to 10 L
Sets the injection volume of the sample in microliters.
When the SampleList is edited in System Control, the
maximum value allowed is set to the syringe size
currently configured in the 3800 GC setup.
During operation, if the sample volume plus solvent
volume, internal standard addition volume, and air
gaps volume specified in the active method on the
3800 exceed the syringe volume, a 3800 hardware
fault will occur. This will cause the Star Workstation
to halt automation and reset the 3800. After changing
the method settings and/or the injection volume to
reduce the total below the installed syringe volume
shown in the 3800 setup screen, you should begin
the SampleList at the selected line to bypass the
samples that have already been run.
2nd Inj Volume
(Duplicate Mode or Dual
Mode operation only)

0.1 to 10 L
Sets the injection volume in microliters for the second
injection of the sample in Duplicate Mode or the
injection of the second sample in Dual Mode. When
the SampleList is edited in System Control, the
maximum value allowed is set to the syringe size
currently configured in the 3800 GC setup.
During operation, if the sample volume plus solvent
volume, internal standard addition volume, and air
gaps volume specified in the active method on the
3800 exceed the syringe volume, a 3800 hardware
fault will occur. This will cause the Star Workstation
to halt automation and reset the 3800. After changing
the method settings and/or the injection volume to
reduce the total below the installed syringe volume
shown in the 3800 setup screen, you should begin
the SampleList at the selected line to bypass the
samples that have already been run.
Injectors Used

Pos 1, Pos 2, 1 then 2, or 2 then 1
Selects the 8400 Injection position to be used for the
sample. If the 8400 is not configured for both

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Field Description
injection positions, entering the wrong position will
cause the sample line to be skipped and a Bad
Injector message entered into the message log.
To run samples in Duplicate Mode or Dual Mode, you
must select either 1 then 2 or 2 then 1.
2nd Injection
Duplicate, Advance, Clean & Dup, or Clean & Adv
Specifies the action that the 8400 will take before
making the second injection during a run.
If you choose Duplicate or Clean & Dup, the same
sample will be used for both injections. This is called
Duplicate Mode.
If you choose Advance or Clean & Adv, the 8400
will advance to the next vial location and will sample
the vial, if any, that is there for the second sample
injection. This is called Dual Mode.
Injection Delay
0.0 and 0.1 through 10.0 minutes
Sets the time delay between the first injection and the
second injection in Duplicate Mode and Dual Mode
operation. When the value is 0.0, the injection time
delay is turned off and not used. For values other
than zero, the 8400 will prepare and load the syringe
for the second injection. When the syringe is loaded,
it will move to the inject position and wait for the
injection delay to time out before injecting.
If the injection delay times out before the sample is
injected, an error message saying that the injection
delay timed out before injection is placed in the
message log.

333
3900 GC Method Command
Reference
3900 GC AutoSampler

When the 8400 AutoSampler or 8410 AutoInjector is selected, the AutoSampler
window may contain up to five sections. The topmost section is common to all
modes of operation. The entries in this section are described below.
In addition, all modes of operation also include a Default Clean section and a
Clean Mode section. When Viscous, Volatile, or User Defined modes are
selected, the Internal Standard section is displayed. In User Defined mode, the
More User Defined button is displayed to provide access to the dialog box to
set the User Defined parameters. The Default Settings for Predefined
AutoSampler Modes contains a table showing the parameters that are used by
the 8400/8410 for each of the predefined modes of operation.

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Item Description
AutoSampler Type 8400, 8410, or None

Specifies whether or not an 8400 AutoSampler or 8410
AutoInjector is installed on the 3900 GC. If an 8400 or
8410 is not installed on the GC or is turned off, select
None. When 8400 or 8410 is selected, the following
items are displayed for editing.
Syringe Size (uL) 5 uL or 10 uL
Selects the size of the syringe that is installed on the
8400/8410 for use with this method. A 5 microliter or a
10 microliter syringe may be used with the 8400/8410.
Injection Mode Std Split/Splitless, Std On Column, Neat, Viscous,
Volatile, or User Defined
Sets the 8400/8410 parameters for the predefined
modes of operation.
Sample Depth (%) 0 to 100 %
Specifies how far the syringe needle is to go down into
the sample vial. 100% is the bottom of the vial. 0% is
the bottom of the vial septum.
Solvent Depth (%) 0 to 100 %
Specifies how far the syringe needle is to go down into
the solvent vial. 100% is the bottom of the vial. 0% is
the bottom of the vial septum.
Default Clean Section

Default Cleaning occurs when the Stop button on the front panel of the 3900 GC,
the Reset button on the 3900 Status Window in Star Workstation System
Control, or the Stop Automation menu item in the Star Workstation System
Control Automation menu is pressed after the 8400/8410 has started its run and
before it has finished its sampling and post-injection washing operations. Default
Cleaning also occurs when the 3900 GC has a fatal automation fault after the
8400/8410 has started its run and before it has finished its sampling and post-
injection washing operations.

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Item Description
Vial I, II, or III
Specifies which of the three solvent vials will be used by the
Default Cleaning
Specifies the amount of cleaning solvent that will be drawn up
with each syringe cleaning stroke.
Strokes 0 to 10
Specifies the number of times the cleaning solvent will be
drawn up into the syringe and expelled into the waste cup.
Speed (uL/sec) 0.1 to 50.0 microliters per second with 10 uL syringe
0.1 to 25.0 microliters per second with 5 uL syringe
Specifies the speed at which the cleaning solvent will be drawn
up into the syringe and the speed at which it is expelled into
the waste cup.
Clean Mode Section

Item Description
Pre-Inj Solvent Flushes 0 to 99
Specifies the number of times each selected
cleaning solvent will be drawn up into the syringe
and expelled into the waste cup before flushing with
next cleaning solvent (if more than one cleaning
solvent source is specified) or the sample.
Pre-Inj Sample Flushes 0 to 99
Specifies the number of times the sample will be
drawn up into the syringe and expelled into the waste
cup before the syringe is loaded for injection.
Post-Inj Solvent Flushes 0 to 99
Specifies the number of times each selected
cleaning solvent will be drawn up into the syringe
and expelled into the waste cup before flushing with
next cleaning solvent (if more than one cleaning
solvent source is specified).
Clean Solvent Source I, II, III, I & II, I & III, II & III, or I & II & III
Selects which solvent vial or sequence of solvent
vials will be used to flush the syringe before and after
injection.

336
Internal Standard Section

Item Description
Use

Yes or No
If Yes, an internal standard addition will be used.
When internal standard addition is used, the internal
standard solution will be drawn up into the syringe
from the specified solvent vial before the sample is
drawn up.
Vial I, II, or III
Selects which solvent vial contains the internal
standard.
Specifies the amount of internal standard to be drawn
into the syringe before the sample.
Drawup Speed (uL/sec) 0.1 to 50.0 microliters per second with 10 uL syringe
Specifies the speed at which the internal standard
will be drawn up into the syringe.
Specifies how long the syringe is to remain in the
internal standard vial after drawing up the internal
standard.
Air Gap Yes or No
If Yes, 1 microliter of room air will be drawn into the
syringe to create an air gap between the internal
standard and the sample.

337
More User Defined Settings Dialog Box

This dialog box is accessed from More User Defined button that is displayed
when the User Defined mode is selected.
Solvent Plug Settings

338

Item Description
Vial I, II, or III
Selects which solvent vial to use for the solvent plug.
Specifies the amount of solvent to be drawn into the
syringe before the sample or internal standard.
Drawup Speed (uL/sec) 0.1 to 50.0 microliters per second with 10 uL syringe
Specifies the speed at which the solvent will be
drawn up into the syringe.
solvent vial after drawing up the solvent.
Air Gap Yes or No
syringe to create an air gap before the solvent plug.
User Defined Settings

339

Item Description
Fill Volume (uL) 0 to 10.0 microliters with 10 uL syringe
Specifies the sample volume that will be used for each
fill stroke.
Fill Strokes 0 to 99
Specifies the number of the times the sample will be
pumped in and out of the syringe before loading the
sample volume into the syringe.

Sample Air Gap Yes or No
syringe to create an air gap before the sample plug.
Air Plug after Sample 0 to 10.0 microliters with 10 uL syringe
Specifies the volume of room air that will be drawn into
the syringe after it is loaded with sample.
Viscosity Settings

Item Description
Viscosity Delay (sec) 0 to 9.9 seconds
sample vial after drawing up the sample.
Fill Speed (uL/sec) 0.1 to 50.0 microliters per second with 10 uL syringe
Specifies the speed at which the sample will be drawn
up into the syringe.
Inject Speed (uL/sec) 0.1 to 50.0 microliters per second with 10 uL syringe
Specifies the speed at which the contents of the
syringe will be expelled into the injector.
Pre-Inj Delay (sec) 0 to 99.9 seconds
Specifies the length of time the syringe needle resides
in the injector before expelling the syringe contents.
Post-Inj Delay (sec) 0 to 99.9 seconds
Specifies the length of time the syringe needle remains
in the injector after expelling the syringe contents.

340
Default Settings for Predefined AutoSampler Modes
The following table lists the parameter settings used for each of the Predefined
8400/8410 modes using a 10 microliter syringe. If the predefined modes do not
work acceptably for your samples, use the User Defined mode to enter settings
that will work better with your samples. The values listed in this table provide a
starting point for setting the various parameters.

Parameter
Std Split/
Splitless
Std On-
Column

Neat

Volatile

Visco
us
Solvent Plug
Settings:
Solvent plug is not used with predefined modes. If you wish to
use solvent plug injections, you must use User Defined mode.
PreDefined
Settings:

Fill Volume 7.5 uL 7.5 uL Not used Not used Not
used
Fill Strokes 5 5 0
0 0
Sample Air Gap No No No No No
Air Plug after
Sample
1 uL 1 uL 1 uL 1 uL 1 uL
Viscosity
Settings:

Viscosity Delay 0 sec 0 sec 0 sec 6 sec 9.9 sec
Fill Speed 2 uL/sec 2 uL/sec 2 uL/sec 1 uL/sec 1
uL/sec
Inject Speed 50 uL/sec 2 uL/sec 50 uL/sec 1 uL/sec 5
uL/sec
Pre-Inj Delay 0 sec 0 sec 0 sec 0 sec 0 sec
Post-Inj Delay 0 sec 6 sec 0 sec 0 sec 12 sec
Instead of fill strokes Neat mode fills the syringe with sample at 2 uL/sec then
expels it into the waste cup at 50 uL/sec. It does this a total of six times. Then it
fills the syringe with sample at 2 uL/sec and expels it back into the sample vial at
50 uL/sec. This pumping action is done three times. After this is completed, the
sample is loaded into the syringe and injected using the parameters in the table.

341
3900 GC Injector Section
1177 Injector

Item Description
Injector Oven On or off.
Turns the 1177 injector oven in the selected position on or
off.
Temperature (C) 50 to 450C.
Spilt Ratio Dialog Box
This dialog is displayed from the 3900 GC Injector section when an 1177 injector
is configured with type 1 EFC.

342

Item Description
Time 0.00 to 999.99 min.
Split State On/Off.
If the split state is ON, then the sample is split according to the
split ratio specified. If the split state is OFF, then all the sample
enters the column.
Split Ratio Off, 1 to 10,000.
Use a split ratio of 100 after injection to vent the injector. Use a
very low split ratio after flushing to conserve carrier gas.
spreadsheet.

343
3900 GC Flow/Pressure Section
Type 1 (for 1177 injector)

Item Description
Pressure (psi) 0.1 to 100.0 psi.
Rate (psi/min) 0.01 to 400.00 psi/min.
edited.
Hold (min) 0.01 to 999.99 min.
Total (min) 0.01 to 999.99 min.
Cannot be edited.
Constant Flow On or Off
Click on Constant flow to disable the spreadsheet and
reveals the constant flow rate value.
Column Flow (ml/min) Specifies the desired constant Column Flow.
Pressure Pulse Yes or No
Click on Yes to enable a pressure pulse injection in
constant flow mode.
Pressure Pulse (psi) 0.1 to 100.0 psi.
Specifies the desired column head pressure during
injection.
Pulse Duration (min) 0.01 to 5.00 min.
Specifies the period of time after the run starts for
which the pressure will be maintained.
spreadsheet.
spreadsheet.

344
3900 GC Column Oven Section

Item Description
Stabilization Time (min) 10.0 min.
Specifies the column Stabilization Time.
Temp (C) 30 - 450 C.
Rate (C/min) 0.01- 100.0 C/min.
The Rate in the first row is always blank and
cannot be edited.
Hold (min) 0.01-999.99 min.
Total (min) 0.01-999.99 min.
Cannot be edited. Column Oven End Time
(Total) is displayed in all time-programmed
windows of the Method.

Insert Inserts a line above the currently selected row in
the spreadsheet.
spreadsheet.

345
3900 GC Method Section
Overview
In the 3900 GC Configuration section, you configured your hardware for an
instrument and opened the System Control Window for the instrument. At this
point, you could simply inject a sample, as described in the following sections.
However, it is not likely that the default Method will have the method settings that
are appropriate for your analysis. Therefore, the default Method will need to be
to view and edit methods. It can be accessed from:

This button on the MS Workstation Toolbar opens
Method Builder and prompts you to create a new
method or open and existing one.

This button on the System Control Toolbar allows
button.

This button on the MS Workstation Toolbar allows
button.

346

to create a method.

Select Custom to create a Method for an instrument that is not attached to the Varian
MS Workstation.
Select the Instrument for which this method will be used.

347

For each detector in the Method, you will be asked to select the channels on
which post-run processing will be performed.

348

analysis.

Title Bar / Menu Bar / Toolbar
This navigation window shows the overall structure of the Method, its sections and
subsections. The branches can be expanded by clicking on the plus sign or
contracted by clicking on the minus sign to show the desired level of detail. The
parameters window shows the parameters for the highlighted item in the navigation
window. Method parameters are viewed and edited in this window.

349
the online help.
Method Notes

The 3900 GC Method Windows

The 3900 GC entry specifies the Varian MS Workstation module address of the
GC that the Method uses. The module Address in the parameter window can be
changed so that a Method developed for an instrument using one module
address can be easily modified for use on another instrument at a different
module address.

350

The 3900 Method section contains two Method windows: GC Control, and
Autosampler. These windows contain all parameters that control the operation of
the 3900 GC during a chromatographic run.
Spreadsheet editing
Certain Method windows contain spreadsheet tables for time, temperature or
flow programming. All spreadsheets behave similarly.

Add a row at the bottom of the spreadsheet.
Insert a row before the currently selected row.
Delete currently selected rows.
Sort rows by time (available in time program spreadsheets).
Select rows by clicking and dragging on the row numbers on the left side of the
spreadsheet.

351

One or more rows can be selected by clicking and dragging on this column.
Spreadsheets that specify time programs can display duplicate times, but all
duplicates must be eliminated before you can save your work.
Checking Method End times
All editing windows other than the column oven window show the current end
time of the column oven program above the Save and Cancel buttons.

The column oven endtime is shown.
When the Method is downloaded to the 3900 GC, component program end times
that exceed the column oven end time will be truncated.

352
GC Control Window
The GC control window contains sections (Flow/Pressure, Injector, and Column
Oven).
Flow/Pressure Section
Use the EFC Programs to specify the pressure ramp of the Type 1 EFC.

Type 1 EFC (for 1177 Injectors)
With a Type 1 EFC is installed, a pressure ramp spreadsheet will appear.

Use the spreadsheet to build a pressure ramp program to control the Type 1 EFC.
The first row of the spreadsheet contains the Initial pressure and hold time for the
completed.

353
each of the ramp segments. Each segment will ramp to the specified pressure at
the specified rate (assuming the rate is achievable), and then hold the pressure
for the specified time. (Note that the Rate in the first row is always blank and
cannot be edited. Also note that the entire Total column cannot be edited.)

Constant Column Flow for Type 1 EFC
Constant Column Flow mode for Type 1 EFC is enabled in the Flow/Pressure
section.

Click on the Radio Button to turn on the Constant Column Flow Mode. This mode
disables the spreadsheet and reveals the constant flow rate value.
Enter the desired Column Flow.
Click on Yes to perform a pressure pulse injection. Upon injection, the pressure will
change to the Pulse Pressure for the Pulse Duration setting.
When the method is activated in System Control, the Varian MS Workstation will
generate and download the appropriate pressure program corresponding to the
Column Temperature program, the Column Setup Length and Diameter, the
Carrier Gas, and the ambient Barometric Pressure. These parameters are
specified in the 3900 GC system control setup, and the Barometric Pressure is
measured by the 3900 at the time the Method is downloaded. The 3900 will run
the pressure program to hold the Column Flow at the specified value as the
Column Temperature is ramped during each run.
Injector Section
Use the Injector Program to specify the temperature setpoints of the isothermal
1177 Injector, and split ratio of the 1177 Injector.

354

1177 Injector
With a 1177 Injector is installed, an Oven Power switch, a Temperature setting
and a Split Ratio table will appear.

Indicate whether or not you will use the installed 1177 injector by clicking on the On
Set the desired Temperature.

355

You can use a split ratio of 100 after injection to vent the injector of any residual
solvent.
completed.
Column Oven Section
The Column Oven window contains the Column Oven Program. Use the Column
Oven Program to specify the Stabilization Time of the Column Oven, and to
specify its programmable temperature ramp.

356
Specify the desired Stabilization Time.
Use the spreadsheet to build a temperature ramp program to heat and/or cool the
Column Oven.
the Column Oven. The Column Oven will equilibrate to this setting, and stabilize
for the specified Stabilization Time, when the method is activated, and will be
restored to this setting when each chromatographic run is completed.
be edited.)
Autosampler Window
The Autosampler window contains sampling parameters for the 8400/8410
Autosampler when attached to the 3900 GC. The parameters include selection of
the sampling syringe size, the penetration depth for sample and solvent wash
vials, the default clean and clean modes, and the injection modes.

Injection Mode

The Injection Mode selection consists of five predefined injection modes:
Standard Split/Splitless, Standard On-Column, Neat, Viscous and Volatile. If any
of these modes cannot satisfy your injection needs, a sixth User Defined mode is

357
available. Selecting User Defined mode allows you access to all 8400
autosampler parameters to fine-tune your injection.
Consult the Online Help for a detailed description of all Injection Mode
parameters.
Auto-configuring the Method to Match the 3900 GC
Hardware
When you edit a 3900 GC Method while the corresponding GC is online in
System Control, you are warned if the Method configuration does not match the
hardware on the GC.

Click on Yes to change the Method to match the GC.
Click on No to accept the Method as is.
If you choose to auto-configure the Method, the following dialog is displayed.

Uploading the Method from the 3900 GC
You can get the Method from the GC and save it in the Varian MS Workstation.
This allows you to do local Method editing on the 3900 GC front panel and then
save this Method for later use on the Workstation.

358

To upload the Method from the 3900 GC to System Control, select Upload Active
Method from Modules from the File menu.
You are then prompted for the name of the file under which to save the Method.
The active Method in System Control is updated to reflect the parameters
obtained from the 3900 GC.
The Startup Method
When you start System Control and display an Instrument Window, the last
active Method for that instrument is activated. When System Control is started, it
will return to the initial settings in the Method that was last used on the
instrument.

Editing Methods from the 3900 Status and Control Window
The 3900 GC Status and Control Window contains a Method button that allows
you to directly edit the active Method corresponding to that GC.

359

Method button
When you click on this button Method Builder is opened with active Method
loaded and the corresponding Instrument Module selected. You can then edit
that section or any other section of the Method as described previously.
changes to the Module.

You may wish to copy sections from one 3900 Method file to another. This can


360
import by clicking on them. If you click on one section and the hold down the shift
key while clicking on another section, all of the sections in between will be
files.


To remove sections from a 3900 Method open the Method containing the
menu.

361

and the hold down the shift key while clicking on another section, all of the


362
Printing the Method

the File menu.



363
3900 GC System Control
Command Reference

The 3900 Status and Control window is divided into four display areas. The left-
most display area is the 3900 Operation Display, which contains information
about the current run and the overall state of the GC.
The middle displays area is the temperature zone status display, showing the
setpoint and current actual temperature of each heated zone in the GC, the Oven
Status, and the Injector EFC Status display.
The right most display is the 8400/8410 carrousel display.
3900 Operation Display
The 3900 operation display is in the left portion of the 3900 Status and Control
window.

364
Item Description
Runtime Shows the elapsed time in minutes since the beginning of
the run. The maximum run time is 999.99 minutes.
Endtime Shows the time at which the run will end.
State Ready, Running, Stabilizing, Equilibrating, Computing, or
Not Ready
Shows the state of the GC. The light appears green if the
GC is Ready or Running. Otherwise, the light is red.
Fault/No Fault indicator No Fault (green light) or Fault (red light).
When a hazardous or disabling fault occurs, any run in
progress will halt and the affected component will shut
down. If the fault is recoverable, then the run +is not
terminated.
Start If the system is Ready, starts the GC Method and sends
a start signal to the GC. The Start button is disabled
unless the 3900 GC is in the Ready state.
Reset Resets the GC, advancing it to the next state. If it is
RUNNING, the GC aborts the current run, goes to the
READY state, and continues with the next injection in the
Sequence.
Method Opens the Method Builder application for editing the
active 3900 GC method.
Setup Opens the GC Setup Dialog Box which is used to set the
configuration of the 3900 GC.
Extend The Extend runtime button allows the runtime to be
extended by 10 minutes each time the button is clicked
on. The extended run time will be used until the method
is either re-activated or a new method is activated. The
extend run feature does not change the method stored in
your Saturn WorkStation.
Oven Off/Oven On Oven On/Oven Off. Turn the column oven heater either
on or off depending on its current state.
End stabilization If the 3900 GC is in a stabilization state, this button will
end the stabilization time and set the gc to ready.
Temp Zones Status Display

The temperature zones status display is in the middle portion of the 3900 Status
and Control window. The display includes the setpoints and actual temperatures
of the column oven, and the injector of the 3900 GC. The display is Fault if a
fault occurs in the zone component or Off if the zone oven is off.
The LEDs indicate the status of each temperature zone. If the zone is not
configured or the zone oven is off, the LED is gray. If the temperature zone is Not
Ready or there is a fault, then the LED is red. Otherwise, the LED is green.

365

Item Description
Col Oven Setpoint Abient+5 C to 450 C
Displays the column oven
programmed temperature setting in
the active method.
Col Oven Actual Abient+5 C to 450 C
Displays the actual temperature of the
column oven at the 3900 GC
1177 Setpoint 50 to 450 C
Displays the 1177 injector oven
programmed temperature setting in
the active method.
1177 Actual 50 to 450 C
Displays the actual temperature of the
1177 injector oven at the 3800 GC.
Oven Status Display

Oven Parameters:
Item Description
Column Ready Yes or No.
The column oven is Ready (Yes) if the setpoints have
been achieved and stabilized. The column oven is Not
achieved or if, during a run, the oven becomes not ready
or goes out of tolerance. Some reasons the GC may go
Not Ready during a run are: the temperature program is
too aggressive, the oven door is opened, the coolant
runs out, the power line voltage drops, etc.
Column Fault Yes or No.
Displays if a fault in the column oven component has
occurred.
Injector Ready Yes or No.
The injector oven is Ready (Yes) if the setpoints have
been achieved and stabilized. The injector oven is Not
achieved or if, during a run, the injector becomes not
ready or goes out of tolerance. .
Injector Fault Yes or No.
Displays if a fault in the injector oven component has
occurred.

366
Item Description
Stabilization Time 0.00 - 10.00 min
Shows the 3900 GC column oven stabilization time in
minutes. The stabilization time counts down from the
programmed method value and then displays 0.00
minutes when the stabilization period is over.
Injector EFC Status Display

Injector EFC Status:
Item Description
Flow Ready Yes or No.
etc.
Pressure Ready Yes or No.
etc.
Type 1 Pressure
Setpoint
0.1 - 100 psi
Displays the programmed column head pressure setting in
the active method.
Actual Pressure 0.1 - 100 psi
Column Flow Displays, in ml/min, the column flow rate calculated from
the column head pressure, column temperature, and
column parameters (carrier gas, column length, and
internal diameter).

367
Item Description
Linear Velocity Displays, in cm/sec, the column linear velocity calculated
column parameters (carrier gas, column length, and
internal diameter).
Total Flow Displays, in ml/min, the total flow rate through the system.
Split Ratio 1 - 10000
Displays the current split ratio of the 1177 injector method.
The split ratio is defined as the Column Flow + the Split
Flow / the Column Flow.
8400/8410 Carrousel Display
When an 8400 AutoSampler or 8410 AutoInjector is connected to your 3900, the
Carrousel display will be visible in the 3900 GC Status and Control window.

8400 AutoSampler Carrousel / 8410 AutoInjector Carrousel
Item Description
Red fill Indicates vials listed in the active SampleList that have not
yet been sampled or are missing.
Green fill Indicates the vial (vials in Dual Mode) currently being
sampled.
Blue fill Indicates the vials in the active SampleList that have been
sampled.

Action Description
Click on a vial position Displays the vial number for that position for 5
seconds.
Double-click on a vial position Opens the Inject Single Sample dialog box to
inject a single sample.
3900 Setup Dialog Box
This dialog box shows the hardware configuration reported by the 3900 GC. This
configuration is compared to and must match the configuration in the Method

368
when it is activated. It also allows the configuration of the 3900 GC to be
changed from the Saturn GC/MS Workstation.

Item Description
Column, Rapid MS Mode On/Off
When a Rapid-MS column is used in the 3900
GC, the Rapid-MS Mode should be set to On.
This will configure the GC to set the proper
parameters for the Rapid-MS column. The
column length and inside diameter entries will
be grayed out.
Column, Length The length of the column in meters. Values
range from 0 to 250 meters.
Column, Inside Diameter Inside diameter of the column in micrometers.
Values range from 0 to 999 micrometers.
Temperature Limit, Column Oven Upper temperature limit of the column oven.
Values range from 50 to 450C.
Temperature Limit, Injector Upper temperature limit of the injector. Values
range from 50 to 450C.
Ready-In Sync Polarity Is Ready-In a closed contact (Checked/Un-
checked). Allows you to specify what switch
state corresponds to External Device Ready.
Injector EFC, Splitless Vent Flow The flow the system will vent when the split
valve is left closed for the duration of the run
such as during an on-column injection. This
flow is diverted before the injector and thus
does not influence the splitless nature of the
run. This entry is ignored during split and

369
Item Description
splitless runs in which the split vent is opened.
Injector EFC, Gas Saver Flow The lowest system flow rate that will be
maintained during the gas saver period. This
has a range of 1-100 mL/min and defaults to
20 mL/min.
Injector EFC, Gas Saver Timeout A non-zero value entered for this parameter
will cause the system to initiate a timer once a
method is activated. If no system actions such
as a run start or another method activation
occurs before the Gas Saver Timeout is
reached, then the system will reduce the flow
through the system to the Gas Saver Flow. A
method activation action will clear the Gas
Saver Flow and bring the system to Ready for
subsequent injections. A zero value entered
for the Gas Saver Timeout will cause the Gas
Saver Flow to be ignored and no Gas Saver
actions will be performed.
Injector EFC, Auto Calibrate EFC
Flow
Automatically calibrate the EFC system.
When it is finished, the screen will display
either a successful completion or detected
problem message. No other GC functions can
be performed during AutoCalibration. Note
that AutoCalibration should be done on a
semiannual basis.
Injector EFC, Calibrate Septum
Purge Flow
Calibrate the septum purge. After
installing a new column, the septum
purge should be calibrated. Set the
desired column head pressure. Then
measure the actual septum purge flow
rate and enter this value in the septum
purge field. The septum purge flow rate is
adjustable but is typically set at 3 - 5
mL/min.
Septum Purge Calibration, Desired
Head Pressure
The desired column head pressure in psi.
Range is 0.1 - 100 psi.
Septum Purge Calibration,
Measured Flow Rate
The septum purge flow rate is adjustable but
is typically set at 3 - 5 mL/min.
Print Actual Sends the 3900 setup parameters to the
default printer.
Close & Update Saves the changed parameters and
reinitialize the 3900 with the new parameters.
AutoSampler, Type None, 8400, 8410
Displays the type of autosampler that is
connected to the 3900 GC.
AutoSampler, Syringe Volume 5 uL, 10 uL and 100 uL.
Enter the syringe volume you will install and
use with your CP-8400/8410. The 3900 will
use this value to set the correct entry
selections and any needed internal settings to
correctly use the indicated syringe size.
Incorrectly setting this parameter may cause

370
Item Description
poor operation but will not harm either the GC
or the AutoSampler.
AutoSampler, Syringe Speed 1 to 30 (cm/sec), default=30
The Injector Injection Speed parameters
define the rate at which the needle will
penetrate the injector septum and descend to
the set Injector Needle Depth.
AutoSampler, Needle Depth 0 to 100, default=100
The Injector Needle Depth parameters define
how far into the designated injector the needle
will penetrate. 100% causes the needle to be
completely inserted to its 2-inch length.
AutoSampler, Plunger Count Limit (1-100,000) This parameter defines the
expected number of strokes the plunger is
expected to survive without significant
degradation. Once the entered value is
exceeded, a message will be displayed on the
CP-8400/8410 Status page indicating the
plunger counter has exceeded the set value.
The default number of strokes is 10,000.
AutoSampler, Enable Buzzer Buzzer at Start of Cycle (On/Off) A sound
will be generated to warn of impending tower
movements when this parameter is set to On.
The default value is On.
AutoSampler, Calibrate
AutoSampler
Displays the 8400/8410 AutoSampler
Calibration Dialog Box.
Calibrate Autosampler Dialog Box
This dialog box helps the user to calibrate the 8400/8410 AutoSampler. Items
that are not active are "grayed" in the actual screen.

