Eksigent Control Software

Software User Guide

D5031167 C
September 2012
This document is provided to customers who have purchased AB Sciex equipment to use in the
operation of such AB Sciex equipment. This document is copyright protected and any
reproduction of this document or any part of this document is strictly prohibited, except as
AB Sciex may authorize in writing.
Software that may be described in this document is furnished under a license agreement. It is
against the law to copy, modify, or distribute the software on any medium, except as specifically
allowed in the license agreement. Furthermore, the license agreement may prohibit the software
from being disassembled, reverse engineered, or decompiled for any purpose.
Portions of this document may make reference to other manufacturers and/or their products,
which may contain parts whose names are registered as trademarks and/or function as
trademarks of their respective owners. Any such use is intended only to designate those
manufacturers' products as supplied by AB Sciex for incorporation into its equipment and does
not imply any right and/or license to use or permit others to use such manufacturers' and/or their
product names as trademarks.
AB Sciex warranties are limited to those express warranties provided in connection with the sale
of its products, and are AB Sciex’s sole and exclusive representations, warranties, and
obligations with respect to its products, and AB Sciex makes no other warranty or any kind
whatsoever, expressed or implied, including without limitation, warranties of merchantability or
fitness for a particular purpose, whether arising from a statute or otherwise in law or from a
course of dealing or usage of trade, all of which are expressly disclaimed, and assumes no
responsibility or contingent liability, including indirect or consequential damages, for any use to
which the purchaser may put the equipment described herein, or for any adverse circumstances
arising therefrom.

For research use only. Not for use in diagnostic procedures.

The trademarks mentioned herein are the property of AB Sciex Pte. Ltd. or their respective
owners. Eksigent is a division of AB Sciex, LLC.
AB SCIEX™ is being used under license.

Eksigent
5875 Arnold Road, Dublin, CA 94568.
© 2012 AB SCIEX.
Printed in Canada.

Eksigent Control Software Software User Guide

2 of 152 September 2012
Contents

Chapter 1 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Install the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Configure the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Import Instrument Calibration Settings and Configure Software Drivers . . . . . . .11
Chapter 2 Acquisition Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Components of the Acquisition Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Status Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Control Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Spectral Absorbance Region . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Main Plot Region . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
Peak Table (UV Detector Systems only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
Contour Plot Region (UV Detector Systems only) . . . . . . . . . . . . . . . . . . . . . .16
File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Output Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
UV Detector Toolbox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
PeakPark ToolBox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Smoothing Toolbox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