371

Item Description
Calibrate Vial 0 Position, Start
Calibration
To start the Vial 0 (or Vial 1) calibration, make
certain a vial with the same form factor and cap
as the ones you will be using for your analyses
is placed in the 0 position of the carrousel (or
the Vial 1 position of the CP-8410). Press the
Start Calibration button.
Calibrating the Vial 0 (or Vial 1) position
involves manipulating the positions of three
different components. The object of the
calibration is to position the syringe exactly over
the center of the sampling target area of the
vial. Upon starting the calibration procedure,
the CP-8400/8410 will rotate the tower, rotate
the carrousel, and lower the syringe sled to the
approximate location of Vial 0 (or Vial 1 if
CP-8410). After the CP-8400/8410 has found
the approximate Vial 0 (or Vial 1) position,
visually check that the syringe sled is not
resting on the vial top. If it is use the Syringe
Up button. Press the button until the syringe
sled is clear of the vial top by approximately 1
mm. Start the calibration process by adjusting
the tower position
Calibrate Vial 0 Position, Save
Calibration
When you have completed the Vial 0 (or Vial 1)
calibration, press the Save Calibration button.
Calibrate Vial 0 Position, Tower
Counterclockwise
Moves the tower 10 steps in the
counterclockwise direction each time the button
is pressed.
NOTE: One basic rule associated with this
calibration concerns rotation of the tower and
carrousel; to assure consistent operation,

372
Item Description
always approach the final calibration position
with clockwise movements. To help facilitate
this rule, the carrousel will backup 10 steps
when a counterclockwise action is selected but
will move one step when a clockwise tower
rotation is selected.
Calibrate Vial 0 Position, Tower
Clockwise
Moves the tower 1 step in the clockwise
direction each time the button is pressed.
Calibrate Vial 0 Position,
Carrousel Counterclockwise
Moves the carrousel 10 steps in the
counterclockwise direction each time the button
is pressed.
Calibrate Vial 0 Position,
Carrousel Clockwise
Moves the carrousel 1 step in the clockwise
direction each time the button is pressed.
Calibrate Vial 0 Position, Syringe
Up
Use the Syringe Up button and adjust the
syringe sled height so that the needle is just
barely above the vial cap (You should be able
to see about a papers thickness of space
between the syringe sled needle guide and the
top of the vial cap. The penetration depth into
the vial is measured from the bottom of the
needle guide, so this height will give you
optimum penetration depth.).
Calibrate Vial 0 Position, Syringe
Down
Use the Syringe Down button and adjust the
syringe sled height so that the needle is just
barely above the vial cap (You should be able
to see about a papers thickness of space
between the syringe sled needle guide and the
top of the vial cap. The penetration depth into
the vial is measured from the bottom of the

373
Item Description
needle guide, so this height will give you
optimum penetration depth.).
Calibrate Injector Position, Start
Calibration
Press the Start Calibration. The CP-8400/8410
will rotate the tower so that it is over the Injector
position and lower the syringe sled so that it is
over the injector. If the needle guide descends
so that it is either resting on the inject switch or
below the needle cone on the inject switch, use
the Syringe Up button and move the sled up
until the needle guide is just above the injector
cone.
Calibrate Injector Position, Save
Calibration
Press the Save Calibration softkey when the
Injector calibration is complete.
Calibrate Injector Position, Tower
Counterclockwise
Using the Tower Counterclockwise button
rotates the tower counterclockwise 10 steps.
Position the tower directly over the injector
Inject Switch Locator cone.
Calibrate Injector Position, Tower
Clockwise
Using the Tower Clockwise button rotates the
tower clockwise 1 step. Position the tower
directly over the injector Inject Switch Locator
cone.
Calibrate Injector Position,
Syringe Up
Using the Syringe Up button adjust the height
of the needle guide such that the sled is just
resting on or very slightly depressing the
Injector Switch and is covering the locator cone.
Calibrate Injector Position,
Syringe Down
Using the Syringe Down button adjust the
height of the needle guide such that the sled is
just resting on or very slightly depressing the
Injector Switch and is covering the locator cone.
Change Syringe, Start Syringe
Change
Selecting Start Syringe Change will cause the
tower to rotate such that the user will have easy
access to the syringe for routine service and
syringe removal and replacement. The buzzer
will sound before any tower movement occurs.
Press the Finish Syringe Change softkey upon
completion of the syringe maintenance.
Change Syringe, Finish Syringe
Change
Selecting Finish Syringe Change will cause the
tower to return to its previous position and
state. The buzzer will sound prior to movement
as designated by the Buzzer at start of cycle
setting.

Change Syringe, Clear Plunger
Counter
Selecting this softkey causes the Plunger
stroke count to be reset to 0.
Use Mouse Buttons to adjust
positions of Tower, Syringe,
and/or Carrousel
Checking this box, changes the Calibrate
AutoSampler Dialog Box for the positions to be
adjusted with the mouse.
Close Closes the dialog box.

374

Item Description
Calibrate Vial 0 Position, Start
Calibration
To start the Vial 0 (or Vial 1) calibration, make
certain a vial with the same form factor and cap
as the ones you will be using for your analyses
is placed in the 0 position of the carrousel (or
the Vial 1 position of the CP-8410). Press the
Start Calibration button.
Calibrating the Vial 0 (or Vial 1) position
involves manipulating the positions of three
different components. The object of the
calibration is to position the syringe exactly
over the center of the sampling target area of
the vial. Upon starting the calibration
procedure, the CP-8400/8410 will rotate the
tower, rotate the carrousel, and lower the
syringe sled to the approximate location of Vial
0 (or Vial 1 if CP-8410). After the
CP-8400/8410 has found the approximate Vial
0 (or Vial 1) position, visually check that the
syringe sled is not resting on the vial top. If it is
use the Syringe Up button. Press the button
until the syringe sled is clear of the vial top by
approximately 1 mm. Start the calibration
process by adjusting the tower position
Calibrate Vial 0 Position, Save
Calibration
When you have completed the Vial 0 (or Vial 1)
calibration, press the Save Calibration button.
Calibrate Vial 0 Position, Use
Mouse Buttons to Rotate Tower
Clicking this button will display the following
dialog box.

375
Item Description

Mouse Buttons to Rotate
Carrousel
dialog box.

Mouse Buttons to Raise/Lower
Syringe
dialog box.

Calibrate Injector Position, Start
Calibration
Press the Start Calibration. The CP-8400/8410
will rotate the tower so that it is over the
Injector position and lower the syringe sled so
that it is over the injector. If the needle guide
descends so that it is either resting on the
inject switch or below the needle cone on the
inject switch, use the Syringe Up button and
move the sled up until the needle guide is just
above the injector cone.
Calibrate Injector Position, Save
Calibration
Press the Save Calibration softkey when the
Injector calibration is complete.
Calibrate Injector Position, Use
Mouse Buttons to Rotate Tower
Position the tower directly over the injector
Inject Switch Locator cone. Clicking this button
will display the following dialog box.

376
Item Description

Calibrate Injector Position, Use
Mouse Buttons to Raise/Lower
Syringe
Using the Syringe Up button adjust the height
of the needle guide such that the sled is just
resting on or very slightly depressing the
Injector Switch and is covering the locator
cone. Clicking this button will display the
following dialog box.

Change Syringe, Start Syringe
Change
Selecting Start Syringe Change will cause the
tower to rotate such that the user will have
easy access to the syringe for routine service
and syringe removal and replacement. The
buzzer will sound before any tower movement
occurs. Press the Finish Syringe Change
softkey upon completion of the syringe
maintenance.
Change Syringe, Finish Syringe
Change
Selecting Finish Syringe Change will cause the
tower to return to its previous position and
state. The buzzer will sound prior to movement
as designated by the Buzzer at start of cycle
setting.

Change Syringe, Clear Plunger
Counter
Selecting this softkey causes the Plunger
stroke count to be reset to 0.
Use Mouse Buttons to adjust
positions of Tower, Syringe,
and/or Carrousel
Un-checking this box, changes the Calibrate
AutoSampler Dialog Box for the positions to be
adjusted with the buttons on the screen.
Close Closes the dialog box.

377
Setup Ethernet Ports Dialog Box
This dialog box is displayed the first time that the Star Assistant guides you
through the setup of your 3900 in System Control. This dialog box is also
accessed from the Instrument/Setup Ethernet Communications menu item of
System Control.

Item Description
Address 44, 45, 46, or 47
Click the Address button to attach to a 3900 GC on the
Ethernet network. If you are running on a company
network, only GCs on the same local subnet appear in
the Select Available Modules dialog box that is displayed
after clicking the Address button.
Module Type None or 3900
This field is set if you select a 3900 GC using the
Address button. If you specify an IP Address or Domain
Name explicitly, then select 3900 from this combobox.
IP Address or Domain
Name
This field is set if you select a 3900 GC using the
Address button. To connect to a GC in a different subnet,
type its IP Address directly into the IP Address or Domain
Name field.
Status Available, Online, In Use By <client>, Not Responding, or
No Address
Displays the connection status of the 3900 GC.

Status Meaning
Available
Online
In Use By <client>
Not Responding
No Address
Not in use by anyone
In use by this
Workstation
In use by another
Workstation
Not responding to
Workstation queries
No IP Address or name
specified

378
Item Description
Actual IP Displays the actual IP address of the connected 3900
GC.
Setup... Click to setup IP address management (BOOTP Server).
The Setup BOOTP Server Dialog Box is displayed.
Setup BOOTP Server Dialog Box
the 3900 GCs must be added to the list of devices requiring IP addresses. IP
addresses must be assigned to GCs using a BOOTP Server. A BOOTP Server
lists Ethernet addresses (which are unique to each communication card installed
in each 3900 GC) along with the IP addresses that are to be assigned to the
corresponding device. You may obtain the Ethernet address for each GC from
the GCs front panel. Turn on the 3900 GC and press any key to allow it to start
in local mode.

379

Item Description
Manage IP addresses
from this Workstation
When IP addresses are managed from a central
location by a Network Administrator, the BOOTP Server
on your Workstation must be disabled (not checked).
Require password entry
for this dialog box
Check this box to restrict access to the BOOTP Server
dialog box to avoid inadvertent or unauthorized changes
to IP address assignments. If this item is checked, the
next time you enter the BOOTP Server dialog box, you
will be prompted for a password. The initial password is
blank (no password). To set your password initially,
enter the desired password in the Enter new password
and Re-enter new password fields. Subsequent entry
into the BOOTP Server will require this password.

Ethernet Address Displays the Ethernet address of any 3900 GCs already
also manually enter an Ethernet address for a 3900 GC
(available from the 3900 GC front panel display).
IP Address Displays the IP address of any 3900 GCs already
also manually enter an IP address for a 3900 GC. Use
the manual entry of IP addresses and Host Names
when individual IP addresses have been reserved for
use by each 3900 GC but IP Address and Host Name
management is not performed by a Network
Administrator.
Host Name You must enter a name for each 3900 GC. The IP
address will not be assigned to the GC until a name is
entered.
Assign IP addresses
manually
Select this entry if you manually enter IP addresses and
Host Name entries in the table.
Assign IP addresses
starting from
Select this entry to consecutively assign IP addresses
beginning from a particular address. Enter the number
of IP addresses to assign automatically and the starting
IP address. As 3900 GCs are powered on, IP addresses
are automatically assigned from the specified address.
Subnet Mask Displays the subnet mask assigned to the Workstation.
This parameter is assigned in the TCP/IP network setup
in the Control Panel application.
Gateway Displays the Gateway assigned to the Workstation. This
parameter is assigned in the TCP/IP network setup in
the Control Panel application.
Domain Displays the Domain name assigned to the Workstation.
This parameter is assigned in the TCP/IP network setup
in the Control Panel application.

380
Advanced BOOTP Settings Dialog Box
This dialog lets you enter advanced settings.

Item Description
Assign Private Class A addresses to Hosts
Manually

Determines whether IP addresses
must be entered in the Setup BOOTP
Server dialog box (checked) or if they
are generated (unchecked).

Use Subnet Mask

Enter the subnet mask here. This is
only used when the Manage IP
addresses from this Workstation
checkbox is checked in the Setup

Use Gateway

Enter the gateway address here. This
is only used when the Manage IP
Use Domain

Enter the domain name here. This is
only used when the Manage IP

381
8200 AutoSampler Instrument
Control Command Reference
8200 AutoSampler Status and Control Window

382

Item Description
RunTime The elapsed time since the start of the run.
EndTime The time when the AutoSampler Method will end.
Mode Standard or SPME. Standard is used with liquid sampling
syringes. SPME is used with Solid Phase MicroExtraction
fibers and holders.
Status light Shows the state of the AutoSampler. When the AutoSampler is
ready to prepare and inject a sample, the light is green.
Otherwise, it is red.
Fault/No Fault
light
Shows whether the AutoSampler has faults that have not been
cleared. The light appears green when the AutoSampler has
no uncleared faults; otherwise it appears red.
Vial 1 - 48 with standard sample vial tray.
1-12 with large sample vial tray.
Name Shows the sample name for the currently active sample in the
Active SampleList.
Location Shows the vial number of the currently active sample.
Injection "m" of "n"
where
m = 1 - 9
n = 1 - 9
Shows the current injection number and the total number of
programmed injections of the current sample.
Activity Lists the operation that the AutoSampler is currently doing.
Inject Starts the AutoSampler Method section and begins execution
of its sample preparation and injection programs. If the
AutoSampler is designated as the Instrument's Autocontrol
Module, the AutoSampler Method will start without the use of
this button.
Reset Terminates the AutoSampler Method section; clears all faults.
Used to stop the AutoSampler Method, return the AutoSampler
state to Ready, and continue with the next automated run. To
prevent sample carryover, the Reset command will not prevent
the AutoSampler from performing and completing the Final
Rinse cycle of an injection.
Advance Advances the AutoSampler to the next state or step of an
automix routine.
Method... Invokes the Method Builder and displays the AutoSampler's
Configuration page of the active Method. The AutoSampler's
programmable parameters may then be modified.
Hide/View
Keypad
Toggles between hiding and showing the keypad. Used to hide
or display the keypad in order to enlarge or reduce the size of
the AutoSampler Carrousel Display.
Run Vial Check Searches the AutoSampler carrousel to determine which vials
are present. Used to update the AutoSampler Carrousel
Display.
Hardware Displays the Hardware Dialog Box. The Hardware Dialog Box
allows the VarianWS 8200 AutoSampler hardware settings to
be set to match the hardware installed in the AutoSampler.

383
AutoSampler Carrousel Display

Item Description
Black dot Indicates the vials found during Vial Check.
Red fill Indicates vials listed in the active SampleList that have not yet
been sampled.
Blue fill Indicates the vial currently being sampled.
Green fill Indicates the vials in the active SampleList that have been
sampled.

Action Description
Click on a vial position Displays the vial numbers for that
position for 5 seconds
Double-click on the center of the carrousel Opens the Active SampleList window
to edit the active SampleList.
Double-click on a vial position Opens the Inject Single Sample
Dialog Box to inject a single sample.
Double-click on the outside of the
carrousel within the display box
Opens the Active RecalcList window
to edit the RecalcList.

384
Hardware Dialog Box

Item Description
Sampling Device Specifies the size and type of syringe installed in the
8200 AutoSampler, either a 10 microliter liquid
sampling syringe, a 100 microliter liquid sampling
syringe, or a Solid Phase MicroExtraction (SPME)
fiber and holder.
Wait for Read In When checked, the AutoSampler waits for a
hardware Ready input signal before starting. When
unchecked, the hardware Ready input is ignored.
Invert Ready In When checked, the hardware Ready input logic is
inverted (a high signal is a true). When unchecked,
the default hardware Ready input logic is used (a low
signal is a true).
Configuration Shows the injector that the current configuration file is
setup for.
OK button Saves the entries and closes the dialog box.
Set Config button Selects the configuration file to use. The
configuration file specifies AutoSampler parameters
to use when injecting into different injector
configurations.
Cancel Discards edits and closes the dialog box.

385
8200 SampleList Window Extensions
When an 8200 is controlled by the Varian MS Workstation, the SampleList for
that instrument contains the following device-dependent fields. Refer to the help
on the generic SampleList Window for a description of the fields not listed here.

Item Description
Sets the AutoSampler vial number of each sample in the
SampleList.
Volume 01. to 8.7 ul with 10 ul syringe, or
1 to 87 ul with 100 ul syringe
Sets the injection volume of the sample in microliters.
Automix routines Click on the button in this column to open the Automix
Routines Dialog Box and enter the automix routine to be
followed for the specified sample.
Carrousel button Opens the Carrousel Dialog Box for automatic updating
of the active SampleList.
Automix Routines Dialog Box

Item Description
Automix Name Descriptive name for the automix step
Selects the AutoSampler vial for the source of
the reagent to be used in this automix step.

386
Item Description
Volume 0.1 to 10 ul with 10 ul syringe, or
Sets the volume in microliters to be drawn
into the syringe and add to the vial to be
sampled.
Mixes 0 to 100
Sets the number of mixing strokes to be done.
Mix Stroke 0.1 to 10 ul with 10 ul syringe, or
Sets the volume to be drawn into the syringe
in microliters for each mixing stroke.
Washes 0 to 9
Sets the number of times the syringe will be
washed after this step.
Reaction Time 0.0 to 99.9 minutes
Pause time to allow reactions to finish before
the next step of the automix routine or sample
injection is performed.
Add button Adds a new automix line to the end of the
automix routine
Insert button Inserts a new automix line before the selected
line.
Delete button Deletes the selected automix routine line.
Automix First Injection Only When checked, this automix routine will only
be performed before the first injection from
the vial. When unchecked, this automix
routine will be performed before each
injection.
OK button Saves the edits and closes the dialog box.
Cancel Discards edits and closes the dialog box.
Set as Default Automix Saves the highlighted line as the default
entry. New lines will be created with these
values loaded.

387
Carrousel Dialog Box

Item Description
Copy Replaces the entire SampleList with a copy of the Default
Sample parameters for each vial in the carrousel.
Delete Deletes each line in the SampleList for which no vial can be
found in the carrousel.
Append Appends a new line to the SampleList for each vial in the
Carrousel that is not entered in the SampleList.
Cancel Cancels the operation and closes this Dialog Box without
changing the SampleList.

388

389
8200 Method Command Reference
8200 Configuration Window

Item Description
Carrousel Type 12 Vials or 48 Vials
Select the tray that is to be used on the 8200
AutoSampler when this Method is run.
End Time
GC Cycle Time (SPME mode)
0 to 640 minutes
Specifies the number of minutes that the 8200
AutoSampler will wait before starting the
sample preparation for the next injection when
Prep Ahead is checked.
Prep Ahead When checked, the 8200 AutoSampler will
begin preparing the sample for the next
injection before the instrument goes to ready.
When unchecked, the 8200 will wait for an
Instrument Ready before starting the sample
preparation for the next injection.
Liquid Sampling Modes Select from the various liquid sampling modes
described in the following table. When a liquid
sampling mode is chosen, the Liquid
Sampling Options subwindow is shown. For a
detailed description of the liquid sampling
modes and their corresponding 8200
AutoSampler parameters, please refer to the
8200 AutoSampler Operators Manual.
Mode Description
Standard Mode Default mode of operation. A solvent flush
sampling mode used for most samples.

390
Item Description
Volatile Sample Used with samples in a high vapor pressure
solvent. A solvent flush sampling mode with
slow plunger speeds and no upper air gap to
minimize flashing of the sample during
sampling.
Neat Sample Used to minimize the solvent that is injected
with the sample. In this mode, solvent flush is
turned off. The syringe is washed several
times with the sample and overfilled with
sample. During injection only the specified
amount of sample is injected from the syringe
and the excess is expelled into the waste arm.
Viscous Sample Used with samples that have a higher
viscosity than water. A solvent flush sampling
mode with slow plunger speeds and longer
pauses to improve reproducibility with higher
viscosity samples.
User Defined Allows you to set the 8200 AutoSampler
parameters. When this mode is selected the
User Defined Parameters subwindow is
displayed with the parameters available for
editing.
SPME Mode When the SPME (Solid Phase
MicroExtraction) sampling mode is chosen,
the SPME Options subwindow is shown.
Liquid Sampling Options

Item Description
Wash Mode Choose from:
Solvent A Wash
Solvent B Wash
A then B Wash
No Wash
Selects the solvent used to wash the syringe
after sampling and to create the solvent plug
before sampling a vial. When the solvent A
then solvent B wash mode is selected, solvent
A will be used for the solvent plug.
Syringe Volume Either 10 microliters or 100 microliters.
Selects the size of the syringe that is installed
on the 8200 syringe.

391
User Defined Parameters

Item Description
Solvent Flush Sampling When Yes is selected, the solvent plug size needs
to be specified and whether upper and lower air
gaps are to be used must be selected. When No is
selected, the solvent plug size and upper and
lower air gaps are turned off.
Syringe Wash Time (sec) 6 to 180 seconds
Sets the amount of time that the wash solvent will
be flushed through the syringe.
Air Dry After Wash This parameter may only be selected when Solvent
Flush Sampling is set to No. When Yes is selected,
the compressed air supplied to the 8200
AutoSampler will be blown through the syringe
after the wash cycle to dry the syringe. When No is
selected, air drying is not done.
Solvent Plug Size (ul) 0.0 to 3.0 microliters (10 microliter syringe)
0 to 30 microliters (100 microliter syringe
The volume of solvent loaded into the syringe used
to flush the sample from the syringe needle during
injection.
Vial Needle Depth (%) 0 to 100 percent
Sets the syringe needle depth in the vial. May be
used for doing ambient headspace or multiple
liquid phase sampling.
Uptake Speed (ul/sec) 1.0 to 5.0 microliters (10 microliter syringe)
Sets the plunger speed to provide the specified
volumetric sample flow into the syringe.
Upper Air Gap
Lower Air Gab
When Yes is selected, room air is drawn into the
syringe to create the corresponding air gap. When
No is selected, the sampling step to create the
corresponding air gap is skipped.

392
Item Description
Pause Time (sec) 1 to 30 seconds
Sets the amount of time that the syringe will be
held in the vial after the sample is drawn into the
syringe. It allows the pressures to equilibrate and
the sample flow into the syringe to stop before
withdrawing the syringe from the vial.
Hot Needle Time (min) 0.00 to 1.00 minute
Sets the amount of time that the syringe needle will
reside in the injector before the sample is expelled
from the syringe.
Injection Rate (ul/sec) 0.2 to 10.0 microliters (10 microliter syringe)
Sets the rate at which the sample will be expelled
from the syringe into the injector.
Needle Residence Time
(min)
0.00 to 10.0 minutes
Sets the amount of time that the syringe needle will
reside in the injector after the sample is expelled
from the syringe.
SPME Options

Item Description
Absorb Time (min) 0.00 to 640.00 minutes
Sets the amount of time the SPME fiber will be
extended into the sample for absorption.
Desorb Time (min) 0.00 to 640.00 minutes
Sets the amount of time the SPME fiber will be
extended into the injector for desorption.
Sample Headspace When checked, the SPME fiber guide will be
inserted just below the septum and the fiber
extended into the vapor space for sampling. When
not checked, the SPME fiber guide will be inserted
further into the vial and the fiber extended close to
the bottom of the vial.
Agitate When checked, the SPME agitation motor will be
turned on during absorption to improve sample
contact with the fiber. When not checked, the
SPME agitation motor will not be run.

393
Automated MS Report Generation
Overview
Once you have added Report sections to your Method, automated reports can be
generated from System Control after each injection, after recalculations, or by
the use of any of the Print actions in the Sequence window.
You may choose to disable automated Report printing during the course of an
automated sequence of injections or recalculations. You can do this by disabling
automated printing from the Automation menu in the Instrument window.

When this item is not checked, report printing is disabled. ASCII file generation is still
performed if specified in the Report Method section.
Disabling automated printing is analogous to disconnecting the printer
automation continues but no reports are printed. This is useful if you are about to
run out of printer paper but do not wish to suspend automation.

394

395
Automation File Editor Command
Reference
Menus
File Menu
New A sub-menu displays RecalcList, SampleList and Sequence.
Selecting one of them displays the Create a New
Automation File dialog box to name a new file of the
selected type.
Open A sub-menu displays RecalcList, SampleList and Sequence.
Selecting one of them displays the Open an Automation File
dialog box to open an existing automation file of the selected
type .
Save Saves the currently displayed automation file with the
existing name.
Save As Displays the Save Automation File As dialog box, allowing
you to save the currently displayed automation file with a
new name.
Print Prints the currently displayed automation file.
Printer Setup Opens the
Print Setup Dialog Box to select a printer and set options for
it. You can open the Print Setup dialog box from the Saturn
Printer Setup dialog box.
Exit Quits the Automation File Editor. If any file is open and
changes have not been saved, you will be prompted to do
so.

396
Edit Menu
Cut Deletes a selection and copies it to the Clipboard. Used to
remove or move a selected part of a spreadsheet.
Copy Copies a selection to the Clipboard. Used to duplicate a
selection and place the duplicate in a new place (using Paste).
Paste Inserts previously cut or copied information that was stored in
the Clipboard into a spreadsheet.
Clear Deletes a selection but leaves the Clipboard unchanged.
Add Adds a new line in a Sequence, SampleList or RecalcList.
Insert Inserts a new line in a Sequence, SampleList or RecalcList.
Select All Selects all lines in a Sequence, SampleList or RecalcList.
Fill Down Causes the contents of the top cell in a series of highlighted
cells to be copied to the cells below it. Used to edit all the cells
in a column quickly.
Edit Notes Opens the Edit Notes dialog box to permit editing of the notes
associated with the currently open automation file.
Help Menu
Product Support
Web Site
If you have Internet access and a web browser installed on your
computer, this option will automatically open the Varian MS
Workstation Product Support Web Site. Here you will find the
latest software and documentation updates for the Varian MS
Workstation suite of products, along with additional notes, tips,
and answers to frequently asked questions.
You may wish to visit this site periodically to see if new
information is available that may be pertinent to you.
About
Automation File
Editor
Displays the About Box for the Automation File Editor
application. The About Box contains information about the
software version, installation information, and a list of the
instrument control modules that you have installed.

397
Main Toolbar

Item Description

A sub-menu displays RecalcList, SampleList and Sequence.
Selecting one of them displays the Create a New Automation File
dialog box to name a new file of the selected type.

A sub-menu displays RecalcList, SampleList and Sequence.
Selecting one of them displays the Open an Automation File dialog
box to open an existing automation file of the selected type .

Saves the currently displayed automation file with the existing
name.

Displays the Save Automation File As dialog box, allowing you to
save the currently displayed automation file with a new name.

Prints the currently displayed automation file.

Deletes a selection and copies it to the Clipboard. Used to remove
or move a selected part of a spreadsheet.

Copies a selection to the Clipboard. Used to duplicate a selection
and place the duplicate in a new place (using Paste).

Inserts previously cut or copied information that was stored in the
Clipboard into a spreadsheet.

Causes the contents of the top cell in a series of highlighted cells to
be copied to the cells below it. Used to edit all the cells in a column
quickly.

398
Open Automation File Dialog Box
This dialog box is used to specify or open an automation file. The Open
Automation File dialog box appears with several different titles, depending upon
how you access it. In all cases, it contains the fields listed below in forms
appropriate for the type of file you are about to open.

Item Description
Look in Lists the available folders and files. To see how the current folder
fits in the hierarchy on your computer, click the down arrow. To
see what's inside a folder, click it. The box below shows the
folders and files in the selected location. You can also double-
click a folder or file in that box to open it. To open the folder one
level higher, click the up arrow button on the toolbar.
File list Lists the folders and files in the selected location. To see what's
inside a folder, double-click it. You can also use the Look In box to
see the hierarchy of folders. To open the folder one level higher,
click the up arrow button on the toolbar.
File name Shows the currently selected file.
Files of type Restricts the list of files to only those matching the selected type.
Recent Files Click on this button to display a list of recently selected files.
When you select a file from this list, its name is displayed in the
File name box.
Notes When checked, displays any notes and/or revision log associated
with the currently selected file.
Open Opens the selected file.
Cancel Cancels file selection.

399
Save Automation File As Dialog Box
This dialog box is used to name an automation file. The Save Automation File As
dialog box appears with several different titles, depending upon how you access
it. In all cases, it contains the fields listed below in forms appropriate for the type
of file you are about to save.

Item Description
Save in Lists the available folders and files. To see how the current folder fits
in the hierarchy on your computer, click the down arrow. To see what's
inside a folder, click it. The box below shows the folders and files in
the selected location. You can also double-click a folder or file in that
box to open it. To open the folder one level higher, click the up arrow
button on the toolbar.
File list Lists the folders and files in the selected location. To see what's inside
a folder, double-click it. You can also use the Save In box to see the
hierarchy of folders. To open the folder one level higher, click the up
arrow button on the toolbar.
File name Shows the currently specified file.
Save as type Specifies the type of file to save.
Recent Files Click on this button to display a list of recently selected files. When
you select a file from this list, its name is displayed in the File name
box.
Notes When checked, displays any notes and/or revision log associated with
the currently selected file.
Save Saves the file with the specified name.
Cancel Cancels file saving.

400
Print Setup Dialog Box
This dialog box is used to specify the printers that will be used by Varian MS
Workstation applications both interactively and during automation.

Item Description
Default Saturn
Printer
Displays the printer that is used when printing interactively from
Varian MS Workstation applications. Click on the Change button
to select a different printer.
Instrument
Printers
Displays the printer that is used when printing under automation
from System Control. Since the Varian MS Workstation is a
single instrument workstation, the printer specifications for
instruments 2-4 will be ignored.

401
Edit Notes Dialog Box
This dialog box allows you to enter descriptive notes associated with an
automation file. These notes can be viewed when selecting the file, and are
included in the file's printout.

Item Description
Notepad Area Shows any notes attached to the file. The notes may describe
the contents of the file, its uses, restrictions, etc. The
Notepad Area is scrollable if the notes exceed the available
space. The notes can be edited here, either by typing text
directly, or by pasting text from the Clipboard by pressing the
keys: CTRL V simultaneously.

402
RecalcList Window
Data Files can be added to a RecalcList by clicking on a cell in the Data File
column and typing the file name, or by pressing the Browse... button and
selecting the file name. Another way of quickly adding one or more Data Files to
a RecalcList is by selecting the files of interest in the Explorer, and dragging
them over the RecalcList Window. When you release the mouse button, the Data
Files are automatically appended to the RecalcList.
Note that a Recalc List may contain standard GC data files (.run extension) as
well as MS data files (.sms extension). Some of the Recalc List items described
below are handled differently for the two data file types. When the list is
processed, the appropriate data handling will be used automatically for each data
file.

Item Description
Data File Shows the name and path of the Data File for each sample.
Sample Name Cannot be edited.
Shows the name of each sample in the RecalcList.
Sample Type Baseline, Analysis, Calibration, Verification, Print Calib, New
Calib Block, AutoLink, Activate Method
Sets the sample type, or automation action, of each line in
the RecalcList.
Cal. Level 1 to 10
Sets the calibration level of each calibration or verification
sample in the RecalcList.
Inj Cannot be edited.
Shows the number of injections made of each sample in the
RecalcList.
Recalc Notes... Up to 180 characters
Opens the Notes window for the selected record to edit or
create a note about the sample. This note is stored
separately from the original injection notes.

403
Item Description
AutoLink... Two AutoLink commands when Sample Type is Baseline,
Analysis, Calibration, or Verification.
One AutoLink command when Sample Type is AutoLink.
One Activate Method Command when Sample Type is
Activate Method.

Opens the AutoLink Parameters dialog box to set the options
for linking to a remote application during automation through
System Control.
Opens the Activate Method Dialog Box to set the path name
for activating a new method during automation of a
RecalcList through System Control.
Unid Peak Factor 0 to 1,000,000.0
Sets a calibration factor for unidentified peaks. Not used by
calibration samples.
Multiplier 0.000001 to 1,000,000.0
Sets a value for the multiplier. Results for the sample are
multiplied by this value. Not used by calibration samples.
Divisor 0.000001 to 1,000,000.0
Sets a value for the divisor. Results for the sample are
divided by this value. Not used by calibration samples.
Amount Standard 0.000001 to 1,000,000.0
GC Files: Sets the amount of the first internal standard.
Used to calibrate results for Internal Standard and
Normalized Percent calculations. Not used by calibration
samples.
MS files: Sets an ISFactor which is used by Analysis and
Verification samples. It will be multiplied by the appropriate
Compound Calibration Level Amount that is in the DH
Method being used. Note that internal standards in Analysis
and Verification samples always use the amount that is
specified in Calibration Level 1.
MultiChannel
MultiStandard

none, multiple, specific channel
GC files: Opens the Data Handling Channels dialog box to
specify the calibration parameters for up to five different
Detector Channels.
MS files: Not used by MS data handling. These are GC
detector channels which are different from the scan function
channels that may be specified in the MS method.
Add Adds a line to the end of the RecalcList.
Insert Adds a new line before the highlighted line.
Delete Deletes the highlighted line in the RecalcList.
cells to be copied to the cells below it. Used to edit all the
cells in a column quickly.
Browse... Opens the Open Data File dialog box to select a Data File to
add to the RecalcList.
Report... Shows the results report for the selected Data File.

404
Item Description
Defaults Displays the Set Defaults dialog box, allowing you to specify
default values for each applicable field in the RecalcList.
Begin Opens the Begin RecalcList Dialog Box to specify a method
to be used while recalculating or printing all RUN files in this
RecalcList, and to then begin recalculating or printing the
files.
Suspend Suspends execution of this RecalcList after the current file
has been completed.
Resume Resumes execution of this RecalcList after it has been
suspended.
Data Handling Channels Dialog Box
NOTE: This dialog box is only used to specify standard GC data handling. MS
data handling uses only one detector channel.
You can specify the Multiplier, Divisor, and Unidentified Peak Factor on a
channel-by-channel basis for up to five different detector channels. And you can
specify up to eight internal standards for each of the five channels, for a total of
forty internal standards. If you only want to specify a single Multiplier,
Divisor, Unidentified Peak Factor, and Amount Standard to be used for all
channels of all detectors, you may do so directly in the SampleList,
RecalcList or Inject Single Sample dialog box and do not need to use this
dialog box.
If you plan to specify parameters on a channel-by-channel basis, before opening
this dialog box make sure that the active method contains the data handling
sections for each channel, and that their peak tables contain the standard peaks
(if any) properly named and checked. The dialog box uses information from the
active method to help you make the proper specifications for the type of
calibration method that you will be using. If you later change the standard
peak names in the peak table, you will need to revisit this dialog for each
sample to update the names and amounts.

405
Item Description
Detector Channel Indicates the detector channel that is specified by the
remaining fields in the row. Channels are indicated by
the detector module name, bus address, and channel
identifier. The combo box contains entries for all
channels having data handling sections in the active
method. If the desired channel is not visible in the
combo box, make sure that the correct method is active
and that it contains data handling sections for the
desired channel.
Calculation Type Internal Std
External Std
Normalized %
No Calibration

Indicates the calibration method specified for the
detector channel in the active method. To change the
calibration method for a specific channel, first click on
the channels row, then click on the Edit Calibration
Setup push-button. If the Calculation Type is not
Internal Std or Normalized %, the Edit Standard
Peak(s) push-button will be disabled.
Unid Peak Factor 0 to 1,000,000
Sets a calibration factor for unidentified peaks.
Multiplier 0.000001 to 1.000,000
Sets a value for the multiplier. Results for the sample
are multiplied by this value.
Divisor 0.000001 to 1,000,000
divided by this value.
Standard Peak 1 40 character standard peak name from peak table
Indicates the name of the first Internal Standard Peak.
The Amount Standard 1 will be applied to the Internal
Standard Peak having the same name. To change the
standard peak name for a specific channel, first click on
the channels row, then click on the Edit Standard
Peak(s) push-button.
Amount Standard 1 0.000001 to 1,000,000
Sets the amount of the first internal standard. Used to
calibrate results for Internal Standard and Normalized
Percent calculations.
Standard Peak 2-8 40 character standard peak name from peak table
Indicates names of the multiple internal standard peaks
present in the specific channels peak table. . To change
the standard peak names for a specific channel first
click on the channels row, then click on the Edit
Standard Peak(s) push-button. If the peak table does
not contain multiple internal standards, these fields will
be disabled.

406
Item Description
Amount Standard 2-8 0.000001 to 1,000,000
Sets the amounts of the second through eighth internal
standards. Used to calibrate results for Internal
Standard and Normalized Percent calculations involving
multiple internal standards. If the peak table does not
contain multiple internal standards, these fields will be
disabled.
Add Adds a line to the end of the list.
Insert Adds a new row before the highlighted line.
Delete Deletes the highlighted row in the list.
Edit Calibration Setup Opens the Calibration Setup Dialog Box to permit
inspection and editing of the calibration parameters in
the method for the indicated detector channel.
Edit Standard Peak(s) Opens the Peak Table Dialog Box to permit inspection
and editing of the Standard Peak names in the method
for the indicated detector channel. Open the Peak Table
and press OK to transfer the standard peak names and
amounts from the Peak Table to the indicated detector
channel row.

407
Open Data File Dialog Box

Item Description
Look in Lists the available folders and files. To see how the current
folder fits in the hierarchy on your computer, click the down
arrow. To see what's inside a folder, click it. The box below
shows the folders and files in the selected location. You can
also double-click a folder or file in that box to open it. To open
the folder one level higher, click the up arrow button on the
toolbar.
File list Lists the folders and files in the selected location. To see
what's inside a folder, double-click it. You can also use the
Look In box to see the hierarchy of folders. To open the folder
one level higher, click the up arrow button on the toolbar.
Files of type Restricts the list of files to only those matching the selected
type.
Run Information Shows information about the currently selected file.
Result
Information
Shows information about the results, if any, calculated from the
current data file.
Channel Specifies the detector channel to show Result Information for.
Note that this applies only to standard GC results.
Delete Results Allows you to delete results from the currently select channel of
the currently selected data file. This button does not appear if it
has been disabled from the Varian MS Workstation Security
Administration application. Note that this only affects standard
GC results. MS results are not deleted.

408
Item Description
Open File Opens the selected data file using the selected channel.

SampleList Window
The SampleList window contains injection parameters that are specific to the
sample introduction device you are using on your instrument. This section
describes the generic SampleList fields. Refer to the appropriate Instrument
Control help topic in the System Control Reference Help for a description of the
device-specific extensions to the SampleList.

Item Description
Sample Name Up to 19 characters
Sets the name of each sample in the SampleList
Sample Type Baseline, Analysis, Calibration, Verification, Print Calib, New
Calib Block, AutoLink, Activate Method
Sets the sample type, or automation action, of each line in
the SampleList.
Cal. Level 1 to 10
Sets the calibration level of each calibration or verification
sample in the SampleList.
Inj 1 to 9
Sets the number of injections to be made of the sample.
Injection Notes up to 180 characters
Opens the Notes window for the selected sample to edit or
create a note about the sample.

409
Item Description
AutoLink Two AutoLink commands when Sample Type is Baseline,
Analysis, Calibration, or Verification.
One AutoLink command when Sample Type is AutoLink.
One Activate Method Command when Sample Type is
Activate Method.
Opens the AutoLink Parameters dialog box to set the options
for linking to a remote application during automation through
System Control.
Opens the Activate Method dialog box to set the path name
for activating a new method during automation of a
SampleList through System Control.
Unid Peak Factor 0 to 1,000,000.0
Sets a calibration factor for unidentified peaks. Not used by
calibration samples.
Multiplier 0.000001 to 1,000,000.0
Sets a value for the multiplier. Results for the sample are
multiplied by this value. Not used by calibration samples.
Divisor 0.000001 to 1,000,000.0
divided by this value. Not used by calibration samples.
Amount Standard 0.000001 to 1,000,000.0
GC Files: Sets the amount of the first internal standard. Used
to calibrate results for Internal Standard and Normalized
Percent calculations. Not used by calibration samples.
MS files: Sets an ISFactor which is used by Analysis and
Verification samples. It will be multiplied by the appropriate
Compound Calibration Level Amount that is in the DH Method
being used. Note that internal standards in Analysis and
Verification samples always use the amount that is specified
in Calibration Level 1.
MultiChannel
MultiStandard

none, multiple, specific channel
GC files: Opens the Data Handling Channels dialog box to
specify the calibration parameters for up to five different
Detector Channels.
MS files: Not used by MS data handling. These are GC
detector channels which are different from the scan function
channels that may be specified in the MS method.
Add Adds a line to the end of the SampleList.
Insert Adds a new line before the highlighted line.
Delete Deletes the highlighted line in the SampleList.
cells to be copied to the cells below it. Used to edit all the
Add Lines Displays the Add Lines dialog box, allowing you to specify the
number of lines to either insert or append to the spreadsheet,
along with the values to use for each applicable field. Certain
fields such as Sample ID and vial number can be
automatically incremented.
Defaults Displays the Set Defaults dialog box, allowing you to specify
default values for each applicable field in the SampleList.

410
Item Description
Data Files Opens the Data File Generation dialog box to specify the
naming scheme being used for Data Files generated from
injections. Note that if the method contains both MS and
standard GC DH method sections, then both sms and run
files will be generated.
RecalcList Opens the RecalcList Generation dialog box to specify the
options for generating or updating RecalcLists after injections.
Note that if the method used contains both MS and standard
GC DH sections, then the generated Recalc List will contain
both sms and run files.
Select SampleList Section Type Dialog Box
A SampleList File may contain multiple SampleList Sections. Each installed
AutoSampler can contribute its own unique type of section, having special
features that correspond to its special hardware. For example, the 8200 has
syringe sampling mode features, while the 8134 has relay control features.
Generally each installed AutoSampler has its own unique SampleList with
special columns for its features. A SampleList File can contain a section for each
type of AutoSampler, similar to the way that a Method file can contain a section
for each type of Instrument Module.
This dialog box lets you pick the specific section that you want to edit in a
SampleList file that may contain more than one section.

Item Description
SampleList section
type listbox
Selects a section type to use in building a new SampleList;
opens the appropriate SampleList window. SampleLists
may contain sections for multiple types of sample handling
devices, depending upon which module drivers have been
installed.
OK Creates a SampleList section of the specified type.
Cancel Cancels the SampleList section creation.

411
Data File Generation Dialog Box

Item Description
Directory for Data Files Shows the currently selected directory where Data Files
will be generated.
New Folder Allows you to create and name a new folder in the
currently displayed directory.
Drives Allows you to specify the drive where Data Files will be
generated.
Data File Names Allows you to enter the Data File name specification. You
may enter as many characters as you wish, but the final
file name (including path) must not exceed 255
characters in length.
You may embed the special symbols listed in the window
to represent sample-specific information in the Data File
name. As you enter the specification, an example file
name is shown.
OK Accepts the name specification.
Cancel Cancels the name specification.

412
RecalcList Generation Dialog Box

Item Description
Do not automatically
create and update a
RecalcList.
No RecalcList will be generated or updated when you
create Data Files as a result of injections.
Create and update a new
RecalcList
Allows you to enter the name of a new RecalcList that
will be created when Data Files are generated as a
result of injections. If the RecalcList name that you
specify already exists when the injections are
performed, a number will be appended to the name so
that it is unique.
Append to an existing
RecalcList
Allows you to browse for an existing RecalcList file.
When Data Files are generated as a result of
injections, their information will be appended to this
file.
OK Accepts the RecalcList specification.
Cancel Cancels the RecalcList specification.

413
AutoLink Parameters Dialog Box
With AutoLink, you can specify a program to be executed after all injections of a
sample have been performed, or two programs to be executed after each
injection of that sample. When AutoLink appears as a sample type in a
SampleList or RecalcList, the associated program is executed at that point in the
SampleList / RecalcList after the previous SampleList / RecalcList line has
completely finished. The AutoLink can also be specified as part of a SampleList
line that has a Baseline, Analysis, Calibration, or Verification sample type. In
such cases, the two AutoLink programs are executed after each injection of the
sample.

Item Description
Command DOS command lines to open DDE applications
Sets the command line that will be used when
AutoLink is invoked.
Other Parameters commands understood by the remote application
Provides information to the remote application when
it is invoked.
Browse... Opens the Select an AutoLink Program dialog box to
select the name of an AutoLink program and enter it
into the Command field.

414
Sequence Window

Item Description
Action Shows the action chosen for each line in the Sequence
Method Shows the Method chosen for each line in the
Sequence
Sample/RecalcList Shows the SampleList or RecalcList chosen for each
line in the Sequence
Add Adds a new line to the end of the Sequence.
Insert Adds a new line above the highlighted line.
Delete Deletes the highlighted line in the Sequence.
Browse... Opens the Select a Method File or Select a
Sample/RecalcList window to browse through
directories and find a Method or Sample/RecalcList file
to add to the Sequence.

415
Automation File Editor
Overview
The Automation File Editor is used for editing and creation of SampleLists,
RecalcLists, and Sequences outside of the Varian MS Workstations System
Control application. The off-line Automation File Editor allows access to these
files without disrupting automated runs that may be occurring in System Control.
SampleLists and Sequences that are active and running in System Control
can not be accessed simultaneously in the off-line Automation File Editor.

Accessing the Automation File Editor

Click on the Automation File Editor icon on the MS Workstation Toolbar
The Automation File Editor is displayed.
Editing or creating a RecalcList

Choose either a New RecalcList or Open an existing RecalcList from the File
menu..

416
The RecalcList window for the open RecalcList is displayed. It contains most of
the same fields contained in the SampleList. Where the SampleList may contain
AutoSampler and sample specific data handling information, the RecalcList
contains the Data Filename and data file specific data handling information. The
fields that are common to both the RecalcList and the SampleList are described
in the sections following the creation of the SampleList.

Enter post calculation operations to be performed.
Enter notes about the recalculation of the Data File.
Press the reports button to view results for the currently selected data file. The
SaturnView application will be started and the data file will be automatically
loaded.

417
Editing or creating a SampleList

Choose either a New SampleList or Open an existing SampleList from the File
menu..

After choosing the SampleList to open the Select SampleList Section Type
dialog box is displayed. This dialog box allows you to choose a SampleList that is
appropriate for the AutoSampler that will be used, e.g. CP-8400, CP-8410, 8200
Standalone AutoSampler. Choose the Generic SampleList if you are not using
the 8200/SPME AutoSampler with your 3800 GC.

The SampleList window for the open SampleList is displayed.

418

Enter information about the samples you plan to inject.
Select the location and name for the Data Files to be generated by the
SampleList.
button. Move columns by dragging them using the right mouse button. Right click
on column headers for formatting options.
be entered directly into this table. Note that for MS data handling, the Amt Std is
used as an IS Factor which is multiplied by the appropriate calibration level
amount in the method.
If you have more complex requirements when doing standard GC data handling,
such as multiple internal standards or multiple detectors requiring different
entries for these data handling parameters, click on the button in MultiChannel
MultiStandard column. For MS data handling, the analogous specifications are
contained in the method.

419

data file.
letter and sub-directory (path) where the data files are to be stored.

would appear.

420
- Unidentified Peak Factor
- Multiplier
- Divisor
- Amount Standard when one Internal Standard is being used
specify them on a per-detector channel basis when doing standard GC data
handling. This is useful if, for example, you have different detectors installed on
your GC. In addition, if you are using multiple internal standards, you can also
specify their amounts on a per sample and per detector channel basis. Note that
when doing MS data handling, the analogous specifications are made in the data
handling method.
Multi-Channel Multi-Standard column in the 8200 SampleList. You will be
prompted for the Method that will be used when this SampleList is run. Then
Data Handling Channels dialog box is displayed. When you select the detector
channel in the Data Handling Channels dialog box, the calculation type, internal
standard peaks and amounts are read from the Method that you just selected.
The values entered for internal standard peaks and amounts will be entered into
the peak table of this method.


421
From the SampleList RecalcList button, you can choose to create a new
RecalcList, append to an existing RecalcList, or not create nor update a
RecalcList. Clicking on the RecalcList button displays the RecalcList Generation
dialog box.


422
SampleList row.


Enter the name of the Method toor pick the Method from a list of files.

is activated.

423
Editing or Creating a Sequence

Choose either a New Sequence or Open an existing Sequence from the File
menu...


Sequence lines.
box.

424

425
GC Batch Report
Overview
The Batch Report application allows you to quickly generate reports for a batch
of Data Files without using System Control. Reports are automatically printed
when you drag and drop Data Files from the Windows Explorer onto the Batch
Report window. You can specify the Method to use when formatting the reports,
and the post-run application that you wish to invoke.

Click on the Batch Reporting icon in the MS Workstation Toolbar.
The Batch Report window is displayed.

Reports are printed using the formatting options stored in the Method last used to
process the Data Files, or from the specified Method. You may specify the post-
run application to invoke. Use REPORT32 for standard reports. Use the
Windows Explorer to drag and drop Data Files into the Batch Report window.
As each report is generated, the Status Messages window is updated.

426
Method Selection

The Batch Report application allows you to generate reports for a set of Data
Files using parameters specified in a Method. You determine whether you to use
the Method parameters from the most recent report generation for each Data File
(the Data File Method), or whether you wish to specify a different Method for all
Data Files in the batch.
To use the Data File Method for Data File in the batch, click on the Use Data File
Method radio button. To use a specific Method, click on the Browse button and
select the Method you wish to use. You can view and edit the selected Method
using the Quick Link button.

427
Generating Reports

To generate reports for Data Files using the report formatting information in the
specified Method drag Data Files from the Windows Explorer and drop them on
the Batch Report window. When you do, the upper list box will show the selected
files. As each file is processed, a status message is added to the lower list box.
During the report generation process, you can click on the Pause button to stop
processing after the current job. When paused, the Resume button becomes
enabled, allowing you to resume the batch.
Changing Report Commands
By default, the Batch Report application generates a Standard Report for each
Data File in the batch (assuming the Method contains a Standard Report section
corresponding to the detector data stored in the Data File). You can select
alternate report applications that you have installed in the Star Workstation by
clicking on the Change button in the Batch Report window. When you do, you
are presented with the Change Application dialog box.

428

The Change Application dialog box displays all post-run applications registered
in the Star32.ini file in your Windows directory. The actual command line is listed
for each:

Command Line Application
Report32.exe The Standard Report application.
Starwr32.exe Star Custom Report Writer
Pvwrai32.exe PolyView
Starfi32.exe StarFinder

Select the application you wish to invoke from Batch Report and click OK.

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GC Data Handling Calibration
Types of Calibration
There are three types of calibration available with the Varian MS Workstation:
External Standard, Internal Standard, and Normalized Percent. Refer to the
section GC Data Handling Fundamentals for a brief description of each
calibration type. Refer to the Regulatory Compliance Manual for a complete
description of the algorithms used by each type to calculate results.
Preparing the Method for Calibration
In order to generate quantitative results for the compounds in your samples, you
must identify the peaks of interest and specify your calibration parameters. This
is done by using the Peak Table and Calibration Setup window in the Data
Handling section of the Method. The Data Handling Method section can be
edited from the Interactive Graphics or the Method Builder application. The
Method Builder application can be invoked anywhere a Method name appears in
a Quick Link button.
Calibration Setup
The Calibration Setup window contains parameters that affect the type of
calibration calculations that will be performed by your Varian MS Workstation.

430
Specify the calibration type.
Up to 10 separate replicates.
Percent of new versus historical data.
Refer to the on-line help in Interactive Graphics for a description of all fields in
this window.
Refer to the Regulatory Compliance Manual for a description of weighting
options.
Peak Table
The Peak Table contains amounts for each level (the number of which is
specified in the Calibration Setup), and the internal standard peak designations.

Specify internal standard peaks.
Refer to the appropriate standard peak.
Enter amounts for each level.
Automated Calibration
You calibrate your Method by injecting calibration samples using System Control.
Calibration samples are specified in the SampleList.

To clear previously stored calibration data, enter a New Calib Block line.
Select the Calibration sample type.
Enter the calibration level for this injection.
You may inject more than one replicate for each level.

431
Specify internal standard amounts.
You can also calibrate your Method using previously collected Data Files,
recalculating them as calibration samples. Add the Data Files to the RecalcList.

Enter the Data Files to be used as calibration samples.
Select the Calibration sample type.
Enter the calibration level for this Data File.
Inspecting Calibration Curves
Calibration Curves can be viewed and edited from System Control. Pull down the
Recalculate menu.

Select View Calibration Curves.
You are prompted for the Method containing the calibration curves to view. The
active Method for the instrument is selected by default.

Select the Method.
If curves exist for more than one channel, you are prompted for the channel. The
Calibration Curve window is displayed for the selected channels curves.

432

You may also view Calibration Curves for the active Method in Interactive
Graphics. Pull down the Results menu.

The Calibration Curve window is displayed.
You may also view Calibration Curves from the Calibration Setup window in the
Data Handling section of the Method.

433

Select View Curves.
Generating Calibration Block Reports
As you create calibration information in System Control, you may wish to
generate a Calibration Block Report documenting the calibration curves and
replicate statistics for each peak. Open the SampleList (shown) or RecalcList
window.

Enter a Print Calib line after all calibration runs are completed.
A Calibration Block Report is printed when the SampleList or RecalcList line is
encountered during automation. The format of the Calibration Block Report is
determined by parameters set in the Calibration Block Report Format window in
the Report section of the Method. Refer to the section Generating GC Standard
Reports for details on the Report Method section.

434
Calibration Verification
You may wish to periodically check the validity of your calibration data as you
perform analytical injections. You do so by injecting a verification sample with
known amounts for each compound and comparing them to amounts calculated
from the calibration curves. If the amounts deviate more than a given tolerance, a
verification failure occurs and a number of failure actions can take place.
Verification failure options are specified in the Verification Setup window in the
Data Handling Method section.

Specify the tolerance.
Select the failure action. Verification failures are documented in the results
report.
Verification samples are entered into the SampleList (shown) or RecalcList.

Select the Verification sample type.
Specify the calibration level corresponding to the known amounts in the sample.
Refer to the on-line help in Report for details on the format of the results report
for Verification runs.

435
GC Data Handling Fundamentals
Introduction
Even after optimizing your chromatographic conditions to provide the best
separation possible, you may still have unresolved peaks or other situations
requiring special post-run Data Handling operations. For instance, you may want
to exclude solvent peaks from the total area when doing area percent
calculations. You may want to ensure that a very small peak in one part of the
chromatogram is detected, and not rejected as a noise peak. Another common
use for special post-run Data Handling is to fine tune your quantitation method.
This section will provide an overview of both how the Varian MS Workstation
software performs the peak processing and how you can use the software to
most efficiently meet your Data Handling needs.
Refer to the Calibration section for more information on calibration and
verification procedures. Refer to the Regulatory Compliance Manual for a
complete description of Data Handling algorithms and calculations. Refer to the
on-line help in Interactive Graphics for descriptions of all of the fields in the Data
Handling section of the Method.
Performing a Pilot Run
You may wish to use a pilot run to adjust the Data Handling parameters to their
proper settings. You can use Interactive Graphics to edit the Data Handling
section of your Method, and save this along with the Instrument Control sections
for automatic data analysis on your production runs.
Data Handling Methods can be developed using an iterative approach. You
change Method parameters, then reintegrate, and then determine if the results of
your changes are appropriate. If not, you repeat these steps until you have the
desired results. The Interactive Graphics application in the Varian MS
Workstation is designed to facilitate this iterative process. You can view your pilot
run and create a Peak Table by clicking on peaks of interest with the mouse. You
can add timed integration events graphically using the Interactive Time Events
window. You can even generate and review calibration curves used to calculate
results. Refer to the section Interactive Graphics for more information on these
procedures.

436
Peak Detection
The Varian MS Workstation software reduces the raw data collected from the
chromatograph into a results report in four steps:
- Peak detection
- Peak integration (and final baseline determination)
- Peak identification (if a Peak Table is present)
- Results calculations
Peak detection is the process in which the peak start, apex, and end points are
determined. This is also the step where fused peaks are identified as a
mother/tangent peak pair, or as two valley separated main peaks.
The programmable time events that affect the peak detection process are Peak
Width, Signal to Noise Ratio, Inhibit Integrate, Tangent Percentage, and Forced
Peak. These are discussed in more detail later in this section.
Once the peaks are detected, the area for the peaks is determined in the peak
integration step. The first part of this step is to process any Split Peak events.
This event causes a previously detected peak to be treated as two separate
peaks. Tied to both peak detection and peak integration is baseline placement.
The four time events which affect baseline placement do not affect peak
detection. These events are Valley Baseline, Horizontal Forward, Horizontal
Backward, and Horizontal Minimum.
After areas for all peaks have been calculated, the optional step of peak
identification is done. Before peaks are identified, they may be excluded from
consideration by the Solvent Reject event or the Peak Reject event. Also, several
peaks may be treated as one peak by the Group Peak event. Peak identification
is the process by which peaks detected in the first step, and integrated in the
second, are matched by retention time with a list of peaks you have previously
entered in the Peak Table. As described below in more detail, Interactive
Graphics provides a fast and efficient means of building the Peak Table using
your pilot run.
The final step is to perform one or more of a large variety of possible calculations
producing the final results. This produces results in a state suitable for printing or
exporting by the Report application.
Peak Width Determination
In general, peaks are wider in liquid chromatography than they are in gas
chromatography. To account for potential wide differences in peak width from run
to run, you can set an initial peak width parameter. The lower the peak width
value, the more accurate the placement of peak events. However, if set too low,
a wide low peak may not be detected.
Peaks tend to widen with the retention time. The Data Handling software can
account for this by automatically programming peak width events at appropriate
times. This way, early eluting narrow peaks can use a low and more accurate
peak width setting, while later eluting wide peaks will be properly detected with a
higher peak width setting. To do automatic peak width programming, the peak
detection software monitors peak widths as peaks are detected. If it determines
that peaks are getting too wide relative to the current peak width setting, it

437
programs a new, wider peak width. Although it is rarely necessary, the software
is also able to automatically program narrower peak width settings.
Instead of letting the software automatically program peak width settings as
needed, you can manually program your own peak width setting. The act of
manually programming a peak width event disables automatic peak width
programming. In the vast majority of cases, automatic peak width determination
is all that is needed.
Adjusting the Signal To Noise Ratio
The Signal to Noise Ratio (S/N ratio) also affects the peak detection process.
When you lower the S/N ratio, more small noise peaks are detected. Conversely,
increasing the S/N ratio causes fewer small peaks to be detected. In the extreme
case, a high S/N ratio may cause some larger peaks of interest to remain
undetected, particularly if you have manually programmed peak width value that
is too low. Another effect of a high S/N ratio value is that peak start and end
events tend to be closer to the peak apex, especially when there is a lot of tailing,
or a sloping baseline. This can result in valley separated peaks incorrectly
considered baseline resolved.
The optimal setting for this value depends on your analyses. You want to set this
value low enough so that all the peaks in which you are interested are detected,
but high enough so that extraneous noise peaks are not detected. If you want
small peaks to be detected in one part of the chromatogram, but not in another,
you can program different S/N ratio values at different times in the
chromatogram.
Rejecting Solvent Peaks
In many types of chromatographic analyses, you will have a large, essentially
unretained solvent peak elute at the beginning of your run. This represents the
solvent in which your sample is contained, and is not pertinent to your results.
You have two options for removing the peak from your resultsusing the Inhibit
Integrate or the Solvent Reject event. Generally you will use Inhibit Integrate
unless an analyte of interest is a shoulder peak or is tangent to the solvent peak.
Remember that Inhibit Integrate occurs at the first step of peak processing,
during the peak detection phase. Its effect is to remove the section of the
chromatogram specified by the event from consideration while peak detection is
in progress. With the Inhibit Integrate event, regardless of the specific location
where the event ended, the next detected peak always starts a new baseline.
This is why a Solvent Reject event is used if your analyte of interest is a shoulder
peak or is tangent to the solvent peak. This allows the peak detection algorithms
to correctly determine the baseline points for the shoulder or tangent peak, while
still removing the solvent peak from your final results calculations.
Skimming Fused Peaks
Fused peaks are peaks that elute next to each other and are not baseline
resolved. The peak detection software treats fused peaks as either valley
separated peaks, tangent peaks, or as fused tangent peaks. The Tangent
Percentage value affects which peaks are considered valley separated peaks
and which are tangent peaks. The Tangent Percentage value represents the
percentage of the peak height of the second peak to the first fused peak. If the
peak height of the second peak is a lower percentage than the Tangent
Percentage value relative to the first peak, then the peak is considered a tangent,

438
otherwise it is considered a main peak. The rule of thumb is that the higher the
programmed Tangent Percentage value, the more peaks are considered
tangents. Note that a tangent peak can only be detected following a main peak.
Tangent skimming cannot be done on leading tangents.

Tangent Skimmed Peak

Valley Separated Peaks
Fused tangent peaks are a special case of tangent peaks. Once it is determined
that more than one peak is tangent to a main peak, the tangents themselves
could be valley separated.
Splitting Fused Peaks
Occasionally, the Data Handling software will not detect a shoulder peak,
especially if there is no clear valley between the fused peaks. It will treat all of the
area as one peak, even if you expect two peaks to be present. In this case, you
would use the Split Peak event. This splits one peak into two valley separated
peaks.
Forcing Peaks
Forcing peaks is a way of defining your own baselines. You might use this if,
after adjusting the S/N ratio and peak width, a peak you are interested in is still
not detected. Alternatively, you can use the Forced Peak event as a way of
grouping multiple peaks so that they are reported as one peak (see also the
Group Peak event).
The Forced Peak event causes peak events to be placed at the start and end
times of the event and a baseline is drawn between the two. The apex is taken to
be the highest data point in the time range for the event. This event supersedes
all other peak detection events, so the Peak Width, Signal to Noise Ratio, Inhibit
Integrate, and Tangent Percentage settings have no effect on the forced peak
placement.

439
Identifying Peaks
Peaks are identified with the use of the Peak Table in the Data Handling section
of the Method. The main purpose of the Peak Table is to list the names of your
compounds and their expected retention times. Since retention times may vary
slightly from run to run, you can specify a window of time during which the
Workstation will try to identify a particular peak. The peak window is the actual
span of time on the chromatogram that the software searches for the peak,
centered around the retention time you entered for that peak. If the peak falls
within that time window, it will be identified, otherwise it will not be identified. You
may choose to report unidentified peaks, but these peaks cannot be accurately
quantified (refer to the on-line help in Interactive Graphics for a description of the
unidentified peak factor).
If your peaks tend to drift, you can automatically modify their peak windows by
marking a peak as a reference peak. Non-reference peaks will have their peak
windows adjusted by the same percentage that the reference peaks have
deviated from their expected retention times, accounting for the direction of
change.
Interactive Graphics provides an easy way to build a Peak Table using your pilot
run. You select the Edit MethodFill Peak Table menu item, and one by one
click on the peaks in your pilot run which you want to identify in your production
runs. As you click on a peak, a new entry is added to the Peak Table with the
retention time and a default name. When you have added all the peaks of
interest, you can change the default names to real compound names.
Building a Calibration Curve
In order to determine absolute amounts of an analyte, you need to compare the
peak area from a run in which the amount is unknown to a run in which you have
injected a known amount of the compound. A sample that contains known
amounts of the compounds to be analyzed (analytes) is called a calibration
standard. When you inject a calibration standard, you designate the run as a
Calibration Run. You enter amounts (for each analyte in the calibration standard)
into the Peak Table. Note that this is the same table used for identifying your
analytes.
Sometimes you will want to do several calibration runs, and in each successive
calibration run you inject different calibration standards with different amounts of
each analyte. This is called multipoint or multilevel calibration. The Varian MS
Workstation allows you to calibrate with up to ten levels. Each level represents
the amount of each analyte injected for each of the different calibration
standards. Multilevel calibration can be more accurate than single level
calibration, because you calibrate over large range of analyte amounts. For more
accuracy, you may want to repeat injections at a given level. This is a way of
averaging out variations from injection to injection.
Regardless of the number of calibration runs you perform, the result of the
calibration runs is a calibration curve. The calibration curve for an analyte is
generated by plotting the peak size on the y axis and the injected amount of the
analyte on the x axis for each calibration run you have performed, and then
calculating the best line through the points. There are options to do a linear,
quadratic or cubic fit through the points.

440
Calibration Curve Report
File: c:\star\tutorial\ext std.mth
Detector: ADC Board, Address: 16, Channel ID: B
2-Octanone
External Standard Analysis Resp. Fact. RSD: 40.84%
Curve Type: Linear Corr. Coef.(R): 0.979546
Origin: Ignore
y = +2.060889e+002x +3.777554e+003
P
e
a
k
S
i
z
e
Amount
25 50 75 100
0
5000
10000
15000
20000
25000
Replicates 2 1 1 1

Sample Calibration Curve Using Linear Fit
When you inject a sample with unknown amounts of your analytes, you
designate the run as an Analysis Run. After identifying a peak as discussed
above, the peak is quantified using the calibration curve. The peak area, which is
determined after the second step of peak processing, is used as the y value in
the calibration curve equation. This lets you calculate the x value which is the
analyte amount.
External Standard Calibration
The External Standard calibration type is the most common method of calibrating
an analysis. To calculate results with this technique, you must first perform a
calibration run with a standard mixture. The calibration curve manager
automatically generates a curve by plotting the known amounts of standards, as
entered in the Peak Table, against the corresponding peak sizes, as calculated
by the software. When you inject a sample in an analysis run, the Varian MS
Workstation calculates the amount of the analyte from the coefficients for the
curve and the size of the sample peak.

441
Internal Standard Calibration
When you use the Internal Standard calibration type, you calibrate with regular
calibration standards but you also add a known amount of another analyte, the
internal standard, to each calibration standard and sample. When you make an
injection, any variation in the injection volume will be reflected by a detectable
variation in the amount of the internal standard. Fluctuations may also be caused
by the process used to prepare the samples. In this case, adding the internal
standards before sample preparation corrects for recoveries. Your Peak Table
may contain as many as eight internal standard peaks. Each non-standard peak
refers to the internal standard peak to use for calculations. Having multiple
internal standards allows you to match each peak to a standard with similar
chemical properties, which should have a similar recovery.
In generating the curve for an Internal Standard Calibration, you plot ratios: the
peak size divided by the standard peak size on the y axis and amount of
standard divided by the amount of internal standard on the x axis. Even if your
injection volume varies slightly, the ratio of the sample to the internal standard
will remain constant.
Normalized Percent Calibration
The Normalize Percent calibration type gives a percentage amount of each
analyte relative to the total amount of all analytes in the sample, adjusted for
varying detector response to the different analytes. It is analogous to a regular
percentage calculation, except that the percentages are based on actual
amounts of sample components rather than on peak size. It is also analogous to
the Internal Standard calibration type in that the amounts are determined using a
calibration curve based on ratios of sample to internal standard. An alternative
method of generating ratios of amounts is to use either Internal Standard or
External Standard calibration types and choose Normalize Results in the
Integration Parameters window in the Data Handling section of the Method.
Choosing a Calibration Type
Your choice of which calibration type to use depends on your regulatory
requirements and sample workup techniques. If you can very accurately
measure your standard amounts, using an external standard calibration type is
the easiest. The Internal Standard calibration type accurately accounts for
variances in injection volume. You would also choose Internal Standard
calibration if you have varying loss during sample preparation. In this case you
would add a known amount of your Internal Standard compound before sample
preparation, and sample loss during preparation will be accounted for.

442

443
GC Data Handling Method
Command Reference
Integration Parameters

Peak Detection:
Item Description
Subtract Blank Baseline checked or not checked
If checked, subtracts the blank baseline in the Method
from each Data File. Used to account for predictable
changes in the baseline for each run, giving a relatively
flat baseline.
Initial S/N Ratio 1 to 256
Sets the initial signal-to-noise ratio for the Method. Used
to set the sensitivity of peak detection. This value is
overridden if you time program a Signal to Noise Ratio
event.
Initial Peakwidth 0.5 to 256
Represents an estimate of the peak width at half height
in seconds. Peak detection uses this with the S/N Ratio
to discriminate between peaks and noise. It
automatically updates the value if you do not program
peak width.

444
Item Description
Initial Tangent Height % 0 to 100
Sets the percentage of a mother peak's size below
which a given peak is considered a tangent peak. Used
to assign tangent peak status as a percentage of the
mother peak size. Can be used to force a peak to be
integrated as a tangent or as a fused peak. This value is
overridden if you time program a Tangent Height
Percentage event.
Monitor Noise:
Item Description
Monitor Noise Before Every Run, Once at Start of Method, Fixed Value
Sets times at which the Workstation monitors noise. The
workstation can monitor noise before each run, once at the
start of each Method, or use a user-specified value between
1 and 10,000 (units depend on detector type).
Peak Measurement:
Item Description
Measurement Type Area, Height, Square Root of Height

Sets the method used to measure the peaks.
Initial Peak Reject Value 0 to 1,000,000
Sets the minimum size peak to be identified. Used
to eliminate very small peaks from the report, to
ensure that insignificant peaks are not mistaken for
peaks of interest. This value is overridden if you
time program a Peak Reject value.
Peak Result Calculation:
Item Description
Report Unidentified Peaks checked or not checked
If checked, tells the Workstation to report all peaks,
whether identified or not.
Report Missing Peaks checked or not checked
If checked, tells the Workstation to report any peaks
in the peak table that were not found. Used to see
which peaks should have been found in the sample
but were not.
Normalize Results checked or not checked
If checked, results for each analyte will be expressed
as a percentage amount relative to the total amount
of all components of the sample. This checkbox is
enabled only for external standard and internal
standard calculations.

445
Peak Table

Item Description
Retention Time 0.001 to 1440.0
Sets the expected retention time of a peak. Specify a
retention time at which you expect a peak to elute.
Peak Name up to 40 characters
Assigns a name to a peak. Specify the compound name
or some form of identification for the analyte.
Ref checked or not checked
If checked, identifies a peak as a reference peak. Used to
account for shifting retention times.
Std checked or not checked

If checked, identifies an internal standard peak. Used to
mark which peak represents the internal standard in IS or
N% calculations.
RRT checked or not checked

If checked, identifies a peak as a relative retention time
peak.
Standard Peak Name Any standard peak
Combobox which allows you to select one of the internal
standards to use for this peak.
Amounts (levels 1 to
10)
0.000001 to 1,000,000
Sets the amount of the standard for each level. The
number of columns displayed depends on the number of
calibration levels specified in the Calibration Setup
window.
Add Adds a peak to the end of the peak table.
Insert Inserts a peak in the peak table above the active row.
Used to insert an entry into the peak table between
existing entries.
Delete Deletes the highlighted peaks from the peak table.
Fill Down Copies the contents of the top cell in a series of
highlighted cells to the cells below it. Used to edit all the
Sort Reorders the table in order of increasing retention time.

446
Item Description
Define Peak
Windows...
Opens the Define Peak Windows dialog box to set time
windows for reference peaks and other peaks or to set an
Unretained Peak Time.
Print Prints the contents of the current peak table.
Define Peak Windows Dialog Box
For both types of peaks, you set an absolute time window and a percentage time
window. The actual time window used will be equal to the absolute time plus the
percentage time.

Item Description
Define Reference
Peak Windows:
Width
0.00 to 200.0
Sets an absolute time that will be added to and subtracted
from the retention time of a reference peak to define a time
window.
Define Reference
Peak Windows:
Retention Time %
0 to 100
Sets a percentage of the retention time of a reference peak
that will be added to and subtracted from the retention time
to define a time window.
Define Other Peak
Windows: Width
0.00 to 200.0
Sets an absolute time that will be added to and subtracted
from the retention time of a non-reference peak to define a
time window.
Define Other Peak
Windows: Retention
Time %
0 to 100
Sets a percentage of the retention time of a non-reference
peak that will be added to and subtracted from the retention
time to define a time window.
Unretained Peak
Time (minutes)
0.00 to 1440.00
Sets the Unretained Peak Time (the amount of time taken
by an unretained compound to pass through the
chromatograph) for the Method. Used in RRT calculations.

447

Calibration Setup

Item Description
Calibration Type % (No Calibration), Internal Standard (IS), External
Standard (ES), Normalized % (N%)
Sets the calculation type for the Method. Determines
what calculations are performed for calibrations and
analyses.
Number of Calibration
Levels
1 to 10 levels
Sets the number of calibration levels you will be using.
Default Curve Origin Include, Ignore, Force
Sets the default treatment of the origin in each curve.
Choose to include, ignore, or force the curves through
the origin.
Default Curve Fit Linear, Quadratic, Cubic

Sets the default for how each calibration curve is fit.
Choose a linear, quadratic, or cubic equation for the
curves.
View Curves... Opens the Calibration Curve window. Used to view,
edit, print, or export the calibration curve.

448
Item Description
Weighted Regression None, 1/n, 1/nX, 1/X2, or 1/nX2
Sets the weighted regression scheme to be used in
determining calibration coefficients.
Replicate Treatment Keep Replicates Separate or Average Calibration
Replicates
Determines whether new replicates are kept separate
or whether they are averaged into an existing historical
value. When keeping replicates separate, there is a
limit of 10 replicates that can be stored. However, you
can indefinitely continue to average new replicates into
the historically maintained value.
Averaging Weight 0-100%
Sets the weight given to new calibration replicates
when averaging into the historical value.
Replicate Tolerance Always add new replicates, Never add new replicates,
Add replicates when within this tolerance (%)
Determines whether a new replicate should be added
to the calibration curve or whether it should be
ignored. Always add new replicates does no
verification of replicates -- they are always added.
Never add new replicates does not add the replicate
and is seldom used. Add replicates when within this
tolerance (%) only adds a replicate to the calibration
curve if within the tolerance specified. This tolerance is
applied the same way as is the Deviation Tolerance for
a Verification run.
Replicate Tolerance % 0 to 500%
Sets the replicate tolerance value.
Replicate Tolerance Out-
of-Tolerance Action
No Action, Increment Error Count, Terminate Sample
List, Halt Automation
Sets which action is taken when a replicate is of
tolerance. Either does nothing (No Action), adds 1 to
the error count (Increment Error Count), stops the run
and goes to the next SampleList (Terminate Sample
List), or halts automation (Halt Automation) each time
a replicate is out of tolerance.
Calibration Range
Tolerance %
0 to 500%
Sets the calibration range tolerance percentage for
which peaks outside the calibration range plus the
tolerance generate calibration range errors. Zero is
always used for the low end of the calibration range
check, even if the valid calibration range does not
extend to the y axis.
Calibration Range Out-of-
Tolerance Action
No Action, Increment Error Count, Terminate Sample
Sets which action is taken when a replicate is of
calibration range. Either does nothing (No Action),
adds 1 to the error count (Increment Error Count),
stops the run and goes to the next SampleList
(Terminate Sample List), or halts automation (Halt
Automation) each time a replicate is out of calibration
range.

449
Item Description
Edit/Lock Calibration
Data...
Opens the Coefficients window to edit calibration
coefficients for the Method.
Coefficients Table

Item Description
Retention Time Shows the retention time of each peak.
Peak Name Shows the name of each peak.
Lock Coeffs. checked or not checked
If checked, coefficients will not be updated on calibration
runs. Prevents specific calibration coefficients from
changing on subsequent calibration runs. Can be used to
manually enter calibration coefficients for peaks that will
not be identified in the calibration standard.
coefficients: X
3
, X
2,
X,
intercept
-100,000,000.0 to 1,000,000
Sets the coefficients that define the calibration curve for
each peak.

450
Calibration Curve Window

Item Description
Curve Type Shows the type of curve fit currently used. Indicates whether
the curve fit has been changed since the calibration (edited).
Origin Shows the origin treatment currently used. Indicates
whether the origin treatment has been changed since the
calibration (edited).
Equation
y = aX
3
+ b X
2
+ cX
+ d
Shows the equation of the calibration curve currently
displayed. Indicates whether the coefficients have been
changed since the calibration (edited).
Response Factor
RSD
Shows the Relative Standard Deviation of Response
Factors.
Corr. Coeff (R
2
) Shows the Correlation Coefficient for the calibration curve.
Print... Opens the This Report Only dialog box to print only the
current calibration curve.
Print All... Opens the Print All dialog box to print all the calibration
curves for the Method.
Export... Opens the This Report Only dialog box to export the current
calibration curve data to another application.
Overlay... Opens the Overlay dialog box to compare different fits and
origin treatments of calibration curves.
Point Info... Opens the Point Info dialog box to edit outliers from the
calibration curve and obtain information about individual
points.
Coefficients... Opens the Coefficients dialog box to edit the coefficients for
the calibration curve.
X <--> Y Opens the X <--> Y dialog box to use the curve to calculate
one coordinate from the other.

451
Item Description
Revert Undoes any changes to the curve since it was last saved.
Peak Name Any peak in the chromatogram

Selects a peak for which to view the calibration curve
Origin Include, Ignore, Force
Sets the treatment of the origin in the curve for the current
peak. Choose to include the origin, ignore it, or force the
curve through the origin.
Curve Fit Linear, Quadratic, Cubic

Sets how the calibration curve for the current peak is fit.
Choose a linear, quadratic, or cubic equation for the curve.
Curve Only checked or not checked
When checked, hides the header information at the top of
the curve display. Used to enlarge the curve display.
X, Y Cursor checked or not checked
Shows X and Y coordinates on the curve.
This Report Only Dialog Box

Item Description
Amount Units Up to 10 characters
Lets you label the units for the amount field of the
current calibration curve.
Show Outliers checked or not checked
If checked, outliers appear on the printed calibration
curve.

452
Print All Dialog Box

Item Description
Curves Per Page 1, 2, 3, or 4
Lets you set how many curves will be printed on each
page.
Lets you label the units for the amount field of the
calibration curves.
Show Outliers checked or not checked
If checked, outliers appear on the printed calibration
curves.
Overlay Window

Item Description
Origin Include, Ignore, Force

Sets the treatment of the origin for an alternate curve for the
selected peak.
Curve Fit Linear, Quadratic, Cubic

Sets the fit for an alternate curve for the selected peak.
Save 1 Saves overlay curve 1 as the curve for the peak.

453
Item Description
Save 2 Saves overlay curve 2 as the curve for the peak.
Point Info Dialog Box

Item Description
Exclude Selected Point from
Calculation
If checked, marks the selected point as an outlier,
excluding it from calibration calculations. Excluded
points are never lost, and can always be included
again at a later time.
Amount Shows the amount of the standard represented by
the selected data point.
Peak Size Shows the size of the peak represented by the
selected data point.
Deviation Shows, as a percentage, the deviation of the
selected data point from the curve. Used to see
how far off the selected point is from the result
expected from the curve.
Data File Shows the name of the Data File represented by
the selected point.
Level Specifies the level from which to select a point.
Replicate Specifies the replicate representing the point.
Select a point among those in the selected level.
Next Select the point at the next highest level on the
curve.
Previous Select the point at the next lowest level on the
curve.
Coefficients Dialog Box

Item Description
coefficients: X
3
, X
2,
X,
intercept
0.000000 to 1,000,000
Sets the coefficients for each peak.
Restore Restores coefficients to their last saved values.

454
Item Description
Overlay Shows what the calibration curve would look like
with changes to the coefficients by overlaying the
new curve on the current curve.
Save Saves the edited coefficients and closes the
Coefficients dialog box.
Cancel Closes the Coefficients dialog box without saving
the edited coefficients.
X <-> Y Dialog Box

Item Description
Amount (X) or Amt/Amt Std (X)
- depending on calculation type
0.000001 to 99,999,992
Before calculation, shows the amount you enter;
after calculation, shows a calculated amount.
Peak Size (Y) or PS/PS Std (Y)
- depending on calculation type
0.0 to 99,999,992
Before calculation, shows the peak size you
enter; after calculation, shows a calculated peak
size.
Calculate Begins the calculation.
Verification Setup

455
Item Description
Deviation Tolerance 0.0 to 500
Sets the percentage of deviation from the calibration
curve beyond which a result is considered out of
tolerance.
Out-of-Tolerance Action No Action, Increment Error Count, Terminate Sample
Sets which action is taken when results for a verification
run are out of tolerance. Either does nothing (No
Action), adds 1 to the error count (Increment Error
Count), stops the run and goes to the next SampleList
(Terminate Sample List), or halts automation (Halt
Automation) each time a verification fails.

Time Events Table

Item Description
Start 0 to 1440.0000
Sets the start time for the selected event.
Event WI, II, GR, VB, SR, FP, SP, HF, HB, HM, SN, TP, and PR.

Sets the event type to be added to the table. Choose to add
a width (WI), inhibit integrate (II), group (GR), solvent reject
(SR), valley baseline (VB) event, forced peak (FP), split
peak (SP), horizontal forward (HF), horizontal backward
(HB), horizontal minimum (HM), signal to noise ratio (SN),
tangent percentage (TP), or peak reject (PR) event.
Value/End Time Depends on event type
For II, GR, SR, VB, FP, HF, HB, and HM events, sets the
end time for the selected event. For WI, there are a discrete
set of values between .5 and 256 seconds. For SP, the
value is not applicable. For SN, the range is 1-256. For TP,
the range is 0-100%. For PR, the range is 0-1000000
counts.
Description Describes the legal values.
Add Adds the active parameters to the Time Events Table as a
new time event.
Insert Inserts a new row above the highlighted row.

456
Item Description
Delete Deletes the highlighted Time Events Table entry from the
table.
Sort Sorts the table in order of increasing start times.

Time Events
Event Description
Peak Width (WI) Changes the data bunching rate to allow for changing
peak widths during a run. If no WI events are
programmed, Data Handling will automatically adjust the
bunch rate as the peak widths increase or decrease. Any
time programming of peak widths prevents automatic
updating. Used to help reject noise spikes or to prevent
gradual baseline changes from being detected as peaks.
If a peak is being processed at the programmed time, the
event will not occur until a baseline segment is detected.
This bunching affects only how Data Handling views the
data; it does not have any effect on the raw data
bunching set in the Detector Information window for the
corresponding detector.
Inhibit Integrate (II) Suppresses integration of peak area or height. While II is
active, peak processing is disabled and no retention
times are displayed on the chromatogram or in the
results. In addition, any peak being processed at the start
of the II event will be aborted. Used to prevent integration
over a section of the chromatogram, sometimes to force
a baseline to be drawn. II disables peak sensing. In
contrast, SR is a post-run filter that rejects detected
peaks whose apices fall within the Solvent Reject
window.
Group Peaks (GR) Sums the areas of all peaks whose retention times fall
within the Group window. This causes all the peaks in
this window to be reported as a single peak with the
separation code GR and a retention time set to the
midpoint of the window. It is a post-integration function.
Used to treat all the peaks in a group as if they were a
single peak. The Peak Reject filter is applied after the
Group function, so that no peaks will be rejected from the
Group window because of size. A group peak is treated
like any other identified peak.
Solvent Reject (SR) Rejects all detected peaks whose apices fall within the
SR window. It is a post-integration filter. Used to exclude
peaks in a certain part of a chromatogram from the
report. Unlike the II event, SR can reject a mother peak
while retaining its tangent peak in the report.
Valley Baseline (VB) Forces peak baselines to be drawn through any valley
point that occurs during the VB window. It is a post-
integration function.

457
Event Description
Forced Peak (FP) Forces integration between the start and end times. A
resolved baseline is drawn from the amplitude of the
chromatogram at the start time and the amplitude of the
chromatogram at the end time. Any Inhibit Integrate
events that overlap with a Forced Peak event are
ignored. The peak apex is the highest point in the forced
peak time range.
Split Peak (SP) Splits one peak into two peaks. A line is drawn from the
chromatogram at the split point to the baseline to
separate the original and new peaks. A Split Peak event
can be used to split into two peaks a weak shoulder that
was not recognized as a separate peak by data handling.
If the Split Peak event falls on a baseline section of the
chromatogram, the event is ignored.
Horizontal Forward (HF),
Horizontal Backward
(HB), and Horizontal
Minimum (HM)
These events cause a baseline to be drawn horizontally
rather than the way it would have been drawn without the
event. It does not force a baseline to be drawn, it merely
changes the way it is drawn. For Horizontal Forward, the
baseline amplitude is at the amplitude of the first peak
start event, for Horizontal Backward, the baseline
amplitude is at the amplitude of the last peak end event,
and for Horizontal Minimum, the baseline amplitude is at
the lowest data point in the baseline time range.
Signal to Noise Ratio
(SN)
Used to set the sensitivity of peak detection. If a peak is
being processed at the programmed time, the event will
not occur until a baseline segment is detected. Time
programming Signal to Noise Ratio overrides the initial
value set in the Integration Parameters Window.
Tangent Percentage
(TP)
Sets the percentage of a mother peak's size below which
a given peak is considered a tangent peak. Used to
assign tangent peak status as a percentage of the
mother peak size. Can be used to force a peak to be
integrated as a tangent or as a fused peak. Time
programming Tangent Percentage overrides the initial
value set in the Integration Parameters Window.
Peak Reject (PR). Sets the minimum size peak to be identified. Used to
eliminate very small peaks from the report, to ensure that
insignificant peaks are not mistaken for peaks of interest.
Time programming Peak Reject overrides the initial value
set in the Integration Parameters Window.

458

459
GC Interactive Graphics Dialog
Boxes
Open Multiple Data Files Dialog Box
NOTE: to quickly open files (when the file list spreadsheet is empty), select them
from the explorer style file list and hit the OK button or the return key. You only
need to add files to the file list spreadsheet if you want to select a channel
different from the default channel.

460

Item Description
shows the folders and files in the selected location. You
can also double-click a folder or file in that box to add it to
the list of files to open. To open the folder one level higher,
Look In box to see the hierarchy of folders. To open the
folder one level higher, click the up arrow button on the
toolbar.
File Name Selects the file to be added to the list of files to be opened.
Files of Type Filters the files that you see in the File Name list box so
that only Data Files are displayed.
Recent Files Shows a menu listing up to eight data files that have been
recently opened. Selecting one from the menu adds it to
the list of files to be opened.
Add To List Adds the data file specified in the File Name item to the list
of files. Up to seven files may be added to the list.
Open Files Opens the files specified in the spreadsheet. If the
spreadsheet is empty, it first adds the files selected in the
explorer view to the list. Dismisses the dialog.
Cancel Closes the dialog and ignores any changes made to the
list.
File Name/Channel Table and related commands
The table section of the Open Multiple Data Files Dialog Box is used to assemble
the list of files to be opened. You add one or more files to the list by selecting
Data File(s) and hitting the Add To List button. Once in the list you can change
the color that is associated with the displayed chromatogram by moving the row
up or down.

Item Description
File Name Column Shows the name of the Data File.
Channel Column Lets you choose the channel for which to see data.
Channels with results have the word "RESULTS" next
to the channel label. When a new file is added to the
table, the last channel with results is automatically
selected.
Delete Results Deletes the results from the selected channel. Used to
remove results from a Data File. The recalculation
date and the date of the results deletion will be
permanently recorded in the Data File and included in
the results report.
Enabled by the Security Administration application.
Clear All Removes all items from the table.
Clear Removes the selected items from the table. The entire
row need not be selected for this button to be enabled.

461
Item Description
Up Moves the selected item up one row. If there is already
an entry in the row above, the two entries are
exchanged with each other. When moving an item in
the top row up, it gets moved to the bottom row.
Down Moves the selected item down one row. If there is
already an entry in the row below, the two entries are
exchanged with each other. When moving an item in
the bottom row down, it gets moved to the top row.
Colored Buttons Selects the corresponding row in the table.
Run Information
Item Description
File Shows the name of the Data File.
Chromatogram Display Shows a thumbnail view of the chromatogram. This has
similar zooming capabilities to the main Interactive
Graphics window: click and drag to zoom, click and hold
to PowerZoom, double click to zoom to full scale. Note
that this autoscales the chromatogram the same way as
does the Main Window as described in the Autoscaling
section.
Remember Scaling Check this item to keep the same scaling as you browse
through data files. If this item is unchecked, or if the
current data file is displayed in full scale, subsequent
data files will be displayed in their full scale
representation.
Unlabeled field below
remember Scaling (left)
Shows the module and address used to collect the data.
Unlabeled field below
remember Scaling (right)
Shows the time between run start and run end.
Sample Shows the name of the sample.
Inject Date Shows the date of the original run.
Run Mode Shows the sample type for the selected channel.
Instrument Shows the instrument used to calculate the current data.
Workstation Shows the name of the workstation used to collect the
data.
Channel Lets you choose the channel for which to see data.
Channels with results have the word "RESULTS" next to
the channel label. When a new file is added to the table,
the last channel with results is automatically selected.

462
Open Method File Dialog Box

Item Description
toolbar.

inside a folder, double-click it. You can also use the Look In box
to see the hierarchy of folders. To open the folder one level
higher, click the up arrow button on the toolbar.
Files of type Filters the files that you see in the File Name list box so that only
method Files are displayed.

463
Item Description
When you select a file from this list, its name is displayed in the
File name box.
Notes When checked, displays any notes and/or revision log
associated with the currently selected file.

Open Original/Recalc Dialog Boxes

Item Description
Use Check this box for the method you wish to open. If you
check a box for which the method file listed does not exist,
you are asked whether you would like to replace the listed
method file with another one.
Method File The method file you to open.
Run File The data file from which the method file name was obtained.
Channel The channel of the data file from which the method file name
was obtained.

464
Save Method As Dialog Box

Item Description
Save in Specifies the folder into which the method is to be saved. To
see how the current folder fits in the hierarchy on your
computer, click the down arrow. To see what's inside a folder,
click it. The box below shows the folders and files in the
selected location. You can also double-click a folder or file in
that box to overwrite the Method with that name. To open the
folder one level higher, click the up arrow button on the
toolbar.
Look In box to see the hierarchy of folders. To open the folder
File name Enter new file name for the method file to save.
Save as type Filters the files that you see in the File Name list box so that
only method Files are displayed. Also, indicates that files
entered without an extension automatically have .mth
appended.
Module Assigns a detector module to the Data Handling section of
the Method. Used to change the detector module to which the
Data Handling section is assigned.
Bus Address Assigns a bus address to the Data Handling section of the
Method. Used to change the bus address to which the Data
Handling section is assigned.
Channel ID Assigns a channel to the Data Handling section of the
Method. Used to change the channel to which the Data
Handling section is assigned.

465
Saturn Printer Setup Dialog Box

Item Description
Default Saturn Printer Shows the printer used by all Varian MS Workstation
applications for interactive printing.
Instrument Printers
(Instruments 1-4)
Shows the printers used during automated report
printing in System Control (one for each instrument).
Change... Opens the Print Setup dialog box. Allows you to
select a different printer or alter the hardware and
software settings for the printer.

Preferences Dialog Box
The Interactive Graphics preferences dialog box is divided into four functional
groups in a tabbed dialog. Select the Layout tab to show or hide a particular
component of the layout, such as the X axis. Select the Trace Settings tab to
affect changes to the Main Window (except for colors), such as whether to show
peak names or whether peak events should be drawn as triangles or lines. Use
the Offsets tab to control the amount of offset between chromatogram when
more than one data file is open and you have selected overlay mode. The Colors
tab allows you to configure the window background color and the trace colors.
Whenever you change one of the options listed below, Interactive Graphics
automatically redraws the screen to reflect the change you have made. The Use
Defaults button sets all of the options to their factory configured settings. Hit the
Cancel button if you want to exit the dialog aborting any changes made. The
display will be redrawn to reflect the settings in place before you opened the
dialog. Use the OK button to exit the dialog and accept any changes you made.

466
Layout Tab

Item Description
Show X Axis Show or hide the time axis.
Show Y Axis Show or hide the amplitude axis.
Show Horizontal Scroll Bar Show or hide the horizontal scroll bar.
Show Vertical Scroll Bar Show or hide the vertical scroll bar.
Show Attenuation Control Show or hide the attenuation control (to the right of
the main window).
Wide Attenuation Control When displayed, the attenuation control displays a
wedge indicating that as you move the slider up,
data is zoomed.
Show Tool Bar Show or hide the chromatogram toolbar.
Show Time Event Log Show or hide the Time Event Log Panel textual
descriptions at the actual times that the Data
Handling time events occurred. Holding the mouse
over an event marker shows a tool tip with
information about one of the thirteen types of Data
Handling events: Width (WI), Inhibit Integration (II),
Grouped Peak (GR), Valley Baseline (VB), Solvent
Reject (SR), Forced Peak (FP) , Split Peak (SP),
Horizontal Forwards (HF), Horizontal Backwards
(HB), Horizontal Minimum (HM), Signal to Noise
Ratio (SN), Tangent Percentage (TP), and Peak
Reject (PR).
Show Visual Method Editing
Panel
Show or hide the Visual Method Edit Panel (below
the x-axis). Use the Visual Method Edit Panel to
define a Peak Table and a Time Events Table using
visual programming and to visually compare the
location of programmed time events versus the
actual time the Data Handling time events occurred.

467
Item Description
Show Offset Perspective Displays perspective lines when more than one
Data File is open in overlay mode and both the time
and amplitude offsets are greater than zero. These
perspective lines are a visual aid to help you see
the amount of the offset, and for lining up points at
the same time on different chromatograms. If the
time offset is too great or the amplitude offset too
small, the perspective lines are automatically
removed.
Locked Zooming (Tile Mode) Lock Zoom (tiled mode): when depressed, locks the
amplitude scaling so that changing the amplitude
scaling in one chromatogram causes all other
chromatograms to also display the same amplitude
range. When not depressed, the amplitude range of
the individual chromatograms may differ.
Layout Mode Tile Chromatograms: displays chromatograms one
above each other with each chromatogram in it own
non-overlapping section in the main window. In tiled
mode, the time axis for all chromatograms is always
the same.
Overlay Chromatograms: displays chromatograms
on top of each other so that portions of each
chromatogram overlap ones that are visually behind
them. In this mode, each trace may be offset from
others (as specified in the Offsets tab of the
Preferences dialog) to provide a 3-D view of the
data.
Trace Settings Tab

Item Description
Show Peak Retention Times When checked, displays peak retention times in the
Main Window for all reported peaks, so even
unidentified peak retention times will be displayed.

468
Item Description
Show Peak Names When checked, displays peak names in the Main
Window for all reported peaks, so even unidentified
peak names will be displayed.
Show Integration Baselines When checked, displays the peak baselines and
lines that drop from valleys to the baseline. If the
Data File has never been reintegrated or if results
have been deleted, then the Data File doesnt
contain baseline information, and this option will
have no effect.
Show Cursor/Peak
Information
Turns the cursor on or off. The cursor follows the
active trace and displays the time and amplitude of it
current position in an info-panel. As you move it
near a peak event, it jumps to the peak event and
sticks to it. If the peak event represents a reported
peak apex, then the info-panel also displays
information such as the peak name, area, and width.
Hold the shift key down to disable the stickiness
feature so that the cursor follows the trace smoothly
and is not affected by peak events. Hold the control
key down to allow the cursor to move anywhere on
Show Run File Information When checked, shows the Run File info-panel which
has information about the active data file.
Show Blank Baseline When checked, displays the blank baseline, if any.
Regardless of whether the blank baseline is
displayed, the chromatogram trace is offset by the
blank baseline data specified by the Preview Blank
Baseline Subtraction (below).
Preview Blank Baseline
Subtraction
When checked, uses the blank baseline data from
the active Method. When unchecked (the default),
uses the blank baseline data from the data file as it
was used for the most recent recalculation. The
blank baseline data is used both for blank baseline
display and to offset the chromatogram trace (see
above). In many cases, there may be no blank
baseline data present in either the method or the
data file, in which case no blank baseline is
displayed and the chromatogram trace is not
adjusted.
When checked and there is blank baseline data in
the method, this lets you visualize the effect of
subtracting a particular blank baseline from a
chromatogram trace without first needing to
recalculate with the blank baseline. Also, in this
mode you can modify individual blank baseline
points.
Plot Type Line Plot: plots chromatograms as a continuous line.
Outline Plot: plots chromatograms as a continuous
line and individual points are outlined with a
rectangle.
Point Plot: plots chromatograms as a series of
points. In point plots, each point represents a single
data point in the raw Data File. Zooming the display
in point or outline mode lets you see individual data
points.

469
Item Description
NOTE: all data points may not be drawn when
zoomed to full or large scale. That is because the
data is reduced at large scales so that only important
data is displayed. This is especially apparent when
the data has been oversampled. Also, when the
trace goes off the screen, additional points may be
drawn at the edge of the window that are not actual
data points, but represent an interpolated point
between the point in the window and the next one
just outside of the window.
Show/Hide Peak Events Show All Events: all traces have peak events drawn.
Peak events for the active chromatogram may be
drawn as a line or triangle (see Active Peak Event
Shape below). The non-active chromatograms
always have their peak events shown as a line.
Show Active Events: only the active trace has peak
events drawn as a line or triangle (see Active Peak
Event Shape below).
Hide All Events: no traces have any peak events
shown.
Active Peak Event Shape Displays the peak events for the active
chromatogram as either a line or a triangle. You can
only move peak events for the active trace, and only
when its peak event shape is a triangle.
Offsets Tab

Item Description
Offset type: Determines whether the number in the Offset by field is
an absolute value or a percentage of the screen height
or width.

470
Item Description
Offset by If more than one chromatogram is open, enter the
amount of vertical or horizontal spacing between
chromatograms. The offset has no effect when only one
chromatogram is open. Note that when entering an
offset by amplitude or time value, the offset at one zoom
level may be too large or small at another zoom level.
Preset Percentage
Offsets
These buttons allow you to quickly change between a
few preset values. These switch the offset type to
Percentage and automatically enter the values indicated
in the Offset by field.
Colors Tab

Item Description
Data File 1 7 These buttons indicate the colors of the seven data
files you can open in Interactive Graphics. Click on a
button to bring up the standard Windows Color dialog
for selecting a color for the trace.
Window Background Select the color for the Main Window background.
Click on a button to bring up the standard Windows
Color dialog so that you can select a new background
color for the window. With a dark background color,
Interactive Graphics automatically chooses white as
the color for axes, info-panels, etc. text. With a light
background color, the text color is automatically set to
black.
Display Faded
Background
When checked, the selected color fades to a lighter
color from the bottom to the top of the window. When
solid black or white is selected, the fading does not
occur.
Themes combo-box Select from one of the color themes to change all of
the color settings at once.

471
Item Description
Save As Saves the current color selection. This opens a dialog
box into which you enter the name of the theme to
save. This saves the colors for the seven data files,
the window background color, and whether the
background color is faded.
Delete Deletes the current theme.

Reintegration List Dialog Box
NOTE: Post-run reporting actions specified in the active Method (such as ASCII
File Conversion) are not done when you perform a recalculation from Interactive
Graphics.

Item Description
Colored buttons Selects the corresponding active row in the table.
Run DH Marks which files will be recalculated. Files without a
check mark will not be recalculated.
File Shows the name of the Data File
Sample Name Up to 19 characters
Shows the sample name for a Data File. This field may
not be edited.
Sample Type Blank Baseline, Analysis, Calibration, Verification
Sets the sample type for a Data File, to establish how
each Data File should be treated during recalculation.
Cal. Level 1-10
Sets the calibration level of a calibration or verification
Data File.
Internal Standard Button which opens the Internal Standard Amounts
Dialog Box to set the amounts of one or more internal
standards. Used to calculate results for internal
standard and normalized percent calculations.

472
Item Description
Unidentified Peak Factor 0.00001 to 999999
Sets a calibration factor for unidentified peaks. Used to
calculate results for unidentified peaks.
Multiplier 0.00001 to 999999
Sets a value for the multiplier. Results for the sample
are multiplied by the value.
Divisor 0.00001 to 999999
divided by the value.
Recalc Notes Button which opens the Recalc Notes Dialog. Notes
entered in this dialog can be displayed by the Report
application by selecting the Notes option in the Results
Format portion of the Report section of the Method.
Incorporate New
Calibrations into Data Set/
Clear Coefficients at Start
of List
If Incorporate New Calibrations is chosen, keeps
existing coefficients and adds new data to them. If Clear
Coefficients is chosen, zeroes all coefficients in the
Method
Save Changes Save changes made and dismiss the dialog.
Calculate Results Saves changes made and starts the recalculation.

Internal Standard Amounts Dialog Box

Item Description
Name of Internal Standard Lists the names of the internal standards. You can
get a copy of this list from the peak table using the
Update List button (see below), but you may not
edit these. Use the Peak Table Dialog Box to edit
these names.
Amount Standard Edit these values to change the amount of internal
standard.

473
Item Description
Update List
or
Update Amounts
Copies the current list of internal standards and
their amounts from the peak table to the table
described above. After copying the list, the button
changes to Update Amounts. This allows you to
recopy just the amounts from the Peak Table after
modifying them.
Cancel Dismisses the dialog box without saving any
changes.
Save Changes Dismisses the dialog box and saves any changes
made.

Fill Peak Table Window
The Fill Peak Table option opens a smaller version of the Peak Table window. It
allows you to fill the table quickly with the peaks in the active chromatogram. In
this mode the cursor is automatically displayed and locks on to the nearest peak
apex. Clicking adds a new peak table entry. If you check the Fill table from
selection checkbox in the Fill Peak Table Window, then all of the peaks in the
region you select are added to the peak table. After peaks have been added to
the table, you can either edit their parameters in this window or in the full Peak
Table window.

Item Description
Retention Time

0.001 to 1440.0
Displays the retention time of the peak that was
clicked on.
Peak Name up to 40 characters
Assigns a name to a peak.
Ref If checked, identifies a peak as a reference peak.
Std If checked, identifies an internal standard peak in IS or
N% calculations.
RRT If checked, identifies a relative retention time peak.
Standard Peak Name List of all peaks marked as an internal standard
Allows selection of the peak that will be used as the
internal standard for this peak.

474
Item Description
Group Any integer
Allows you to assign an arbitrary group number to a
peak. A report can be generated organized by
number.
Amounts (levels 1 to 10) 1e-6 to 1,000,000
Sets the amount of the standard for each of the
calibration mixtures, level by level.
Add Adds a peak to the peak table as a new entry.
Insert Inserts peak in the peak table above the active row.
Delete Deletes the highlighted peaks from the peak table.
Sort Sorts the rows by retention time.
Fill table from selection Sets the mode so that all of the peaks in the region
you select are added to the peak table as opposed to
just the individual peak on which you click.

Exact View Dialog Box

Item Description
Start Time (Minutes) Sets the time at which the plot will start.
End Time (Minutes) Sets the time at which the plot will end.
Low Amplitude Sets the lowest amplitude that will appear on the plot.
Enter this in the units as currently displayed by the y-
axis.
High Amplitude Sets the highest amplitude that will appear on the
plot. Enter this in the units as currently displayed by
the y-axis.

475
GC Interactive Graphics Menus
File Menu
Add/Remove
Chromatogram
Opens the Open Multiple Data Files dialog box to select a
list of up to seven data files and view their
chromatograms; all currently open chromatograms are
replaced with chromatograms selected in the dialog.
New Method Opens a new Untitled Method to edit; closes any
previously open Method.
Open Method Opens the Open Method dialog box to open an existing
Method file to edit; closes any previously open Method.
Open Original Method

Opens the Open Original Method dialog box to open for
editing the Method used with the original injection; closes
any previously open Method.
Open Recalc Method

Opens the Open Recalc Method dialog box to open for
editing the Method used with the most recent
recalculation; closes any previously open Method.
Build Method from
Datafile
Extracts the data handling method used for the most
recent recalculation which is stored in the data file. You
will be prompted to save the method file with the default
name DatafileName-Channel.mth. Closes any previously
open Method.
Save Method Saves the Method with all changes to Data Handling
sections. You can use this Method for future runs or
recalculations.
Save Method As Opens the Save Method As dialog box to save a
Method under a new name.
Print Prints the Main Window as viewed on the screen except
that the background is drawn white. When printing to a
monochrome printer, any colors on the screen are drawn
black instead. Opens the standard Windows print dialog
allowing you to select the printer and number of copies to
print. When the dialog is first opened, the Default Saturn
Printer is selected.
Print Method Prints the Data Handling section of the Method.
Print Preview Opens the Print Preview Window, which displays the
Chromatogram as it will be printed. In some cases there
are minor layout differences between the main window
display and the printed output. In particular, colors will be
modified as described in the Print menu item above.
From the Print Preview Window, you can print the window
and zoom in to examine details.

476
Print Setup Opens the Saturn Printer Setup dialog box to set
preferences for printing. You can open the Print Setup
dialog box from the Saturn Printer Setup dialog box.
Exit Closes Interactive Graphics.

Edit Menu

Undo Undo is not available.
Cut Cut is not available.
Copy Copies the main window as a Picture (Windows enhanced
metafile format) to the clipboard. This Picture can be
resized and the contents will stretch to fit the new frame.
This copies a picture with a white background. Any white
traces are drawn black; other colors are preserved.
Copy Bitmap Copies a Bitmap to the clipboard. The bitmap is the size
of the main window and cannot be resized. In addition to
the main window, this also includes the chromatogram
toolbar, the attenuation control, and the Visual Method
Edit Window if these are shown. This copies the screen
exactly as drawn without changing background or trace
colors.
Copy Picture to Disk The same as Copy (above) except that it copies a Picture
(placeable enhanced metafile format) to a disk file, rather
than to the clipboard.
Paste Paste is not available.
Delete Deletes any time events or peak events selected in the
Visual Method Edit Window.

View Menu

Locator Window Shows or hides the locator window. This window displays
a full scale version of the active chromatogram. When you
select a region in this window, it zooms the main window
instead. The active chromatogram is either the top most
trace in overlay mode, or the bottom most trace in tile
mode.
Method Quick Link
Button
Shows or hides the Method Quick Link Toolbar containing
the Method Quick Link Button. The Method Quick Link
button lets you view or print the method file currently open
in Interactive Graphics.

477
Main Toolbar Shows or hides the main application tool bar, which
contains buttons such as the Add/Remove Chromatogram
button, the Print button, and the reintegration buttons.
Status Bar Shows or hides the Status bar at the bottom of the
Interactive Graphics window.
Visual Method Edit
Window
Shows or hides the a window beneath the x-axis that you
use to interactively edit the peak table and the time events
table.
Chromatogram Toolbar Shows or hides the tool bar associated with the
chromatogram, which contains buttons such as the Full
Scale Button, the Cursor Display Button, and the Tile and
Overlay Buttons.
Attenuation Control Shows or hides the Attenuation Control to the right of the
main window. This allows you to scale the amplitude of the
displayed trace(s).
Preferences Displays the Preferences dialog box to configure settings
for how chromatograms are displayed in Interactive
Graphics.

Results Menu

Reintegration List Opens the Reintegration List dialog box to recalculate
results for one or more Data Files. This lets you enter
sample related information: whether to run data handling
at all for a data file; whether its an analysis, calibration,
baseline, or verification run; recalc notes; etc.
Reintegrate Now Uses the settings in the Reintegration List to perform a
recalculation on the open chromatograms. Used to
recalculate results for one or more Data Files without
opening the Reintegration List dialog box.
Reintegrate Now/Clear
Moved Events
Same as Reintegrate Now, except that any user defined
peak start and end points are reset before reintegrating.
Autosave method
before Reintegration
When checked, any changes to the method are saved
before reintegrating without prompting. When unchecked,
you are prompted whether to save any changes to the
method before reintegrating. If the method is a memory
based method (like a new Untitled method), then you are
always prompted to save the method regardless of the
setting.
View Calibration
Curves
Opens the Curve Manager window to view calibration
curves for the current Method.
Data File
Name/Channel
Displays the Quick Link menu for each open Data File.
This is equivalent to Data File Operations Quick Link
Button on the MS Workstation Toolbar.

478
Edit Method Menu

Set Password Opens the Add Password Dialog Box which allows you
to add or change the password for a method file.
Method Notes Opens the Method Notes window to edit notes for the
Method

Opens the Integration Parameters Dialog Box to edit
the integration parameters for a Method.
Peak Table Opens the Peak Table Dialog Box to edit the peak table
for a Method.
Time Events Opens the Time Events Table Dialog Box to edit the
time events for a Method.
Calibration Setup Opens the Calibration Setup Dialog Box to specify
calibration parameters.
Verification Setup Opens the Verification Setup Dialog Box to specify
verification parameters.
Fill Peak Table Opens the Fill Peak Table window to fill the peak table
quickly.
Add Method Item Contains a submenu which allows you to add a Peak
Table Entry or one of the 13 Time Events to the Visual
Method Edit Window. A better way to add Peak Table
Entry or a Time Event is to click with the right mouse
button in an empty section of the window. This will bring
up the same menu, with the advantage that the event is
placed at the location of the right mouse click.
Select All Method Items Selects all the Peak Table Entries and Time Events in
the Visual Method Edit Window.
Delete Selected Method
Items
Deletes all selected Peak Table Entries and Time
Events in the Visual Method Edit Window.

479
Help Menu
Product Support Web
Site
If you have Internet access and a web browser installed
on your computer, this option will automatically open
the Varian MS Workstation Product Support Web Site.
Here you will find the latest software and
documentation updates for the Varian MS Workstation
suite of products, along with additional notes, tips, and
answers to frequently asked questions.
About Interactive
Graphics
Displays the About Box for the Interactive Graphics
application. The About Box contains information about
the software version, installation information, and a list
of the instrument control modules that you have
installed.

480

481
GC Interactive Graphics Toolbars
Toolbar Overview
There are two toolbars on the main window: the Main Toolbar and the Method
QuickLink Toolbar. These can each be dragged with the left mouse button to a
docked or undocked location. The third toolbar is the Chromatogram Toolbar. It
may not be dragged or undocked, however, it can be scrolled out of view by
clicking on the green minimizer button.
Each toolbar can be hidden or closed. If the toolbar is hidden, it may be
displayed by selecting the appropriate menu item from the View menu of
Interactive Graphics.
Main Toolbar

Opens the Open Multiple Data Files dialog box to select a list of up
to seven data files and view their chromatograms; all currently open
chromatograms are replaced with chromatograms selected in the
dialog.

Copies the main window as a Picture (Windows enhanced metafile
format) to the clipboard. This Picture can be resized and the
contents will stretch to fit the new frame. This copies picture with a
white background. Any white traces are drawn black; the other colors
are preserved.

Prints the Main Window as viewed on the screen except that the
background is drawn white. When printing to a monochrome printer,
any colors on the screen are drawn black instead. Opens the
standard Windows print dialog allowing you to select the printer and
number of copies to print. When the dialog is first opened, the
Default Saturn Printer is selected.

Displays the help you are now viewing.

Reintegration List: opens the Reintegration List dialog box to
recalculate results for one or more Data Files. This lets you enter
sample related information: whether to run data handling at all for a
data file; whether its an analysis, calibration, baseline, or verification
run; recalc notes; etc.

Reintegrate Now: uses the settings in the Reintegration List to
perform a recalculation on the open chromatograms. Used to
recalculate results for one or more Data Files without opening the
Reintegration List dialog box.

482

Reintegrate Now/Clear Moved Events: same as Reintegrate Now,
except that any user defined peak start and end points are reset
before reintegrating.

View Preferences: displays the Preferences dialog box to configure
settings for how chromatograms are displayed in Interactive
Graphics.

View Locator Window: shows or hides the locator window. This
window displays a full scale version of the active chromatogram.
When you select a region in this window, it zooms the main window
instead. The active chromatogram is either the top most trace in
overlay mode, or the bottom most trace in tile mode.

Method Quick Link Toolbar

This button lets you view or print the
method file currently open in
Interactive Graphics.

Chromatogram Toolbar

Shows or hides the toolbar.

Full Scale: zooms all traces to their full scale values. This button is
the same as double clicking in the main window.

Vertical Full Scale: in overlay mode zooms the amplitude range
such that all traces are visible in the given time range. In tile mode
the active (bottom) chromatogram is zoomed such that all of the
trace is visible within the given time range. If zooming is locked,
then the other chromatograms are zoomed to the same vertical
scaling as the active chromatogram. If zooming is not locked, then
only the bottom chromatogram is affected. This command only
affects the displayed amplitude range, the time range is unaffected.
This button is the same as double clicking in the Y axis of the main
window.

Horizontal Full Scale: in overlay mode, zooms such that the entire
time range is visible for all chromatograms. In tile mode, the active
(bottom) chromatogram is zoomed such that the entire time range
is visible. The other chromatograms are zoomed to the same time
range as the active chromatogram. This command only affects the
displayed time range, the amplitude range is unaffected. This
button is the same as double clicking in the X axis of the main
window.

483

Previous Scaling: zooms to the previous time and amplitude range.
Each time you scale chromatogram(s), Interactive Graphics adds
the new scaling rectangle to the end of a list of scaling rectangles.
Previous scaling zooms the display to the value stored in the
previous position on the list. This item is disabled when at the start
of the list.

Next Scaling: zooms to the next time and amplitude range. Each
time you scale chromatogram(s), Interactive Graphics adds the
new scaling rectangle to the end of a list of scaling rectangles. Next
scaling zooms the display to the value stored in the next position
on the list. Since new scaling rectangles are added to the end of
the list, it implies that Next Scaling is only available when you had
formerly hit the Previous Scaling button. That is, this item is
disabled when at the end of the list.

Exact View: opens the Exact View dialog which lets you specify the
time and amplitude ranges numerically.

Cursor Display: turns the cursor on or off. The cursor follows the
active trace and displays the time and amplitude of it current
position in an info-panel. As you move it near a peak event, it
jumps to the peak event and sticks to it. If the peak event
represents a reported peak apex, then the info-panel also
displays information such as the peak name, area, and width.
Hold the shift key down to disable the stickiness feature so that
the cursor follows the trace smoothly and is not affected by peak
events.
Hold the control key down to allow the cursor to move anywhere on

Select Background Color: opens the standard Windows Color
dialog so that you can select a new background color for the
window. With a dark background color, Interactive Graphics
automatically chooses white as the color for axes, info-panel, etc.
text. With a light background color, the text color is automatically
set to black. Select Display Faded Background so that the
selected color fades to a lighter color from the bottom to the top of
the window. When solid black or white is selected, the fading does
not occur.

Tile Chromatograms: displays chromatograms one above each
other with each chromatogram in its own non-overlapping section
in the main window. In tiled mode, the time axis for all
chromatograms is always the same.

Overlay Chromatograms: displays chromatograms on top of each
other so that portions of each chromatogram overlap ones that are
visually behind them. In this mode, each trace may be offset from
others (as specified in the offsets tab of the preferences dialog) to
provide a 3-D view of the data.

Lock Zoom (tiled mode): when depressed, locks the amplitude
scaling so that changing the amplitude scaling in one
chromatogram causes all other chromatograms to also display the
same amplitude range. When not depressed, the amplitude range
of the individual chromatograms may differ.

Fill Peak Mode: opens the Fill Peak Table Window which allows
you to quickly build a peak table using peaks from the current
chromatogram. In this mode the cursor is automatically displayed
and locks on to the nearest peak apex. Clicking adds a new peak
table entry. If you check the Fill table from selection checkbox in
the Fill Peak Table Window, then all of the peaks in the region you
select are added to the peak table.

484

485
GC Interactive Graphics Window
Locator Window
Use the Locator Window to view the entire active chromatogram and to select a
section of the chromatogram to view in greater detail in the Main Interactive
Graphics Window. The active chromatogram is either the top most
chromatogram in overlay mode, or the bottom most trace in tile mode.
The Locator Window is a window that floats above the main Interactive Graphics
window. Interactive Graphics draws a full scale version of the active
chromatogram in this window. As implied by the name, you can use this window
to quickly locate and zoom to a particular part of the chromatogram by dragging
the mouse to create a rectangular selection. This section of the chromatogram is
then expanded to fill the entire Main Window. Selecting a section in the Locator
Window to view may be faster than scrolling in the Main Window. The section of
the chromatogram displayed in the Main Window is indicated by an inverted
background in the Locator Window.
An info-panel display lists the currently displayed data file name in the Locator
Window along with the channel and last recalc data.

The following mouse actions are possible for the Locator Window:

Left mouse button click and drag a
selection.
Expands selected section of chromatogram to
fill the entire Main Window.
Left mouse button double click. Expands the Main Window to display the entire
active chromatogram

486
Main Window
Use the Main Window to view and manipulate between one and seven
chromatograms. This is the main window you use when working with Interactive
Graphics.

The Main Window occupies the center of the Interactive Graphics window. The
following other panels may optionally be displayed around the periphery of the
Main Window:

Panel Location
Relative to Main
Window
Purpose
Amplitude Axis Panel To Left Y-axis display, vertical
zooming
Time Axis Panel Below X-axis display, horizontal
zooming
Visual Method Edit Panel Below Time Axis Interactive peak table entry
and time event table editing.
Time Events Log Panel Above Display log of time events and
the time that they actually
occurred.
Chromatogram Toolbar
Panel
Above Time Events
Log
Quick access to often used
functions.
Attenuation Control Panel To Right Adjust amplitude range using
logarithmic scaling.
Active Chromatogram
When in overlay mode, the Main Window always displays one active
chromatogram, and may also show up to six more inactive chromatograms. The
active chromatogram is the front-most chromatogram and is the only
chromatogram for which you can:
1. Modify the baseline by moving a peak start/end event to a new location.

487
2. Show a cursor and its associated info-panel containing the time and
amplitude of the cursor and peak information.
3. Display baselines and droplines.
4. Display peak names and retention times.
5. Show the Time Events that were performed by data handling.
6. Display a blank baseline.
7. Display peak events in the shape of a triangle.
8. Display the run file info-panel.
9. Use the scaling buttons from the Chromatogram Toolbar: Full Scale, Vertical
Full Scale, Horizontal Full Scale, Previous Scaling, Next Scaling, and Exact
View.
You can make an inactive chromatogram the active one, by clicking directly on
the chromatogram in the Main Window with the right mouse button and select the
Move to Front menu item from the menu displayed.
When in tile mode, all chromatograms are considered active, however, the
Chromatogram Toolbar buttons only apply to the chromatogram at the bottom.
Opening Data Files
Use the Open Multiple Data Files dialog box to provide a list of which Data Files
will be displayed in the Main Window. You can also use this dialog box to change
the order of already open chromatogram(s) which also has the affect of
displaying the trace in a different color.
Zooming and Scrolling
The primary purpose of the Main Window is to allow you to inspect sections of
the chromatogram and review the placement of peak events as determined by
data handling. To do this you may want view a part of the chromatogram in high
detail. You do this by zooming, that is, selecting a rectangular section of the
chromatogram by dragging the mouse in the Main Window. When you release
the mouse, the chromatogram is redrawn so that the selected area fills the entire
Main Window. You can zoom similarly by selecting a chromatogram section in
the Locator Window. By repeatedly selecting rectangles in the Main Window, you
view the chromatogram ever finer detail. Interactive Graphics will not allow
further zooming if the amplitude range would become less than 0.0001 and the
time range would become less than 0.05 minutes. Double clicking in the Main
Window displays the chromatograms at their full scale zoom levels.
PowerZooming is an alternative way of zooming. You PowerZoom by clicking
and holding the left mouse button down without moving it. This zooms in on that
point isometrically, or, if your are holding the control key down, zooms out from
that point. Once PowerZooming begins, you can move the mouse around while
the mouse button is still down to change the point at which you are zooming.
You can view other sections of the chromatogram while maintaining the same
zoom level by scrolling. Scroll bars are shown only if the time or amplitude range
of your zoomed view is less than the maximum time or amplitude range of the
chromatograms as determined by autoscaling. Scrolling horizontally lets you see
sections of the chromatogram earlier or later than the current section. Scrolling
vertically lets you see sections of higher or lower amplitude.

488
You can scale vertically using the Attenuation Control to the right of the Main
Window. This adjusts the amplitude range on a logarithmic scale. When using
the attenuation control, the lowest point of the active trace is fixed, and the
amplitude range is adjusted to a smaller range as you slide the position indicator
up and to a larger range as you slide it down.
You can zoom in the amplitude and time axes in the same way as you do in the
Main Window. You can select a rectangular section of the axis, PowerZoom, and
double click in the axis. These actions zoom just like they would in the Main
Window, except that only the amplitude scaling is affected when zooming in the
amplitude axis and only the time scaling is affected when zooming in the time
axis.
Autoscaling
Interactive Graphics automatically determines the maximum and minimum
values in the chromatogram. In determining these values, it ignores any
chromatogram sections during which an Inhibit Integrate (II) or a Solvent Reject
(SR) time event is in effect. It uses these values when displaying a
chromatogram at full scale. So when you double click in the Locator Window to
expand the Main Window to display the entire active chromatogram, the
chromatogram is displayed so that the minimum and maximum amplitudes are at
the bottom and top of the window.
Moving Baselines
You can modify baselines and droplines by clicking on a peak start/end event for
the active chromatogram and dragging it to a new location. Notice that as you
drag a peak event, the Main Window Information Panel will display the type of
event being moved, and will constantly update the time and amplitude of the new
peak event location. You must reintegrate to view the effects of the moved peak
events on the results. Peak information for affected peaks will not be available
once a peak event is moved.
NOTE: You can only modify baselines when the peak event shape is a triangle.
Moving baseline points is disabled when the peak event shape is a line, or when
peak events are not shown.
All events can be moved other than peak apices or events generated by the use
of a Forced Peak (FP) and Split Peak (SP) time events. An easy visual way to
determine if a peak event can be moved is to slowly move the mouse over a
peak event. If the peak event can be moved, the mouse cursor will change from
the cross cursor to the arrow cursor, otherwise, the cursor looks like: In
either case, a tool tip window is displayed showing the time, amplitude, and type
of peak event.
A peak event can be moved to within one tenth of one data point in time of an
adjacent peak event. By default, a peak event can only be moved so that it
touches the chromatogram trace. Hold the control key down while dragging the
peak event to move it away from the chromatogram trace. Peak events are
drawn as solid triangles or thick lines when moved as opposed to hollow
triangles or thin lines when in the original position determined by data handling.
To reset a peak event to the original position determined by data handling, click
on the event with the right mouse button and select the Reset to Original Position
menu item displayed. To reset all moved peak events to their original position,
select Reintegrate Now/Clear Moved Events from the Results menu.

489
When a peak event has been moved manually, peaks whose areas are affected
by the moved event are marked in the report with a U, designating a user
defined endpoint.
Viewing Options and Mouse Operations
You can customize the appearance of the Main Window with many options that
you can set using the View Menu Commands and the Preferences dialog box.
The following mouse actions are possible for the Main Window:

Left mouse button click and drag
a selection.
Expands selected section of chromatogram to
fill the entire Main Window.
Left mouse button double click. Zooms to full scale.
Left mouse click and hold Zooms isometrically from the mouse position
Left mouse button click on a
peak event and drag to a new
location.
Moves the peak event to a new location to
change the position of baselines and droplines.
You must reintegrate to view the affects of the
moved event on the results.
Right mouse click on a
chromatogram trace.
Brings up a context sensitive menu with actions
to be taken for the selected chromatogram. The
menu will vary depending on your installation.
However, Remove, Move to Front, and Show
Run File Info are always present.
Right mouse click on a peak
event.
Brings up a context sensitive menu with the
action to be taken for the selected peak event.
Select the menu choice to reset a moved peak
event to its original position.
Info-Panels

Info-panels are rectangular panels that are drawn in the Main Window. There are
several of these panels containing information. Some, like the peak counter in Fill
table from selection mode, appear only while a particular operation is taking
place. Others, like the run file info-panel, are shown or hidden depending on a
preference setting.
When you move the mouse over an info-panel, the hand cursor is shown
indicating that the info-panel can be moved by dragging it to a new location. Info-
panels retain their position relative to the nearest corner of the Main Window, so
that when the Interactive Graphics window is temporarily sized to be small and
then the size is restored, the original info-panel position is retained.
You can configure the information shown in an info-panel by right clicking on the
info-panel and checking or unchecking items from the menu that is presented.

490
Neither the position of an info-panel, nor the configured list of items are retained
when the data file is closed and then reopened. These are reset to default values
when the data file is reopened.
Cursor Info-Panel

When the cursor display is enabled, the cursor info-panel is automatically also
displayed. The contents of this info-panel varies depending on the location of the
cursor. Usually, it displays only the time and amplitude of the cursor location.
When the cursor is at a peak apex, the info-panel also shows peak apex
information, such as the name and its area (see below). When moving a peak
event it shows the peak event type as well as the time and amplitude of the peak
event position. The peak event info-panel is automatically shown while you are
dragging a peak event even when the cursor display is disabled.
NOTE: to show the cursor, select the ViewPreferences menu item, then select
the Trace Settings Tab and check the Show Cursor/Peak Information checkbox.
Alternatively, click on the Cursor Display button on the Chromatogram Toolbar.
Item Description
Time The time of the cursor location.
Amplitude The amplitude of the cursor location.
Name The name of the peak.
Result or
Rsp. Ratio
The calculated results for the peak. For a calibrated peak,
this will show the response ratio instead of the results.
Area, Height, or
Sq. Root Height
The area, height, or square root of height for the peak,
depending on the Peak Measurement type selected in the
Integration Parameters Data Handling Method section.
Width The peak width at half height in seconds.
Type The type of peak event being moved.
Run File Info-Panel

The Run File info-panel shows information about the active data file.
NOTE: to show the Run File information, select the ViewPreferences menu
item, then select the Trace Settings Tab and check the Show Run File
Information checkbox. Alternatively, right click any chromatogram trace and
select the Show Run File Info menu item. Remember that regardless on which
chromatogram trace you click, only the run file information for the active trace is
displayed.

491

Item Description
File The full path name of the active chromatogram.
Channel To displayed channel of the active chromatogram.
Last recalc The date and time the file was last reintegrated.
Fill Peak Table Info-Panel
This info-panel displays the time range of the selection and the count of peaks
when filling a peak table from a selection.
NOTE: to show the Fill Peak Table Info-Panel, select the Fill Peak Table item
from the Edit Method menu, then and check the Fill table from selection
checkbox. Alternatively, click on the Fill Peak Mode button on the Chromatogram
Toolbar and check the Fill table from selection checkbox.

Item Description
Start time The start time of the selected region.
End time The end time of the selected region.
Num peaks The number of peaks that are in the selected region and that
will be added to the peak table when the mouse is released.
Visual Method Edit Window
Use the Visual Method Edit Window to define a Peak Table and a Time Events
Table using visual programming and to visually compare the location of
programmed time events versus the actual time the Data Handling time events
occurred.
To use the Visual Method Edit Window, first make the window visible by
selecting Visual Method Edit Window from the View menu. Alternatively, select
Show Visual Method Editing Panel from the Layout tab of the Preferences dialog.
Then you can add, remove, move the position, and edit peak table entries and
time events using left and right mouse actions. Although most of these actions
are also available from the Edit Method menu, once you are familiar with them,
you will find the mouse actions a much faster and more direct way of editing time
events.
Types of Peak Table Entries
There are four different types of peak table entries. They are all drawn as a solid
bar with handles at each end. Click and drag in the middle of the bar to adjust the
time of the peak table entry. Click and drag on a handle at either end to adjust
the peak window retention time percentage for all peaks. The color of the peak
table entry indicates its type. Note that an entry may have more than one color:

492

Color Type of Peak Table Entry
Blue Reference peak
Red Standard peak
Green Relative retention time peak
Yellow None of the above a normal peak
Types of Time Events
There are two types of time events possible. How they are defined, how they are
drawn, and the actions you can take depend on whether it is a time range event
or a value event:

Type of Time
Event
How Defined Events of this
type (color)
How
Displayed
Time range time
event.
Start time and end
time.
II (green)
GR (yellow)
VB (purple)
SR (dark blue)
FP (red)
HF (light brown)
HB (brown)
HM (black)

Up triangle at
start time, down
triangle at end
time, and
connecting line
all drawn in
color of the
event.
Value time event. Value -- units
depend on type of
event, for instance,
area counts for the
Peak Reject event.
WI (light blue)
SP (olive)
SN (dark green)
TP (dark purple)
PR (orange)
Rectangle in
color of the
event.
Adding New Peak Table Entries and Time Events
You add a new peak table entry or time event by right clicking an empty spot (i.e.
not on an existing time event) in the Visual Method Edit Window and selecting
from the displayed menu listing all time events and the peak table entry. The item
is added to the window at the location which you clicked. Alternatively, you can
add a new time event by selecting from the Add Method Item submenu in the
Edit Method menu. If the item is a range time event, the time range is given a
default value of one twentieth of the currently displayed time range. If the item is
a value time event, the Time Events Table dialog box is displayed with the newly
added line selected. This presents an opportunity to set the value of the event.
No dialog is presented for the Split Peak value time event since there is no value
associated with this event.

493
Editing Peak Table Entries and Time Events
You can later change any aspect of any time event or peak table entry by double
clicking on an item in the Visual Method Edit Window. If you double click on a
peak table entry, the Peak Table dialog box is displayed with the row containing
that peak event selected. If you double click on a time event, the Time Events
Table dialog box is displayed with the row containing that time event selected.
You can change any time or value in these dialog boxes, and when you dismiss
the dialog, any changes will be reflected in the Visual Method Edit Window.
Selecting Peak Table Entries and Time Events
You select a peak table entry or time event by clicking on it with the left mouse
button. If you click on another peak table entry or time event, any selected ones
are deselected before the one you clicked on is selected. If you are holding the
shift key while clicking on peak table entries or time events, all items you click on
will become selected. If you are holding the Control key down while clicking on
peak table entries or time events, the selection state of the item is toggled. That
is, selected items are deselected, and unselected items are selected.
You can also select a range of peak table entries and time events by clicking with
the left mouse button on an empty spot in the Visual Method Edit Window and
dragging the mouse cursor. Any items that intersect the displayed rectangle are
selected when you release the mouse. As with single clicks, holding the shift key
down while selecting a range of peak table entries or time events selects any
previously unselected items. Holding the control key down while selecting a
range of items toggles the selection state of any item; any previously selected
items are deselected while any previously unselected items are selected.
Moving Peak Table Entries and Time Events
You move time events by clicking on them and dragging them to a new location.
If you click on the left or right handle of a peak table entry, then you adjust the
peak window retention time percentage for all peaks. If you click on the triangle
section of a range time event, then you move only the start or end time of the
event, the other end stays at the same time. Note that if you move the end time
before the start time or vice versa, when you let go of the mouse, the ends will
automatically be switched to the right order. If you click on the connecting line
section of a peak table entry or range time event, or if you click on a value time
event, or if more than one event is selected, then when you drag the mouse, you
move the item(s) to a new time. The ability to move multiple time events while
maintaining the same time spacing is an easy yet powerful way of making global
changes to the method. In particular with peak table entries, this is the easiest
way to interactively adjust for retention time drift.
Deleting Peak Table Entries and Time Events
Delete peak table entries and time events by selecting them and hitting the
Delete key, using the Delete Selected Method Items from the Edit Method menu,
or hitting the Control-D key combination.

494
Info Window and Mouse Cursor Types
Moving the mouse and pausing over a time event in the Visual Method Edit
Window brings up a window containing information about the peak table entry or
time event in a condensed format. The window is automatically hidden as soon
as you move the mouse.
Notice that as you move your mouse in the Visual Method Edit Window, the
mouse will change from a cross cursor to the arrow cursor when over a time
event. The arrow cursor indicates you can do one of the several actions with the
left or right mouse. If you click with the left mouse on a range time event triangle,
notice that the cursor changes to a double-pointed cursor with arrows pointing
left and right. This indicates you can move the start or end time for this event.
Right Mouse Menus
Clicking on a peak table entry or time event with the right mouse button displays
a context sensitive menu of actions you can do with that item. If only one peak
table entry or time event lies underneath the mouse you can edit or delete the
item. If there are multiple peak table entries or time events at the same location
as where you clicked the mouse, all of these items are listed in the menu, each
with Move to Front, Edit, and Delete menu items. If there are multiple selected
items, then the menu will contain a list of all the selected items rather than the
items at the location you clicked. For peak table entries and time events that lie
underneath the front most time event, the Move to Front menu item deselects all
other items, selects the indicated peak table entry or time event, and moves if to
the front enabling you to more easily manipulate that item.
As described in Adding New Peak Table Entries and Time Events, clicking with
the right mouse button in an empty section of the Visual Method Edit Window
displays a menu allowing you to add a new peak table entry or time event to the
window.
The following mouse actions are possible for the Main Window:

Hold mouse still over a peak table
entry or time event
Displays a window containing information
about the item in a condensed format.
Left mouse button click on a peak
table entry or time event.
Selects items as described in the Selecting
Peak Table Entries and Time Events section.
Left mouse button click in an empty
section.
Deselects all peak table entries and time
events.
Left mouse button click on a peak
table entry or time event and drag.
Moves or sizes items as described in the
Moving Peak Table Entries and Time Events
section.
Left mouse button click in an empty
section and drag.
Selects items as described in the Selecting
Peak Table Entries and Time Events section.
Left mouse button double click on a
peak table entry or time event.
Displays the Peak Table or Time Events
Table dialog box with the row containing the
item selected.

495
Right mouse button click on a peak
table entry or time event.
Brings up a context sensitive menu with
actions to be taken for one or more items.
Select from the list of Move to Front, Delete,
or Edit menu items as described in Right
Mouse Menus above.
Right mouse button click in an
empty section.
Brings up a context sensitive menu allowing
you to add a new peak table entry or time
event as described in Adding New Peak
Table Entries and Time Events.

496

497
GC Interactive Graphics
Viewing Chromatograms in Interactive Graphics
Interactive Graphics is the Varian MS Workstation application that allows you to
review chromatograms, edit Data Handling Method parameters, and recalculate
results. Interactive Graphics may be launched from the MS Workstation Toolbar.

Click on the Interactive Graphics / Data Handling button.
If the Data File you wish to view appears in a QuickLink button, select View/Edit
Chromatogram from the menu.
If you did not select View/Edit Chromatogram from a QuickLink menu, you are
prompted for up to seven Data Files to open when Interactive Graphics starts.

Select files to open by double-clicking on the file name, or select the filename and
click on the Add To List button, or drag and drop the files over the list of files below.
If necessary, change the detector channel.
You may re-order the files.
Click on Open Files to view the files.

498
Elements of the Interactive Graphics Window
Once you have selected the file or files to view, they are displayed in the
Interactive Graphics window.

Main Toolbar
Chromatogram Display
Chromatogram Display Window
Visual Method Editing
Attenuation Control
Locator Window
The Locator Window

The Locator Window shows the active chromatogram in full scale. Click and drag
in this window to view a portion of the chromatogram. When you do, the
Chromatogram Display Window is updated and the Locator Window shows the
zoomed area as a highlighted rectangle. Double-click in this window to return the
display to full scale.

499
You can size and position the Locator Window anywhere on the screen. The
Locator Window can be closed by clicking on the button in the upper right corner,
or by toggling the Locator Display button in the main toolbar, or by deselecting
the Locator menu item in the View menu. The display state and position of the
Locator Window is retained the next time you start Interactive Graphics.
The Chromatogram Display Window
The Chromatogram Display Window shows any portion of chromatograms that
you have opened. Click and drag to zoom on a specific area, or click and hold
the mouse button down to continuously zoom on the area beneath the mouse
cursor. Hold the control key down while clicking the mouse button to reverse the
zooming direction. If the Locator Window is displayed, it is updated to show the
zoom area on the full scale chromatogram trace. Double-click in the
Chromatogram Display Window to restore the display to full scale.
If you have opened multiple chromatograms, they may be displayed in overlaid
or tiled modes. When overlaid, all chromatograms are show on the same time
and amplitude axes. By default, the chromatogram traces are offset both in time
and amplitude to facilitate viewing. The offset amounts can be adjusted; refer to
Changing Viewing Options on page 501 for details.

This panel contains information about the active, or front-most chromatogram. The
panel may be moved with the mouse, and you may select the information displayed
by right-clicking in the panel.
Information about peak events is displayed when you move the mouse over the event
marker.
When tiled, each chromatogram trace is displayed separately. All panels share
the same time axis, but each trace can be independently scaled in the amplitude
axis.

500

A separate attenuation control appears for each chromatogram.
When you right click on a chromatogram trace, either in overlay or tiled mode,
you are presented with a popup menu containing options for that chromatogram.
Included in these options are report generation and viewing, along with the ability
to remove the chromatogram, or bring the chromatogram to the active, or top-
most position (in overlay mode only).
The Chromatogram Display Toolbar
The toolbar at the top of the Chromatogram Display Window allows you to adjust
the chromatogram display settings.

Show/Hide toolbar.
Display the chromatograms full scale for both axes, the amplitude axis only, or the
time axis only.
Toggle between current and next or previous zoom settings.
Specify an exact viewing region in time and amplitude units.
Display the position of the cursor on the chromatogram trace.
Change the background color.
Toggle tile or overlay mode.
Lock amplitude settings of tiled chromatograms.
Add peaks to peak table by clicking on the chromatogram display.

501
The Attenuation Control
Located on the right side of the chromatogram display is an attenuation control,
similar to a scrollbar which allows you to adjust the scaling of the amplitude of
the chromatogram trace. As you move the thumb tab up, the vertical scale is
magnified.
The Visual Method Editing Window
The area beneath the Chromatogram Display Window is the Visual Method
Editing Window. Timed integration events and peak table entries are graphically
displayed in this panel. New events can be added by right clicking in the panel
and selecting the desired event from the popup menu. Once inserted, events can
be moved in time and their duration can be edited by dragging their endpoints
with the mouse.
The Main Toolbar
At the top of the Interactive Graphics window is the applications main toolbar.
This toolbar provides shortcuts to frequently used functions that are also
available as menu items. The main toolbar and the Method Quick Link button can
each be repositioned in the window or undocked and displayed as a floating
window by clicking in an empty area in the toolbar and dragging with the mouse.

Open chromatograms.
Copy the chromatogram display to the clipboard.
Print the chromatogram display.
Display the About box.
Display the Reintegration List, reintegrate using the current settings, or reintegrate
and restore any moved baseline endpoints.
Display the Preferences dialog box.
Toggle the Locator Window display.
Quick Link button to method operations for the currently active method.
Changing Viewing Options
There are many options available for the way chromatograms are displayed in
the Interactive Graphics window. Pull down the View menu to display the options.

502
Toggle display of the Locator Window, the Method Quick Link button, the main
Toolbar, or the Status Bar (at the bottom of the window).
Toggle display of the Visual Method Edit Window, the Chromatogram Toolbar or the
Attenuation Control.
Display the Preferences dialog box.
The Preferences Dialog Box
Select Preferences from the View menu to display the Preferences dialog box.
The dialog box contains four tabs at the top, each corresponding to a different
category of preferences. As you make changes in the Preferences dialog box,
the Interactive Graphics display is immediately updated so that you can preview
the change. Refer to the on-line help in Interactive Graphics for a complete
description of all of the fields in the Preferences dialog box.
Layout
The layout preferences determine the appearance and behavior of all elements
in the Chromatogram Display Window other than the chromatogram trace itself.

Accept the changes and close the dialog box. Use the previously saved preferences.
Return all preferences to default values.
Trace Settings
The Trace Settings preferences determine the appearance of the chromatogram
trace in the Chromatogram Display Window.

503

These settings affect what additional information is displayed with the chromatogram.
See the explanation of this option below.
These settings affect the way the chromatogram traces are drawn.
These settings determine whether peak start, end and apex events are drawn on all
chromatograms, only the active chromatogram, or no chromatograms.
These settings affect the display of peak start, end and apex points.
When Preview Blank Baseline Subtraction is selected, the blank baseline stored
in the Method can be edited by clicking and dragging points with the mouse. The
chromatogram is drawn as if the baseline has been subtracted. To actually
subtract the baseline, you must select Subtract Blank Baseline in the Integration
Parameters window in the Data Handling Method Section. If you subtract a blank
baseline that has been manually edited, it will be documented in the report.
Offsets
Time and amplitude offsets affect the 3D appearance of multiple
chromatograms when displayed in overlay mode. When offsets are performed by
percentage, the distance between traces appears fixed regardless of the scaling.
When offsets are performed by a value the distance between traces changes as
the scaling changes.

504
You may specify the colors for each of the seven possible chromatogram traces
that can be displayed simultaneously in Interactive Graphics. You may also
specify the background color of the Chromatogram Display Window, and whether
the background is a solid color or is a faded gradient. You may save your color
settings as a theme, which can be restored later.

Click on the color buttons to choose a new color.
Select an existing color theme, or save the current settings as a new theme.
Selecting a Method
When a chromatogram is initially opened in Interactive Graphics, the Method
used to perform the most recent calculation of the chromatogram is automatically
opened. If this method cannot be found, a new untitled Method will be opened.
If multiple chromatograms are opened at once and more than one Method was
used on the set, you are prompted to select the Method to open, or you can
browse for another Method.

Select the method you wish to use with the chromatograms you opened.
If you wish to use another method, you may browse for it here.

505
If you wish to use Data Handling parameters from a Method file already stored
on disk but not automatically opened when you selected the chromatogram, you
can choose one from the File menu.

Select the Open Method command.
The Open Method dialog box is displayed.

Select the Method containing the Data Handling section you wish to use.
You can select from a list of recently opened methods here.
If the Method you select contains more than one Data Handling section, you will
be prompted for the section to use.

506
Select the method section you wish to open.
If you wish to open the Method originally used with any chromatogram that is
currently opened in Interactive Graphics, you may do so by selecting Original
Method from the File menu.

This item allows you to select from the methods used when the chromatograms were
originally generated.
Building a Method from the Data File
When a calculation is performed on a Data File using parameters in the Data
Handling section of a Method, that Method section is copied into the Data File.
You may build a new Method from the Data Handling parameters stored in a
Data File. Modifications to the new Method do not affect the Method file that was
used originally when the Data File was acquired from the detector. You may use
the Method created from one chromatogram channel to recalculate results for
another Data File.
Build a new Method from an open chromatogram by using the File menu.

Select Build Method from Data File. If multiple chromatograms are open, a cascading
menu allows you to select the Data File to use.

507
When you select Build Method from Data File, you are prompted for the name of
the Method file to be created. This new Method then becomes the active Method.
Changing the Data Handling Parameters
The Edit Method menu provides access to the Data Handling Method section
windows for the open Method.

Select the Data Handling section window to edit.
Edit the Notes associated with the Method. Method notes are printed with the
method, and can be viewed when selecting the method.
The following Method editing windows can be opened from the Edit Method
menu.
Integration parameters affect peak detection, peak size calculation and results
calculation. Refer to the on-line help in Interactive Graphics for details on all
Integration Parameters fields.

508
Peak Table
The Peak Table is used to identify peaks so that results may be calculated. Refer
to the on-line help in Interactive Graphics for details on all Peak Table fields.
Right-click in a column header for formatting option. Refer to page 510 for the
procedure for filling a Peak Table.

Specify peak identification windows.
Select a column then click here to replicate the first entry on all subsequent rows.
Sort peaks by retention time.
When you click on the Define Peak Windows button, the Peak Identification
Window dialog box is displayed.

Peak windows are defined by an absolute time plus a percentage of the retention
time. These values are added to and subtracted from the retention time to determine
the peak window.
Reference peaks are marked in the Peak Table with a check in the Ref column.
This is used with relative retention time peaks (RRT) to compute relative retention
times for all peaks in the Peak Table.
Time Events
Time events affect peak detection and baseline placement. Refer to the on-line
help in Interactive Graphics for details on all Time Events fields. See page 511
for details on graphically editing time events.

509

This field describes acceptable values for the Value / End Time cell.
Calibration Setup
Calibration Setup parameters determine the type of calibration to be performed,
as well as calibration acceptance criteria. Refer to the on-line help in Interactive
Graphics for details on all Calibration Setup fields.

Parameters in this window only apply when a calibrated calculation type is selected.
The number of levels determines the number of amount columns shown in the Peak
Table.
Displays calibration curves.
Specify action taken when a calibration point is not within the given tolerance.
Specify action taken when an analysis run is outside the calibrated range.

510
Edit calibration coefficients. Locked coefficients are not updated by calibration runs.
Verification Setup
Verification Setup options affect the behavior of verification runs. Refer to the on-
line help in Interactive Graphics for details on all Verification Setup fields.

Filling the Peak Table
The fastest way to build a Peak Table is to create one from the detected peaks in
the active chromatogram. To do so, pull down the Edit Method menu.

Select the Fill Peak Table command.
The Fill Peak Table window is displayed at the top of the screen, above the
Chromatogram Display Window.

511
When you check this, peaks detected in any region that you select in the
Chromatogram Display Window are automatically added to the peak table.
The Fill Peak Table window is nearly identical to the Peak Table window, except
that you may click on any peak displayed in the Chromatogram Display Window
to add an entry into the table. A default name and peak parameters are entered
with the retention time of the selected peak. Click on the peaks of interest in the
display, zooming and scrolling if necessary to bring the peaks into view. After all
peaks have been added, click on the Save button.
Interactive Editing of Timed Events
Certain integration parameters can be set to affect only portions of the
chromatogram. This is useful to account for changes in the chromatographic
signal during the course of the run, or to better integrate partially fused peaks or
peaks that occur on a drifting baseline.
These timed integration events can be edited from the Time Events window
displayed from the Edit Method menu, or they can be graphically placed on the
chromatogram display. Peak table entries can also be graphically placed on the
chromatogram using the same technique. Time events that are added to the
chromatogram take effect when you perform a reintegration.
The Visual Method Editing Window is displayed below the chromatogram.

Events that have already taken effect (by reintegrating the chromatogram) are
displayed above the chromatogram trace.
Double-click on a marker to see the entire event table.
Event names and values are shown when you move the mouse over the event
marker.
Peak table entries are displayed as yellow boxes. Double-clicking on the marker
displays the peak table.

512
To add a new time event, right-click in the Interactive Time Events window at the
time where you wish the event to occur.

When you right-click, a menu of events is displayed. Select the desired event type.
The event is added at the point where you right-clicked.

Drag a time range endpoint to change the range.
Drag the center of a time range to move the entire range.
When you change the width of a peak table entry (the yellow boxes), all peak
table entries are adjusted to reflect the new window size. Refer to Peak Table on
page 508 for more information on peak identification windows.
You may select multiple events by holding the Ctrl key down while clicking on
them, or by dragging over the all the events with the mouse.

These events are selected.
Use the delete key to delete selected events, or right-click on the event to see a
menu of options.

513
Moving Peak Start and End Points
Peak start and end points are indicated on the chromatogram as lines or
triangles (depending on the options selected in the Preferences dialog box). You
may change the position of these points by dragging them with the mouse.

Right-click on a point to return it to its original position or view the peak event
information.
Manually positioned points are drawn as solid triangles.
Drag a point to change its position.
When you perform reintegration on a chromatogram with manually positioned
peak events, you are asked whether you wish to include the changes when
calculating results.

Use the manually placed peak events and reintegrate.
Discard the manually placed peak events and reintegrate.
Abort reintegration.
If you use the manually positioned peak events, peaks whose areas are affected
by the event will be flagged with a U (user-modified) in the results report.
Calculating Results
Results can be calculated for all opened chromatogram channels using the Data
Handling parameters in the active Method. Open the Reintegration list by clicking
on the button in the Main toolbar, or by selecting it from the Results menu.

Open the Reintegration List.

514
The Reintegration List is displayed.

Set the run type (analysis, calibration, verification, baseline).
If you are calculating results using an Internal Standard, edit the amount for standard
peaks here.
Indicates channels on which to run Data Handling. An unchecked row indicates that
no new results will be calculated for the corresponding chromatogram.
If a calibration run is specified, either add calibration points to existing data, or
replace existing data with new calibration points.
Save changes but do not run Data Handling.
Save changes and calculate results.
After reintegration, the chromatogram display will be redrawn with any changes
to peak events and colored markers indicating where timed integration events
took place.
You may also quickly reintegrate all open chromatograms using the parameters
in the Reintegration List by using the Reintegrate Now command, selected from
the Main toolbar or the Results menu.

Run Data Handling using parameters stored in the Reintegration List.
Reintegrate peaks after clearing any manually positioned peak events.

515
Viewing Results
You may view results for each peak by enabling the Cursor/Peak Information
display from the Chromatogram Display Toolbar.

Click on this button to enable the display of peak information.
The Cursor/Peak Information display can also be enabled from the Trace
Settings tab in the Preferences dialog box.

The Peak Information window is updated with peak data when you move the cursor
over the peak.
Other results viewing functions are available by right-clicking on the
chromatogram trace. When you do, a popup menu lists all report options
available. This list will vary depending upon the post-run applications that you
have installed. The same list is also available from the Results menu, listed
under the Data File name.

516
Viewing Calibration Curves
If you are performing calibrated calculations (external standard, internal standard
or normalized percent), you may view the calibration curves associated with the
active Method. Pull down the Results menu.

The Calibration Curve window is displayed if calibration data exists in the active
Method. If you have not yet performed any calibration runs with the active
Method, or if you have cleared calibration coefficients without adding any new
calibration data, a message box will tell you that no calibration data exists in the
Method.

You may print or export the selected curve or curves for all peaks in the peak table.
You may overlay curves with different fit parameters to determine the best type of fit
to use for your data.
You may manually enter calibration coefficients.
Right-click on a calibration point to exclude it from the curve fit calculation.

517
Double-click on a calibration point to see more information.
Select the peak whose curve you wish to view.
Changes made here only affect the stored calibration data and are documented in the
results report and calibration block report.
Refer to the on-line help in Interactive Graphics for a complete description of all
fields in the Calibration Curve window.
Printing and Copying the Chromatogram Display
You may wish to print the image displayed in Interactive Graphics, or paste it into
another document. To print the image displayed in the Chromatogram Display
Window, pull down the File menu.

Select Print to print the image.
Select Print Preview to view the image as it will be printed.
To copy the image to the clipboard for use in other Windows applications, pull
down the Edit menu and click on the Copy item.

Copy the image as a picture which can be resized without losing resolution.
Copy the image in the zoom window as a bitmap. Bitmaps cannot be resized without
becoming distorted.
Create a Windows metafile that can be imported into Windows graphic applications.

518

519
GC Standard Report Method
Command Reference
Print Options

520
Single Run Reports:
Item Description
Title Up to 60 characters

Assigns a title to the report.
Print Chromatogram When checked, the Workstation prints the
chromatogram from System Control during automation.
Print Results When checked, the Workstation prints the results report
from System Control during automation.
Suppress Printout on
Injections
When checked, only prints automated reports for Recalc
and Print Sequence actions. Used to insure that printer
errors do not interrupt an automated sequence of
injections
Convert Results to
ASCII
When checked, the Workstation converts the results to
ASCII. Used to generate results for use in other ASCII-
compatible programs.

Calibration Block Reports:
Item Description
Print Report Selects whether or not a Calibration Block Report is printed
when a Print Calib sample type is used in a SampleList or
RecalcList (from System Control/Automation).
Convert Report to
ASCII
When checked, converts the calibration block report to ASCII
format when a Print Calib sample type is used in a
SampleList or RecalcList (from System Control/Automation).
Other Commands:
Item Description
Print Copies 1 to 9
Sets the number of copies of the report to be printed.

521
Results Format

Item Description
Units Any units, up to 10 characters
Assigns a name for the units used in the results report.
Number of
Decimal Digits
0 to 6
Sets the number of digits in which results are to be expressed.
Run Log If checked, includes the method and the Time Events Log at the
end of the report. Entries in the Time Events Log correspond to the
actual times when the events occurred.
Error Log Includes error messages that occurred during the run at the end of
the report. Error messages generated by post-run Data Handling
are always printed whether the error log option is active or not.
Calibration
Report
Includes the text of the calibration block report as part of the results
report.
Notes Includes notes you entered when you made the injection (original
notes) and when you recalculated (appended notes) as part of the
report.

522
Chromatogram Format

Item Description
Start Retention
Time, mins
0.00 to 1440.00
Specifies a start time after injection for the chromatogram display
and printout.
End Retention
Time, mins
0.01 to 1440.00
Specifies an end time for the chromatogram display and printout. If
the End Retention Time is greater than the actual end time in the
data file, the actual end time is used.
Initial
Attenuation
1 to 4096
Sets the initial scaling of the display or printout. Attenuation is
relative to the maximum full scale value of the detector. An
attenuation of 1 scales the chromatogram so that a signal 1/4096
th

of the detector's full scale is the largest signal that will be printed.
The attenuation can be changed to other values at various times
by time programming. The initial attenuation value is ignored if you
select Auto Scale.
Zero Offset, % -100 to 100
Sets the zero point of the displayed or printed chromatogram as a
percentage of the full page. Larger values let you record negatively
drifting baselines or negative chromatographic peaks. The zero
offset value is ignored if you use Auto Scale.

523
Item Description
Length in
Pages
0 to 9
Sets the number of pages used to print a chromatogram. This
option takes precedence over the chart speed value. The chart
speed is calculated by dividing the total length in pages by the run
time.
Initial Chart
Speed, cm/min
0.0 to 30.0
Sets the initial chart speed for the printout. This speed does not
change unless you time program the chart speed. Set the Length
in Pages to 0 to use this option.
Minutes per
Tick
0.0 to 10.0
Sets the interval between time tick marks on the printout.
Auto Scale If checked, adjusts the attenuation and zero offset so that the
chromatogram fills the screen or page.
Time Events If checked, annotates the right margin of the chromatogram to
show when time events occurred. Shows when peak width (WI),
inhibit integrate (II), solvent reject (SR), group (GR), valley
baseline (VB), chart speed (CS), and attenuation (ATT) changes
occurred.
Chromatogram
Events
If checked, annotates the chromatogram with tick marks that
denote peak event for peak starts, peak ends, apices, and valley
points.
Retention
Times
If checked, annotates the chromatogram with the retention times
for all detected peaks.
Peak Names If checked, displays peak names for identified peaks.
Baseline Draws baseline segment lines under the peaks.
Edit Time
Program...
Opens the Report Time Program dialog box to edit a report time
program.
Report Time Program Dialog Box

Item Description
Retention
Time
0.00 to 1440.0

524
Item Description
Chart Speed 0 .1 to 30.0
Sets the program chart speed.
Attenuation 1 to 4096
Sets the program attenuation.. Attenuation is relative to the
maximum full scale value of the detector. An attenuation of 1
scales the chromatogram so that a signal 1/4096
th
of the detector's
full scale is the largest signal that will be printed.
Add Adds the active parameters to the program list.
To add a change in chart speed or attenuation to the report time
program.
Delete Deletes the highlighted line in the program.
To delete a line in the report time program, canceling that change
in chart speed or attenuation.

Calibration Block Report Format

Item Description
Print Text Report
Only/
Print Text and Curves
Selects whether the Workstation prints only a text report or
prints the calibration curves when a Calibration Block
Report is printed. Calibration Block Reports are printed
when a Print Calib sample type is used in a SampleList or
RecalcList (from System Control/Automation).
Show Outliers on
Curve

If checked, prints the excluded points on the calibration
curve.
Labels the amount units used in the calibration block
report.

525
Generating GC Standard Reports
The Standard GC Reports Method Section
Note that information about using other reporting applications such as the
Custom MS Report Writer are documented in the manuals specific to those
applications.
Report formatting parameters are specified in the Report section of the Method.
The Report Method section is a post-run application section and applies to a
specific detector channel. You create a Report Method section for each channel
of each detector for which you wish to generate a report. Refer to the Data
Acquisition Operation Manual for details on the procedure for creating and
editing Method sections.
The Report Method section contains four editing windows. Each one is described
below.
Print Options
Print options allow you to specify the report title, whether the report includes the
chromatogram, results or both, along with other parameters that affect report
generation.

Only prints when performing recalculations or print actions from System Control. Use
this to avoid automated injection delays due to printer problems. Refer to Batch
Reports for details on batch recalculations.

526
Creates an ASCII file containing the results report. The file is named based on the
Data File name and channel label, with the extension .txt.
Results Format
Results format specifies the layout and contents of the results report. Refer to the
on-line help in Report for details on the results report fields and format.

Uses the group number set in the Peak Table.
Contains the Method used during the injection, along with the Module Information
specified in System Control.
Calibration coefficients and replicate statistics for each peak.
Date, time and Method name logged for each recalculation of the Data File.
Notes entered for the Sample in the SampleList and RecalcList in System Control, or
the Reintegration List in Interactive Graphics.
Chromatogram Format
Chromatogram Format specifies the length of the chromatogram, the scaling of
the plot, and the plot annotations.

527

Fits the high and low amplitudes to the page. Peaks inhibited with II or SR time
events are ignored.
When not using Auto Scale, you can time program attenuation and chart speed
settings.
When not using Auto Scale, sets the magnification of the amplitude axis. 4096
displays the maximum detector range, 1 displays the highest magnification.
When not using Auto Scale, sets the offset of the baseline as a percentage of the full
page.
Set the chromatogram printout length in pages or in cm/minute.
Integration time events and attenuation/chart speed changes.
Peak start, end and apex.
Calibration Block Report Format
These options affect the Calibration Block Report generated when a Print Calib
entry is added to a SampleList or RecalcList in System Control.

528

Amount units label the X axis of the curve.
Refer to the on-line help in Report for details on all fields in the Report Method
section.
Automated Report Generation
Once you have added Report sections to your Method, automated reports can be
generated from System Control after each injection, after recalculations, or by
the use of the Print action in the Sequence window.
You may choose to disable automated Report printing during the course of an
automated sequence of injections or recalculations. You can do this by disabling
automated printing from the Automation menu in the Instrument window.

When this item is not checked, report printing is disabled. ASCII file generation is still
performed if specified in the Report Method section.
Disabling automated printing is analogous to disconnecting the printer
automation continues but no reports are printed. This is useful if you are about to
run out of printer paper but do not wish to suspend automation.

529
Automated Printing to Multiple Printers
If you are running automation on more than one instrument, you may wish to
designate a separate printer for each instrument to avoid interleaving of reports.
Pull down the File menu in System Control (or any Varian MS Workstation
application).

Select Printer Setup.
The Saturn Printer Setup dialog box is displayed.

This printer is used when you print documents from any Varian MS Workstation
application interactively.
Changes the printer and sets printer options.
These printers are used during automated report generation from System Control.

530
Batch Report Printing without Recalculating
When you perform batch recalculations in System Control, reports are
automatically generated using the Report parameters in the active Method. You
may wish to print reports for a batch of Data Files without recalculating them.
Batch Printing in System Control
Create or open a Sequence from the File menu or toolbar.

Specify a Print action.
Specify a Method containing the Report sections that you wish to apply.
Specify a RecalcList containing the names of the Data Files for which you wish to
generate reports.
Refer to the Automation File Editor section for details on creating, editing and
saving RecalcLists. Refer to the Automation File Editorsection for more
information on the Sequence window.

531
Batch Printing with Batch Report
You may print reports for a set of Data Files without using System Control.

Click on the GC Batch Reporting icon in the MS Workstation Toolbar.
The Batch Report window is displayed.

Reports are printed using the formatting options stored in the Method last used to
process the Data Files, or from the specified Method.
You may specify the post-run application to invoke. Use REPORT32 for standard
reports.
Use the Windows Explorer to drag and drop Data Files into the Batch Report window.
As each report is generated, the Status Messages window is updated.
Viewing a Report for a Single Run
Note that other reporting applications such as the Custom MS Report Writer can
be used to view reports for Data Files. Details about these applications are
documented in the manuals specific to the application.
Report viewing and printing options are available from any Data File Quick Link
button, or by right-clicking on a chromatogram trace in Interactive Graphics. You
may also select a Data File and view its chromatogram and results report by
invoking the Standard GC Reports application from the MS Workstation Toolbar.

532

Click on the Standard GC Reports icon in the MS Workstation Toolbar.
The Open Data File dialog box is displayed.

Select the Data File.
Select the channel in the Data File whose report you wish to view.
The chromatogram and results report are displayed.

You can search for a peak name or other text in the results report using the Search
menu.

533
Specify report formatting parameters.
The Data File and Method Quick Link buttons provide access to additional operations,
such as reintegrating the chromatogram or editing the Method.
The chromatogram is shown with the magnification, offset and time range
specified in the Report Method section most recently used on this Data File
channel. The results report is shown as it will appear when printed. When you
zoom in on the chromatogram display, the chromatogram options in the Report
Method section are updated.
Click on the Report Title, Chromatogram Options, or Results Options buttons in
the toolbar, or select the corresponding items from the Options menu, to change
the report format.
From the Report application you may print the report, generate an ASCII
representation of the results report, or load the current Data File channel into
Interactive Graphics. Pull down the file menu.

Print the chromatogram and/or the results.
Generate the ASCII results file.
You can also access these functions from the Report toolbar.

534

535
Method Builder Dialog Boxes
Create/Open Method File Dialog Box

Item Description
Select a method file action If Create a New Method File is selected, then the
Star Assistant is started to guide you through
adding any hardware modules or post-run
processing to a new Method file. If Open Existing
Method File is selected, then the Open Method File
dialog box is displayed for selecting the Method file
to open.
Do not display this dialog at
startup
When not checked, this dialog box is always
displayed whenever the Method Builder application
is started. When checked, this dialog box is not
displayed. To redisplay the dialog box at startup,
select Prompt for Action at Startup from the Method
Builder File menu.
OK Either starts the Star Assistant to configure a new
method file or displays the Open Method File dialog
box to select an existing Method file to open.
Cancel Cancels the Method file action and closes the
dialog box.

536
Open Method File Dialog Box

Item Description
Look in Lists the available folders and files. To see how the
current folder fits in the hierarchy on your computer,
click the down arrow. To see what's inside a folder, click
it. The box below shows the folders and files in the
selected location. You can also double-click a folder or
file in that box to open it. To open the folder one level
higher, click the up arrow button on the toolbar.
File list Lists the folders and files in the selected location. To
see what's inside a folder, double-click it. You can also
use the Look In box to see the hierarchy of folders. To
open the folder one level higher, click the up arrow
button on the toolbar.
Files of type Restricts the list of files to only those matching the
selected type.
Recent Files Click on this button to display a list of recently selected
files. When you select a file from this list, its name is
displayed in the File name box.

537
Item Description
Save Method File As Dialog Box

Item Description
Save in Lists the available folders and files. To see how the current
toolbar.
Save In box to see the hierarchy of folders. To open the folder

538
Item Description
File name Shows the currently specified file.
Save as type Specifies the type of file to save.
When you select a file from this list, its name is displayed in
the File name box.
Save Saves the file with the specified name.
Cancel Cancels file saving.
Add Password Dialog Box

Item Description
Enter New Password Enter password to be used in this box. Asterisks
will appear as you type it.
Re-enter New Password Enter password again. This password will be
compared to the previously entered one to guard
against typing errors.
OK Applies the password to the Method and closes
the dialog box.
Cancel Closes the dialog box without applying the
password to the Method.

539
Change Password Dialog Box

Item Description
Enter Current Password Enter the password currently used to protect the
Method.
Enter New Password Enter password to be used in this box. Asterisks will
appear as you type it. If you leave this box blank,
password protection will be removed from the
Method.
Re-enter New Password Enter password again. This password will be
compared to the previously entered one to guard
against typing errors.
OK Applies the new password to the Method and closes
the dialog box.
Cancel Closes the dialog box without changing the
password to the Method.

540
Print Method Sections Dialog Box

Item Description
Sections to Print Lists the sections of the Method. Selected sections will be
printed. To print only certain Method sections, click on
each section to print, then click on Print.
Select All Selects all sections in the Method.
Print Prints selected sections of the current Method and closes
the dialog box.
Cancel Closes the dialog box without out printing sections of the
current Method.

541
Star Printer Setup Dialog Box

Item Description
Default Star Printer Displays the printer that is used when printing
interactively from Varian MS Workstation
applications. Click on the Change button to select a
different printer.
Instrument Printers Displays the printer that is used when printing under
automation from System Control. A separate printer
can be configured for each instrument (up to four).
Click on the Change button to select a different
printer for each instrument.

542
Delete Method Sections Dialog Box

Item Description
Sections to Delete Lists the sections of the Method. Selected sections will be
deleted. To delete only certain Method sections, click on
each section to delete, then click on Delete.
Delete Deletes selected sections of the current Method and
closes the dialog box.
Cancel Closes the dialog box without out deleting sections of the
current Method.

543
Import Method File Sections Dialog Box

Item Description
Sections to Import Lists the sections of the Method. Selected sections will
be imported. To import only certain Method sections,
click on each section to import, then click on Import.
Import Imports selected sections to the Method being edited
and closes the dialog box.
Cancel Closes the dialog box without out importing sections into
the Method.
Star Assistant Wizard
The Star Assistant Wizard guides you through the process of creating a new
Method or adding instrument control or post-run processing sections to an
existing Method. You are prompted for information about the instrument on which
you will be running the Method, the detectors whose data you wish to process,
and the post-run applications that you wish to include in your Method. When
finished, you will be given an opportunity to review the sections that will be added
to your Method before continuing.

Click on the following steps in the Method building process for more information.

544
Select Configuration

Item Description
Select a Configuration Select Custom in order to add any configuration of
hardware modules to the Method file. Select the
Instrument button in order to add only the hardware
modules for that instrument configuration to the Method
file. The Instrument configuration is the configuration of
hardware modules and the associated Varian MS
Workstation bus address defined by the user in the
System Control application. The Instrument configuration
is not available until the user has configured the
hardware modules for the Instrument in System Control
and has exited the Configuration screen of System
Control or closed the System Control application.
Configuration
Description
If you select the Instrument configuration, then a list of
the hardware modules and the address of each module
on the Varian MS Workstation bus is displayed for the
selected Instrument.
Back Displays the Introduction screen for the Star Assistant.
Next Displays the next step of the Star Assistant.
Cancel Closes the Star Assistant. Nothing is added to the
Method file.

545
Configure Modules

Item Description
Available Modules Lists the hardware modules that can be configured in the
Method file.
Configured Modules Lists the hardware modules that have been configured in the
Method file. The modules are listed in the order they are
added.
Add Adds the selected hardware module from the Available
Modules list to the Configured Modules list. The Varian MS
Workstation bus address is automatically assigned.
However, the address can be reassigned by selecting the
drop-down arrow for the address in the Configured Modules
list.
Add All Adds one of each hardware module in the Available
Modules list to the Configured Modules list. The Varian MS
Workstation bus address is automatically assigned.
However, the address can be reassigned by selecting the
drop-down arrow for the address in the Configured Modules
list.
Remove Removes one or more selected hardware modules from the
Configured Modules list. Selecting the header for either the
Address or Module column removes all of the added
hardware modules from the Configured Modules list.
Show existing
modules
If checked, any existing hardware modules in the Method file
are listed in italics in the Configured Modules list. If not
checked, any existing hardware modules are not listed in the
Configured Modules list. The addresses of existing
hardware modules cannot be changed in the Configured
Modules list. The addresses can only be changed from the
Method Parameters window for that hardware module.
Back Displays the Select Configuration screen for the Star
Assistant.

546
Item Description
Cancel Closes the Star Assistant. Nothing is added to the Method
file.
Select Detectors for Post-Run Processing

Item Description
Detector Modules Specifies the detectors for which you
want to add post-run processing to
the Method file. If the detector is
checked, subsequent steps allow you
to configure the post-run processing
for the detector.
Select All When clicked, all of the listed
Detector Modules are checked and
configured for post-run processing. If
all of the Detector Modules are
checked, then the button text is
changed to Unselect All.
Back Displays the previous screen for the
Star Assistant.
Next Displays the next step of the Star
Assistant.
Cancel Closes the Star Assistant. Nothing is
added to the Method file.

547
Create Sections for Post-Run Processing

Item Description
For the following module Specifies the detector module and address for which
post-run processing is added. This Star Assistant
screen is repeated for each detector modules selected
in the previous Select Detectors for Post-Run
Processing screen.
Select the channel(s) to
process
If checked, the selected channel is configured for post-
run processing. When this Star Assistant screen is first
displayed, the default channel for the detector module
is selected. The selected (or checked) channels apply
to all of the selected post-run processing.
Select the Post-Run
processes to perform
If checked, the selected post-run processing is added
to the Method file for all of the checked channels. Any
existing post-run processing in the Method file is not
overwritten so you may safely select any combination
of channel and post-run processing for the detector
module.
Select All When clicked, all of the listed detector channels are
checked and all of the listed post-run processing are
checked. If all of the detector channels and post-run
processing are checked, then the button text is
changed to Unselect All.
Back Displays the previous screen for the Star Assistant.
Cancel Closes the Star Assistant. Nothing is added to the
Method file.

548
Confirm Configuration

Item Description
Added Configuration Displays the hardware modules, hardware control
methods, and any post-run processing for detector
modules that are to be added to the Method file. Any
existing hardware control methods and post-run
processing are not overwritten and are not listed in the
configuration to be added.
Back Displays the previous screen for the Star Assistant.
Finish After you have confirmed the configuration to be added to
the Method file, clicking Finish will add the configuration to
the Method file. The Method Directory pane for the Method
will be updated to reflect the added configuration.
Cancel Closes the Star Assistant. Nothing is added to the Method
file.

549
Method Builder Menus
File Menu

New Starts the Star Assistant Method Configuration dialog to aid
and guide you through creating the Method sections that you
need for an instrument connected to Varian MS Workstation.
Open... Opens an existing Method file to edit. Opens the Open Method
File Dialog Box.
Close Closes the currently selected Method.
Save Saves the current settings under the name of the current
Method file.
Save As... Saves a Method under a new name. Opens the Save Method
File As Dialog Box
Set Password Opens the Add Password Dialog Box or the Change Password
Dialog Box.
Prompt for Action
at Startup
Enables (checked) or disables (unchecked) the Create/Open
Method File dialog box when Method Builder is started.
Print Prints one or more sections from the current Method.
Print Preview Allows user to view any or all sections of the Method in printer
format prior to printing.
Print Setup... Sets preferences for printing. Opens the Star Printer Setup
Dialog Box.
Add Module
Control
Starts the Star Assistant Method Configuration dialog to aid
and guide you through creating the Method sections that you
need for an instrument connected to a Varian MS Workstation.
Add Post-run
Processing
Starts the Star Assistant Method Configuration dialog at the
start of the Post-run Processing section to aid and guide you
through creating the data handling and printing method
sections.
Delete Section Opens the Delete Method Sections Dialog Boxlisting the
sections of the Method. Highlight the sections to be deleted
and click on the Delete button.
Import Section... Imports (copies) Method sections from another Method into the
current Method. Used to create a new Method with some of the
settings from another Method. Opens the Import Method File,
File Sections Dialog Box.
Recent Files List This is a section of the File menu that lists the previously
opened Method files for quick access.

550
Exit Closes Method Builder. If you have made any changes to the
Method, you are prompted to save the changes before closing
Method Builder.
Edit Menu

Undo Undoes the last edit to an item. If the last edit cannot be
undone, this menu item is disabled (grayed).
Cut Copies selected items to the clipboard and removes them
from the Method.
Copy Copies selected items to the clipboard.
Paste Pastes the clipboard contents to the selected item.
Delete Deletes selected items. If a Method section is selected, the
Delete Method Sections Dialog Box is opened..
Fill Down Replicates the first selected table line to the other selected
table lines.
View Menu

Toolbar When checked, the Main Toolbar
is displayed.
Window Toolbar When checked, the Window Toolbar is displayed.
Directory Toolbar When checked, the Directory Toolbar is displayed.
Status Bar When checked, the Status bar at the bottom of the Method
Builder window is displayed.
Method Directory When checked, the Window Toolbar pane is displayed. This
pane provides a tree-structured view of the Method and allows
mouse click selection of Method sections.
Window Menu

New Window Opens a second window into the same Method. This is
useful for setting up side by side comparisons of different
Method sections.
Cascade Arranges the open Method Windows in a cascaded
format for easy switching between multiple Methods and
sections.

551
Tile Vertically Tiles the open Method Windows vertically (side by side).
Tile Horizontally Tiles the open Method Windows horizontally (one above
the other).
Arrange Icons Arranges iconized Method Windows along the bottom of
the Method Builder Window.
Next Pane Switches between The Window Toolbar pane and The
Method Builder Window pane.
Open Window List A list of the currently open Method Builder windows.
Provides quick access to windows that are hidden behind
other windows.
Help Menu

Product Support Web Site If you have Internet access and a web browser
installed on your computer, this option will
automatically open the Saturn GC/MS
Chromatography Workstation Product Support Web
Site. Here you will find the latest software and
documentation updates for the Saturn GC/MS
Chromatography Workstation suite of products,
along with additional notes, tips, and answers to
frequently asked questions.
You may wish to visit this site periodically to see if
new information is available that may be pertinent to
you.
About Method Builder Displays the About Box for the Method Builder
application. The About Box contains information
about the software version, installation information,
and a list of the instrument control modules that you
have installed.

552

553
Method Builder Toolbars
Overview
There are three toolbars on the main window: the Main Toolbar, the Directory
Toolbar, and the Window Toolbar. The Main Toolbar can be used to open, save,
or print Method files; the Directory Toolbar is used to traverse the Method
Directory pane; and the Window Toolbar is used to position the Method windows.
By clicking an area of the toolbar between buttons, each toolbar can be dragged
with the left mouse button to a docked location along any side of the Method
Builder main window, or positioned independently anywhere on the screen. In
addition, each toolbar can be hidden or closed. If the toolbar is hidden, it may be
displayed by selecting the appropriate menu item from the View menu of Method
Builder.
Main Toolbar

Starts the Star Assistant Method Configuration dialog to aid and
guide you through creating the Method sections that you need for
an instrument connected to a Varian MS Workstation.

Opens an existing Method file to edit. Opens the Open Method File
Dialog Box.

Saves the current settings under the name of the current Method
file.

Saves a Method under a new name. Opens the Save Method File
As Dialog Box.

Opens the Add Password Dialog Box or the Change Password
Dialog Box.

Starts the Star Assistant Method Configuration dialog to aid and
guide you through creating the Method sections that you need for
an instrument connected to Varian MS Workstation.

Starts the Star Assistant Method Configuration dialog at the start of
the Post-run Processing section to aid and guide you through
creating the data handling and printing method sections.

Opens the Delete Method Sections Dialog Box listing the sections
of the Method. Highlight the sections to be deleted and click on the
Delete button.

Copies selected items to the clipboard and removes them from the
Method.

554

Copies selected items to the clipboard.

Pastes the clipboard contents to the selected item.

Deletes selected items. If a Method section is selected in the
Method Directory pane, the Delete Method Sections dialog box is
opened..

Replicates the first selected table line to the other selected table
lines.

Prints one or more sections from the current Method.

Displays the help you are now viewing.
Directory Toolbar

From the current selection in the Method Directory pane, selects the
previous directory item that is a collapsible / expandable branch. The
displayed Method Parameters pane is used to reassign Varian MS
Workstation bus addresses for hardware modules and to reassign
channels for post-run processing of detector module data. The module
Method sections can also be accessed from the displayed Method
Parameters pane.

previous directory item that is a Method Parameters window for a
section in the Method file. Pressing this toolbar button will step
backward from the current selection through each section of the open
Method.

next directory item that is a Method Parameters window for a section
in the Method file. Pressing this toolbar button will step forward from
the current selection through section of the open Method.

next directory item that is a collapsible / expandable branch. The
displayed Method Parameters pane is used to reassign Varian MS
Workstation bus addresses for hardware modules and to reassign
channels for post-run processing of detector module data. The module
Method sections can also be accessed from the displayed Method
Parameters pane.

555
Window Toolbar

When pressed, the RecalcList Generation Dialog Box pane is
displayed. This pane provides a tree-structured view of the
Method and allows mouse click selection of Method sections. This
toolbar button toggles to show or hide the Method Directory pane.

Opens a second window into the same Method. This is useful for
setting up side by side comparisons of the same or different
Method sections.

Arranges the open Method Windows in a cascaded format for
easy switching between multiple Methods and sections.

Tiles the open Method Windows horizontally (one above the
other).

Tiles the open Method Windows vertically (side by side).

556

557
Method Builder Window
Overview

The Method is displayed in a window that is split into a left and a right pane. The
left pane is the Method Directory pane and provides a tree-structured view of the
Method. The right pane is the Method Parameters pane and provides the
capability to configure various method parameters. The items displayed in the
Method Parameters pane correspond to the selected item in the Method
Directory pane.
The splitter bar that separates the panes is used to size the panes. When the
mouse cursor is over the splitter bar, click and drag the mouse to size the area
displayed in each pane. You can also hide the Method Directory (or left) pane by
clicking the Hide Directory toolbar button on the Window toolbar.
By default, the toolbar buttons are arranged at the top of the main window below
the Method Builder menu. There are three toolbars: the Main toolbar for opening,
saving, and printing Method files; the Directory toolbar for traversing the tree
displayed in the Method Directory pane; and the Window toolbar for positioning
the Method windows. By positioning the mouse cursor over a toolbar button, a
short description of it is displayed for a brief time. In addition, a status bar is
displayed at the bottom of the Method Builder main window. Any of the toolbars
and the status bar may be hidden or shown by selecting the appropriate item
from the Method Builder View menu.
Only one instance of the Method Builder application is used to display and edit
Method files. If the Method Builder application is already running when you
choose to edit a Method file, a new window is displayed for the Method file. Any
previously open Method file can be accessed by selecting the appropriate

558
window from the Window menu. In addition, if you open another Method file from
the File menu of Method Builder, the Method file is displayed in a new window;
any previously open Method file is not closed. From the Window menu or using
the Window toolbar, the Method file windows can be selected, cascaded, or tiled
in order to compare the same sections in different Method files.
Method Directory

The Method file is displayed in the Method Directory pane as a tree-structured
view of the Method consisting of items that can be expanded in further detail (a
+ or - is displayed to the left of the labeled icon) and items that cannot be
further expanded in the tree (no + or - appears to the left of the labeled icon).
The top-most item in the tree is the name of the Method file. An asterisk (*)
follows the name if the Method file has been modified since it was opened or last
saved. The Method Notes are always displayed as a branch below the Method
file name. All of the next level of branches of the directory tree represent
hardware module components (detectors, pumps, etc.). The hardware modules
are listed in ascending order of their addresses on the Varian MS Workstation
bus.
If the hardware module is a detector component, then the branch for that module
is expanded into the control method for the detector and a branch for each
channel of the detector. The branches for the control method represent the
groups of editable parameters for detector control and data acquisition by the
detector. The branches for the channels are expanded into the post-run
processing applications that can be applied to the channels. For each post-run
application, the branch for that application is expanded into the groups of
editable parameters for the application.
If the hardware module is not a detector component, then the branch for that

559
module is expanded into the groups of editable parameters for the control
method of that module.
If a minus (-) sign is displayed to the left of the name in the directory tree, then
that branch in the tree can be collapsed by either clicking the minus sign or by
pressing the minus key on the keyboard. If a branch is collapsed, then a plus (+)
sign is displayed to the left of the name in the directory tree. Clicking the plus
sign or pressing the plus key on the keyboard expands that branch of the tree.
You may also double-click the name of the branch in order to expand or collapse
the branch.
Clicking on an item in the Method Directory pane will display the corresponding
parameters for that selection in the Method Parameters (or right) pane. For
example, clicking Method Notes in the Method Directory pane will display the
Method notes for the Method file in the right pane.
Method Parameters
The Method Parameters pane displays the corresponding item of the Method
Directory tree selected in the Method Directory pane. There are four types of
windows that can be displayed in the Method Parameters pane: Method file
information, Method Notes, hardware component section descriptions, and
hardware component editable parameters.
If the Method file name is selected in the Method Directory (left) pane, then the
Method Parameters (right) pane displays the file information. The Method file
information includes the fully qualified path name of the file, creation and
modification dates, file size, file attributes, and the Revision History of the
Method file.
If Method Notes is selected in the Method Directory (left) pane, then the
Method Parameters (right) pane displays the notes for the Method file as free-
form text. The Method notes can include any information about the Method such
as setup or how the Method is to be run. The Method notes are always printed
with the Method.
For the low-level branches of a hardware component in the Method Directory
tree (those that cannot be expanded), the Method Parameters pane displays
editable parameters for controlling the hardware module and data acquisition,
and for post-run processing of detector data.
For all other hardware component branches of the Method Directory tree, the
Method Parameters pane displays a description of the Method sections
associated with that hardware component branch. The user can reassign the bus
address of a hardware module, reassign the bus address or channel for post-run
processing, or select the particular group of processing or control parameters to
edit. In addition, the time of last modification of the processing or control
parameters is also listed. In the list containing the names of the Post-Run
Processing Parameters or Method Control Parameters, double-click the list item
in order to display the editable parameters. You may also select the name and
press the ENTER or RETURN key on the keyboard in order to display the
editable parameters for that list item. To reassign the address or channel for all
of the listed Method Control or Post-Run Processing Parameters, select the new
channel or address from the drop-down list in the Method Parameters pane. Any
addresses or channels for which a Method section already exists are omitted
from the drop-down lists.

560

561
Module Information Editor
Module Information Editor
Information about the hardware modules composing your instrument(s) can be
maintained and included in all data files produced by this instrument. This
information can be included in the reports along with the Run Log.
The module information editor lets you define and update the information you
want or need to save along with your data. Within loose guidelines, what
information you save is entirely up to you. The information for module XX is kept
in MODULEXX.MDF in the Workstation directory, where xx is the module
address.
You can edit module information in System Control for any module that is on-line
by clicking on the EditEdit Module Info menu command or the Edit Module
Info Toolbar button. The module information for the currently active module
window will be accessed. If no module window is active, the Toolbar button will
display a list of the available modules. Select the desired module. The menu
command will be disabled if no module window is active.
For purposes of routine maintenance, it is possible to automatically keep track of
the numbers of injections in any or all of the module information files. See
Designing Documentation Structures for details.
The information saved for each module is structured in sections. Each section
contains entries, which have the form Item = value. In the table below, the first
column shows a typical module information file. The second column describes
the elements of this file.

Entry Description
Module Section name
S/N = 1234 Item1 = value1
Description = 2000 Mass Spec Item2 = value2
Name = Old Faithful Item3 = value3

Service Section name
Date First Used = June 5, 1998 Item1 = value1
Service Contract = A123456 Item2 = value2
Support Number = 800 555 1212 Item3 = value3
Date Last Serviced = Item4 = value4
Purchasing Section name

562
Entry Description
PO# = 123456 Item1 = value1
SO# = A12345B Item2 = value2
Current Limitations
There is no protection against duplicated section names or entries. Duplicated
section names or entries cause no harm other than confusion if their contents
differ.
There is no built-in mechanism for copying part or all of the information to
another module address. If you need to change the address of a module, rename
or copy the MODULEXX.MDF accordingly.
Creating a Section

1.
Using the Mouse or the arrow keys, select a section name or the '...'
at the end of the list. (The new section will be inserted at the
selected location).
2.
Press the Add button and enter the name of the section to be
created. Use any name you want, but do not use any bracket
characters. Press OK when done.
3.
The name of the new section appears, and the next blank line is
selected.
4.
Press Add again to create an Entry in this section.
Deleting a Section

1.
With the mouse or the arrow keys, select the section to be deleted -
ALL ENTRIES WILL BE DELETED.
2.
Press the Delete button.
3.
You are prompted to confirm the deletion. Press OK, if appropriate.
4.
You cannot selectively undo the deletion. If you accidentally delete a
section, exit the program without saving the changes. You will lose
all edits made since the last save.
Renaming a Section

1.
Double-Click on a section name. (Alternatively, select a section name
and press the Edit button).
2.
Provide the new name.

563
Adding an Entry to a Section

1. Using the mouse or the arrow keys, select the line within the section
where you want to insert a new entry. To add an entry at the end of a
section, select the blank line at the end of the section.
2. Press the Add button.
3. Provide the item and the value for the entry. To define a new entry
like 'Date Serviced = January 12, 1998', type 'Date Serviced' in the
'Key' field, then 'January 12, 1998' in the 'Value Field''. To move to
the next field, use the Tab key or the mouse.
4. Press OK to accept your selection. The new entry is added to the list.
If it is not correct, double-click on it to edit it.
NOTE:
Entries for which the Value field is left blank will not be followed by an '=' sign.
This allows you to enter free-from text if appropriate. However, you then limit
your capability of retrieving information from DATA files retrieve for such lines.
Advanced Tip:
Double-click on the blank line at the end of a section to add an entry in this
location.
Deleting an Entry from a Section

1. With the mouse or the arrow keys, select the entry to delete.
2. Press the Delete button (this button is disabled if you select an empty
line).
3. You are asked to confirm your request. If appropriate, press OK. If
you accidentally delete an entry, you cannot selectively undo the
deletion, but you can exit the program without saving any edits to
revert to the last saved version.
Editing an Entry or Renaming an Item

1. Double-click on the entry you wish to modify. Alternatively, select the
desired entry and press the Edit key.
2. Modify the item and/or the value field(s).
3. Press OK to replace the old entry with the modified entry. You cannot
selectively undo this action.

564
Creating a Default Module Information Template
New .MDF files can be created based on a template file. If MODULE00.MDF is
found in the Workstation directory, the new file will be a copy of the template. If
the template does not exist, the new file will be created based on the program's
built-in defaults.
Note that the template is only used to create new files. To recreate an existing
.MDF file based on the template, delete the old file (MODULEXX.MDF, where XX
is the module address) and edit the module information.
Designing Documentation Structures
First, you need to decide what instrument information you want to track. For
example:
- Name and Serial Numbers of components
- Miscellaneous parameters (Column information, ...)
- Usage Information (Injections, ...)
- Purchase and Warranty Info
- Service History
Then, you need to decide what information should be attached to which module:
In a system where you only acquire data with an ADCB from instruments that are
not controlled by the Workstation, you would attach all information about all
system components to the ADCB module.
In a system composed of a 3800 GC, an 8200 AutoSampler, and a 2000 Mass
Spec, each module would have its own information file documenting its serial
number, name, etc. You would likely attach the Column information to the GC
module.
Within each Module Information File, create sections named after the major
components or operating concepts. You can have as many sections as you want,
although there is a 64K limit to the total size of the information saved in a file.
Within each section, the Injections field is available to keep track of
consumable. The value of this item is expected to be numerical, and each
occurrence of this item will have its value incremented every time the
corresponding module starts. As a result, you can keep track of the number of
injections performed on a column, on a septum, etc...
Septum
Injections = 25
Last Replaced = June 12, 1998
Free-Form Text line ...
Column
Manufacturer = XYZ
Serial Number = A12345
Type = CP-5MS
Length = 30 m
I.D. = .25 mm
Film = 0.25 um
Injections = 123

565
When you replace a hardware component, zero out (or adequately edit) the
associated number of injections.
You can also save free-form text by creating entries with empty Value fields.
However, you then won't be able to use the programming interface to retrieve
information from such free-form lines.
NOTE: It is important that you keep this information current, as the copy of the
module information stored in the data files cannot be erased or edited. It may be
appropriate to include the updating of this information in your Standard Operating
Procedures.
Retrieving Information from Data Files
The module information is included in reports when the Run Log option is
selected.
For Application Programmers only!
Additionally, a function call is available to application programmers needing to
write programs retrieving module information from run files. This function resides
in the WSMDIN32.DLL dynamic-link library, and its "C" prototype and calling
syntax are as follows:
int PASCAL GetRunInfoString
(
LPSTR lpRun, // File Specification for DATA File
WORD wAddress, // Module Address
LPSTR lpSection, // Section name
LPSTR lpItem, // Item name
LPSTR lpValue // Buffer for returned entry value
)
If the function is successful, it will return the length of the returned entry value.
If the function fails, it will return one of the following error codes:
-3 No info for this Module Address in the DATA file
-2 No such section
-1 No such item
Commands
Buttons
Button Description
Add When a section name is highlighted, this button opens the
Create New Section dialog box.
When an item is highlighted, this button opens the Create
New Entry dialog box.
Edit When a section name is highlighted, this button opens the
Rename Section dialog box.
When an item is highlighted, this button opens the Modify
Entry dialog box.
Delete The highlighted line will be deleted. The user is prompted to

566
confirm this deletion before it is done.
File Menu
The File menu contains the following commands:
Item Description
Save Save the contents of the listbox into the module
information file.
Print Prints the contents of the listbox.

Exit Aborts the current session. If you have made changes,
you will be prompted to save the file before exiting.
Help Menu
The Help Menu provides access to on-line Help and basic Program Information:
Item Description
Contents Display on-line Help
About ModEdit Display basic program information
Dialog Boxes
The Entry Dialog

This Dialog box is used to create and modify entries. It is displayed as a result of
selecting an entry or a blank line and pressing the Add or Edit buttons.
When creating an entry, the item and value fields are empty, and the focus is on
the item field. Type in the new item, then use the Tab key or the mouse to switch
the focus to the value field.
When editing an existing entry, the item and value fields are filled with their
current values. The focus is on the value field, as it is most likely the one you
want to modify. If you need to rename the item, use the Shift+Tab key
combination or the mouse to move to the item field.
Press OK if you wish to save the new or modified entry, otherwise Cancel.
The Section Dialog

This dialog box is used to create and modify sections. It is displayed as a result
of selecting a section and pressing the Add or Edit buttons.
When creating a section, the name field is empty. Type in the name of the
section to create.

567
When renaming an existing section, the name field is initialized with its current
value. Type in the new name for the section.
Press OK if you wish to save the new or modified entry, otherwise Cancel.
Select
To select a line in the list box, single-click on it with the mouse. The line is then
highlighted and would be acted upon by the Add, Edit and Delete buttons as
appropriate. Double-clicking on a line will access the appropriate edit dialog
directly.
From the keyboard, use the up and down arrow keys to move the selected line
up and down. If the listbox does not have the input focus, pressing the up or
down arrow key a few times should restore the input focus to the listbox.

568

569
Security Administration
Overview
The Security Administration window contains three window tabs that can be used
to select the categories of security parameters that can be specified for Varian
MS Workstation applications. Click on the category names below for more
information on each:
Passwords
Application Locking
File Revision Settings
Passwords

570
Item Description
Password for this application Allows you to specify a password required to enter
the Security Administration application. Note that
there is no way to recover this password if it is lost,
so it is recommended that you document the
password in a secure location.
Change Method Passwords Method passwords can be added, changed and
removed from the Security Administration
application. Click on the Select Method button to
browse for and select the desired Method. After the
Method has been selected, you are either prompted
for a new password (if no previous password exists
for the Method), or are prompted for the old and
new password (if the Method already contains a
password). Note that if creation of new passwords is
disabled in the File Revision tab, you will not be
able to add a new password to a Method that does
not already contain one.
Method passwords can also be added and changed
in the Method Builder and Interactive Graphics
applications.
Remove Method Passwords Method passwords can be removed by the Security
Administration application without entering the
existing password. This is useful if the password for
a Method has been lost. Click on the Select Method
button, select the desired Method, and the
password is removed.

571
Application Locking

Item Description
Unlocked Applications This list box shows all top level windows currently
running and are not locked. You may select any number
of them and click on the Lock button. When you do, they
are moved to the Locked Applications list box and their
windows are disabled (they will not respond to mouse or
keyboard input).
Note that applications that are locked by the Security
Administration application remain locked even after the
Security Administration application is closed.
Locked Applications This list box shows all top level windows that are
currently running and are locked. You may select any
number of them and click on the Unlock button. When
you do, they are moved to the Unlocked Applications list
box and their windows are enabled (they respond to
mouse or keyboard input).

572
File Revision Settings

Item Description
Require Revision Log entry when
changes to Methods are saved.
When checked, the user is prompted
for a description of changes when a
Method file is altered and saved. This
Revision Log appears in the Notes
portion of the File Open dialog box, is
listed in the Method Builder application
window when the Method is open, and
is included in the Method printout.
Update Revision Log in Data Files with
recalculation date, time and Method
name.
When checked, Data Files are
updated with a time stamp and Method
name when they are recalculated
(either from System Control or from
Interactive Graphics). The Data File
Revision Log can be included in
printed reports.
Enable results deletion from "Open Data
File" dialog boxes.
When checked, a button appears in
the Open Data File dialog box allowing
results to be deleted from a specified
channel of a Data File. Results
deletion is logged in the Data File's
Revision Log. This option only affects
standard GC results. GC/MS results
will not be deleted.

573
Item Description
Disable creation of new passwords in
Method files.
When checked, new passwords
cannot be added to Methods. Methods
already containing passwords will still
prompt you for the password before
changes are saved.

574

575
Standard GC Reports Command
Reference
File Menu

Open Displays the Open Data File dialog box.
Print Displays the Print dialog box.
Convert
(ASCII)
Converts the text results report into an ASCII file. The name of the
ASCII file is based on the data file name, with the channel number
appended to it. The ASCII file ends with a ".txt" extension.
Printer Setup Displays the Printer Setup dialog box.
Exit Quits the Standard Report application.
Search Menu
This menu is displayed when the results window is active.

Find Displays the Find dialog box.
Find next Repeats the search last performed with the Find dialog box.
Font Menu
This menu is displayed when the results window is active.
Menu
Item
Description
Small Uses a small font to display the results report. This font is for display
only.
Medium Uses a medium font to display the results report. This font is for
display only.
Large Uses a large font to display the results report. This font is for display
only.

576
View Menu
This menu is displayed when the chromatogram window is active.

Change Plot
Color
Displays a dialog box allowing you to select a color for the
chromatogram plot. This plot color is used in the display only.

Options Menu

Report Title Displays the Report Title dialog box.
Chromatogra
m
Displays the Chromatogram Options dialog box.
Results Displays the Results Options dialog box.
Save
Changes to
Data File
Saves any changes made to the report title, chromatogram options
or results options to the currently open data file. The next time you
display the data file in the standard report application, these new
settings will be used.

Windows Menu

Tile Arranges the chromatogram and results windows in a tiled fashion.
Cascade Arranges the chromatogram and results windows in an overlapped
fashion.
Arrange Icons If either the chromatogram window or results window (or both
windows) are iconized, the icons are arranged in the report
window.
Chromatogra
m Window
Activates the chromatogram window.
Results
Window
Activates the results window.

577
Help Menu
Product
Support Web
Site
If you have Internet access and a web browser installed on your
computer, this option will automatically open the Saturn GC/MS
Workstation Product Support Web Site. Here you will find the
latest software and documentation updates for the Saturn GC/MS
Workstation suite of products, along with additional notes, tips,
and answers to frequently asked questions.
About Report Displays the About Box for the Standard Report application. The
About Box contains information about the software version,
installation information, and a list of the instrument control
modules that you have installed.

578

579
Standard GC Reports Dialog Boxes
Open Data File Dialog Box

Item Description
Look in Lists the available folders and files. To see how the current folder
fits in the hierarchy on your computer, click the down arrow. To see
what's inside a folder, click it. The box below shows the folders and
files in the selected location. You can also double-click a folder or
file in that box to open it. To open the folder one level higher, click
the up arrow button on the toolbar.
inside a folder, double-click it. You can also use the Look In box to
see the hierarchy of folders. To open the folder one level higher,
Files of type Restricts the list of files to only those matching the selected type.
Recent Files Click on this button to display a list of recently selected files. When
you select a file from this list, its name is displayed in the File name
box.

580
Item Description
Run
Information
Shows information about the currently selected file, including a
thumbnail view of the chromatogram.
If you are looking at several files and you wish to use a fixed
attenuation in the thumbnail display, check the Remember Scaling
box.
Select the channel you wish to open in the Channel selection box.
When you do, the chromatogram thumbnail and Run Information is
updated.
Del Results Allows you to delete results from the currently select channel of the
currently selected data file. This button does not appear if it has
been disabled from the Varian MS Workstation Security
Administration application.
Open File Opens the selected data file using the selected channel.

Print Dialog Box

Item Description
Chromatogram When checked, prints the chromatogram as part of the report.
Results When checked, prints the results as part of the report.
Copies Sets the number of copies of the report to be printed.

581
Printer Setup Dialog Box

Item Description
Default Saturn
Printer
Displays the printer that is used when printing interactively
from Varian MS Workstation applications. Click on the
Change button to select a different printer.
Instrument Printers Displays the printer that is used when printing under
automation from System Control. A separate printer can be
configured for each instrument (up to four). Click on the
Change button to select a different printer for each
instrument.

Title Dialog Box

Item Description
Title Assigns a title to the report. The title appears in both the
chromatogram and results portion of the printed report.

582
Chromatogram Options Dialog Box

Item Description
Start Retention
Time, mins
0.00 to 1440.00
Specifies a start time after injection for the chromatogram
display and printout.
End Retention
Time, mins
0.01 to 1440.00
Specifies an end time for the chromatogram display and printout.
If the End Retention Time is greater than the actual end time in
the data file, the actual end time is used.
Initial Attenuation 1 to 4096
Sets the initial scaling of the display or printout. Attenuation is
relative to the maximum full scale value of the detector. An
attenuation of 1 scales the chromatogram so that a signal
1/4096
th
of the detector's full scale is the largest signal that will
be printed.
The attenuation can be changed to other values at various times
by time programming. The initial attenuation value is ignored if
you select Auto Scale.
Zero Offset, % -100 to 100
Sets the zero point of the displayed or printed chromatogram as
a percentage of the full page. Larger values let you record
negatively drifting baselines or negative chromatographic peaks.
The zero offset value is ignored if you use Auto Scale.
Length in Pages 0 to 9
Sets the number of pages used to print a chromatogram. This
option takes precedence over the chart speed value. The chart
speed is calculated by dividing the total length in pages by the
run time.

583
Item Description
Initial Chart
Speed, cm/min
0.0 to 30.0
Sets the initial chart speed for the printout. This speed does not
change unless you time program the chart speed. Set the
Length in Pages to 0 to use this option.
Minutes per Tick 0.0 to 10.0
Sets the interval between time tick marks on the printout.
Auto Scale If checked, adjusts the attenuation and zero offset so that the
chromatogram fills the screen or page.
Time Events If checked, annotates the right margin of the chromatogram to
show when time events occurred. Shows when peak width (WI),
inhibit integrate (II), solvent reject (SR), group (GR), valley
baseline (VB), chart speed (CS), and attenuation (ATT) changes
occurred.
Chromatogram
Events
If checked, annotates the chromatogram with tick marks that
denote peak event for peak starts, peak ends, apices, and valley
points.
Retention Times If checked, annotates the chromatogram with the retention times
for all detected peaks.
Peak Names If checked, displays peak names for identified peaks.
Baseline Draws baseline segment lines under the peaks.
Edit Time
Program...
Opens the Report Time Program dialog box to edit a report time
program.

Report Time Program Dialog Box

Item Description
Retention
Time
0.00 to 1440.0
Chart Speed 0 .1 to 30.0
Sets the program chart speed.

584
Item Description
Attenuation 1 to 4096
Sets the program attenuation.. Attenuation is relative to the
maximum full scale value of the detector. An attenuation of 1 scales
the chromatogram so that a signal 1/4096
th
of the detector's full
scale is the largest signal that will be printed.
Add Adds the active parameters to the program list.
To add a change in chart speed or attenuation to the report time
program.
Delete Deletes the highlighted line in the program.
To delete a line in the report time program, canceling that change in
chart speed or attenuation.

Results Options Dialog Box

Item Description
Units Any units, up to 10 characters
Assigns a name for the units used in the results report.
Number of
Decimal Digits
0 to 6
Sets the number of digits in which results are to be
expressed.
Run Log If checked, includes the method and the Time Events Log at
the end of the report. Entries in the Time Events Log
correspond to the actual times when the events occurred.
Error Log Includes error messages that occurred during the run at the
end of the report. Error messages generated by post-run
Data Handling are always printed whether the error log option
is active or not.
Calibration
Report
Includes the text of the calibration block report as part of the
results report.

585
Notes Includes the notes you entered when you made the injection
(original notes) and when you recalculated (appended notes)
as part of the report.
Find Dialog Box

Item Description
Find Sets which string of characters the Workstation will find
Match Case If checked, tells Report to find only character strings with the same
use of upper and lower case

586

587
Standard GC Reports Format
Descriptions
Results Report
Below is an example of a results report generated from an analysis run. The
exact format of your results reports may vary depending on the following
parameters:
- Options set in the Results Format portion of the Method
- The type of run being performed (blank baseline, calibration, analysis, or
verification)
- The peak measurement type (area, height or square root of height)
- The calculation type (percent, normalized percent, internal standard or
external standard)
- The presence of an RRT peak, designated in the peak table (which
determines whether relative retention time is shown)
The format of the ASCII text file generated when ASCII file conversion is
performed is identical to the format in the printed report.
Following this example is a legend of the fields that appear in the report.

588

Title : Title
Run File : Data File name
Method File : Method File name
Sample ID : Sample name
Injection Date: Date/Time Calculation Date: Date/Time
Operator : Operator Name Detector Type: Detector Type/Range
Workstation: Volume Label Bus Address : module bus address
Instrument : Instrument Name Sample Rate : Sample Rate (Hz)
Channel : Channel ID/Name Run Time : Run Time (min)
*********** Star Chromatography Software
*********************************************************
Run Mode : Run Mode
Peak Measurement: Measurement Type
Calculation Type: Calculation Type
Standard Ret. Time Rel. Width
Peak Peak Result Peak Time Offset Area Ret. Sep. 1/2 Status
No. Name (units) Name (min) (min) (counts) Time Code (sec) Group Codes
--- ------------ ---------- ------------ ------- ------- -------- ------- ---- ----- ----- ----
--
1 2-Octanone INT STD 2-Octanone 5.677 0.004 4270 1.000 BB 1.5 1 SR
2 1-Octanol 7.5438 2-Octanone 6.996 0.022 749 1.232 BB 3.3 1
3 n-Decane 30.1366 2-Octanone 7.514 0.002 1511 1.324 BB 1.6 1 C
4 2,6-dimetphe INT STD 2,6-dimetphe 8.479 0.001 2414 1.494 BB 1.7 2 S
5 n-Dodecane 16.8705 2,6-dimetphe 8.998 -0.005 4608 1.585 BB 1.8 2 C
6 2,4-dimetani 16.8549 2,6-dimetphe 9.325 -0.004 3545 1.643 BB 1.8 2 C
7 n-Tridecane 16.8653 2,6-dimetphe 10.856 -0.006 3569 1.912 BB 1.9 2 C
--- ------------ ========== ------------ ------- ======= ======== ------- ---- ----- ----- ----
--
Group 1 37.6804 0.028 6530
Group 2 50.5907 -0.014 14136
------------ ========== ======= ========
Totals: 88.2711 0.014 20666
Status Codes:
R - Reference peak
* - No result could be calculated; check calibration curve
M - Missing peak
C - Out of calibration range
S - Internal Standard peak
U - User-defined peak endpoint(s)
Total Unidentified Counts : 0 counts
Detected Peaks: 7 Rejected Peaks: 0 Identified Peaks: 9
Standard Peak Amounts:
2-Octanone Amount = 12
2,6-dimetphe Amount = 12
Multiplier: 1 Divisor: 1
Baseline Offset: -20 microVolts
Noise (used): 1 microVolts - monitored before this run
Manual injection
Run Log:

589
[Module Run Logs]
Time Events:
[Data Handling Time Events]
Error Log:
[Module Error Logs]
Calibration Report:
[Calibration Report Text]
Revision Log:
[Revision Log]
Original Notes:
[Original Note Text]
Appended Notes:
[Recalc Note Text]
*******************************************************************************

Item Description
Title Set in the Print Options portion of the Report section of the
Method.
Run File The file name of the Data File containing the results.
Method File The file name of the Method used to generate the current
results. This may differ from the Method used when the data
was first generated.
Sample ID Set in the SampleList when the injection was performed.
Injection Date The date and time of the injection.
Calculation
Date
The data and time of the most recent calculation.
Operator Set in the System Control Instrument Parameters dialog box.
This is the name of the operator at the time of the injection.
Detector Type The type of the detector used to collect the data (for example,
9050, 9065, or ADC Board).
Workstation The name of the Workstation on which the data was collected.
The Workstation name is the volume label of the hard disk on
which System Control is running at the time of the injection.
Bus Address The bus address of the detector used to collect the data.
Instrument Set in the System Control Instrument Parameters dialog box.
This is the name of the instrument at the time of the injection.
Sample Rate The rate (frequency) of the data stored in the Data File.
Channel The channel ID corresponding to the data for which results are
shown.
Run Time The length of the run in minutes. Set in the instrument control
Method section corresponding to the detector that collected
the data.
Run Mode Set in the SampleList or SampleLog (in System Control) or
Reintegration List (in Interactive Graphics). Either Blank
Baseline, Analysis, Calibration or Verification. If blank baseline
subtraction has occurred (set in the Integration Parameters
window in the Data Handling Method section), it is indicated
on this line.
Peak Set in the Integration Parameters window in the Data Handling

590
Item Description
Measurement Method section. Either Area, Height or Square Root of Height.
Calculation
Type
Set in the Integration Parameters window in the Data Handling
Method section. Either Percent, Normalized Percent, Internal
Standard or External Standard. If results have been
normalized (set in the Integration Parameters window in the
Data Handling Method section), it is indicated on this line.
Peak No. The number of the peak in the results table.
Peak Name Set in the Peak Table Window in the Data Handling Method
section. Peak names are shown for peaks that have been
identified as being in the peak table.
Result (units) The calculated results. The units (set in the Results Format
portion of the Data Handling Method section) are displayed in
the results column header.
Standard Peak
Name
This column is shown when internal standard calibration is
used and there exists more than one standard peak. This
refers to the name of the standard peak used for the given
non-standard peak.
Ret. Time The actual retention time of the peak, in minutes.
Time Offset
(min)
The amount of time, in minutes that the actual retention time
differs from the retention time for the peak in the peak table.
The retention time in the peak table is automatically updated
with the actual retention time to account for peak drift.
Area (counts) The measured peak size. This will either be the area, height or
square root of height, depending upon the peak measurement
type (set in the Integration Parameters window in the Data
Handling Method section). The column header will reflect the
appropriate measurement type.
Rel. Ret. Time Reported when an RRT peak has been designated in the
peak table (in the Data Handling Method section). The
Workstation calculates relative retention times from the
retention time of the RRT peak and the unretained peak time
(set in the Define Peak Windows dialog box accessed from
the peak table).
Sep. Code A two letter code indicating the relationship of the peak start
and end to the baseline. Possible separation codes are
BV: Baseline to valley
BB: Baseline to baseline
VB: Valley to baseline
VV: Valley to valley
TS: Separated Tangent Peaks
TF: Fused tangent peaks
GR: Group Peak
BM: Baseline to mended end
MB: Mended end to baseline
MM: Mended end to mended end
MV: Mended end to valley
VM: Valley to mended end
Width 1/2
(sec)
The width of the peak at half its height.

591
Item Description
Group This column is shown when the Show Peak Group Totals
checkbox is checked in the Results Format portion of the
Report Method section. The group number for each peak is
set in the peak table in the Data Handling Method section.
Status Codes A code or codes specific to a peak in the results table.
Possible status codes are
R: Reference Peak (designated in the peak table)
*: No result can be calculated, check the calibration curve.
+: More than one result can be calculated, the first solution is
shown in the results field. Check your calibration curve or use
a lower order curve fit (specified in the peak table).
V: Peak fails verification (verification runs only)
M: Missing peak (if Report Missing Peaks is set in the
Integration Parameters Window in the Data Handling section
of the Method)
C: Result out of calibration range, check the calibration curve
and the range tolerance setting in the Method.
S: Internal Standard Peak (designated in the peak table for
internal standard and normalized percent calculations only)
U: User-defined peak endpoint (the peak size is affected by an
endpoint that was manually placed in Interactive Graphics).
Total
Unidentified
Counts
The total number of counts accounted for by peaks not
identified in the peak table.
Detected
Peaks
The total number of peaks detected during integration. Peak
detection is affected by parameters set in the Integration
Parameters Window in the Data Handling Section of the
Method.
Rejected
Peaks
The total number of detected peaks that were rejected based
on values set in the Integration Parameters Window in the
Data Handling Section of the Method.
Identified
Peaks
The total number of detected peaks that were identified in the
peak table.
Standard Peak
Amounts
Set in the SampleList or SampleLog (in System Control) or the
Reintegration List (in Interactive Graphics). This is used with
Normalized Percent and Internal Standard calculations and
identifies the amount of the Standard Peak(s) (designated in
the Peak Table Window in the Data Handling Section of the
Method).
Multiplier Set in the SampleList or SampleLog (in System Control) or the
Reintegration List (in Interactive Graphics). The result for each
peak is multiplied by this value.
Divisor Set in the SampleList or SampleLog (in System Control) or the
Reintegration List (in Interactive Graphics). The result for each
peak is divided by this value.
Baseline
Offset
The distance the chromatographic signal is above or below
zero at the start of the run. Baseline offset is measured in
microunits (units are volts or absorption units, depending upon
the detector). The baseline offset is equivalent to the
amplitude of the first data point in the Data File.
Noise Noise is the peak-to-peak noise measured in microunits (units
are volts or absorption units, depending upon the detector).

592
Item Description
The noise used by Data Handling depends upon the noise
options set in the Integration Parameters Window in the Data
Handling section of the Method. The report includes the noise
value for this run, and the noise value actually used, if it is
different.
Manual
injection
(injection
information)
Indicates the type of injection device used (for example,
manual injection, 8200 AutoSampler, or AI-200 AutoSampler),
and the rack, vial and injection volume, if appropriate.
Run Log The Run Log is included in the report if the Run Log checkbox
is checked in the Results Format portion of the Report section
of the Method. The Run Log is the instrument control Method
that was used in the run that generated the Data File. For
3400 and 3600 GCs, it is the Method as it was downloaded
before the run began. The 3400 or 3600 Event Log (included
in the Run Log) will describe any changes that occurred after
run start. For all LC modules, the Run Log is the Method that
was actually executed on the LC module itself. Any changes
that occurred during the execution of the Method will be
incorporated into the Run Log. Also included with the Run Log
is information from the Module Information Log, which can be
edited in System Control on a per-module basis.
Time Events Data Handling timed events (programmed in the Time Events
Window in the Data Handling Section of the Method) are listed
with the times that they actually occurred.
Error Log The Error Log is included in the report if the Error Log
Report section of the Method. The Error Log is a list of errors
that occurred during the run that generated the Data File.
Calibration
Report
The Calibration Report is included in the report if the
Calibration Report checkbox is checked in the Results Format
portion of the Report section of the Method. The Calibration
Report is the text portion of the Calibration Block Report for
the Method used to calculate results. It includes the calibration
responses and curve coefficients for each peak.
Revision Log The Revision Log is included in the report if the Revision Log
Report section in the Method. The Revision Log contains the
date/time and Method name used every time a recalculation is
performed on the Data File. Results deletion is also
documented in the Revision Log. Documentation of
recalculations can be disabled from the Security
Administration application.
Original Notes The Original Notes are included in the report if the Notes
Report section of the Method. The Original Notes are the
notes set in the SampleList in System Control when the
injection was performed that generated the Data File.
Appended
Notes
The Appended Notes are included in the report if the Notes
Report section of the Method. The Appended Notes are the
notes set in the SampleLog (in System Control) or in the
Reintegration List (in Interactive Graphics) during the most
recent recalculation performed on the Data File.

593
Verification Report
Below is an example of a results report generated from a verification run. The
exact format of your verification reports may vary depending on the following
parameters:
Options set in the Results Format portion of the Method
- The type of run being performed (blank baseline, calibration, analysis, or verification)
- The peak measurement type (area, height or square root of height)
- The calculation type (percent, normalized percent, internal standard or external
standard)
- The presence of an RRT peak, designated in the peak table (which determines
whether relative retention time is shown)
The format of the ASCII text file generated when ASCII file conversion is
performed is identical to the format in the printed report.
Following this example is a legend of the fields that appear in the report. Only
those fields that differ from the Analysis Report are listed. See the Results
Report Format Description for a listing of the additional fields.

Verification Report
Title : Title
Run File : Data File name
Method File : Method File name
Sample ID : Sample name
Injection Date: Date/Time Calculation Date: Date/Time
Operator : Operator Name Detector Type: Detector Type/Range
Workstation: Volume Label Bus Address : module bus address
Instrument : Instrument Name Sample Rate : Sample Rate (Hz)
Channel : Channel ID/Name Run Time : Run Time (min)
*********** Star Chromatography Software
**************************************
Run Mode : Verification
Peak Measurement: Measurement Type
Calculation Type: Calculation Type
Level : Verification Level
Tolerance : 100.0%
Expected Calculated Ret. Time
Peak Peak Result Result Dev. Time Offset Area Status
No. Name () () % (min) (min) (counts) Codes
--- ------------ ---------- ---------- ----- ------- ------- -------- ------
1 Peak 1.841 N/A INT STD 0.0 1.841 -0.000 220494 S
2 Peak 2.004 1.0000 2.004 VM
3 Peak 2.205 1.0000 2.205 VM
4 Peak 2.756 1.0000 2.4122 141.2 2.754 0.000 102519 CV
5 Peak 3.297 1.0000 2.0112 101.1 3.298 0.001 1212397 RV
6 Peak 3.798 1.0000 2.0191 101.9 3.799 -0.000 493782 V
7 Peak 4.791 1.0000 1.9279 92.8 4.789 -0.001 700782
8 Peak 5.125 1.0000 4.7624 376.2 5.104 -0.000 328998 CV

594
9 Peak 5.580 1.0000 1.4435 44.3 5.586 -0.001 297265
--- ------------ ---------- ========== ----- ------- ======= ======== ------
Totals: 14.5762 -0.002 3356238
Status Codes:
R - Reference peak
V - Out of verification tolerance
M - Missing peak
C - Out of calibration range
S - Internal Standard peak
Total Unidentified Counts : 0 counts
Detected Peaks: 7 Rejected Peaks: 0 Identified Peaks: 9
Standard Peak Amount:
2-Octanone Amount = 12
Multiplier: 1 Divisor: 1
Baseline Offset: -20 microVolts
Noise (used): 1 microVolts - monitored before this run
Manual injection
******************************************************************************
*

Item Description
Level Set in the SampleList or RecalcList (in System Control) or in the
Reintegration List (in Interactive Graphics). This corresponds to
the concentration level used in the verification sample, which can
be the same as one of the calibration levels, or can be between
levels used in calibration. The value in the peak table at this level
is assumed to be the amount of the compound used in the
verification sample.
Tolerance Set in the Verification dialog box accessed from the Peak Table
Window in the Data Handling section of the Method. This is the
maximum acceptable deviation percentage allowed before
considering a peak to be out of tolerance.
Expected
Result
This is the amount obtained from the peak table corresponding to
the designated verification level.
Calculated
Result
This is the result calculated from the calibration curve using the
detector response from the verification run. If no drift has occurred
in the system, and the amount of the compound in the verification
sample is identical to the amount of the same compound in the
calibration sample at the same level, then this value will be the
same as the expected result.
Dev. % The percentage that the calculated result deviates from the
expected result. If this value is larger than the tolerance, then a
verification failure occurs.

595
Standard GC Reports Toolbar
Main Toolbar

Displays the Open Data File dialog box.

Displays the Print dialog box.

Converts the text results report into an ASCII file. The
name of the ASCII file is based on the data file name,
with the channel number appended to it. The ASCII file
ends with a ".txt" extension..

Displays the Find dialog box.

Displays the Title dialog box.

Displays the Chromatogram Options dialog box.

Displays the Results Options dialog box.

The Data File Quick Link button shows the current Data
File. Use this Quick Link button to perform additional
operations on the Data File.

The Method Quick Link button shows the Method used
for the most recent recalculation of the selected channel
for the data file. Use this Quick Link button to view, edit
or print this Method.
This selection box contains all channels for the selected
data file and allows you to switch between them without
re-opening the file.

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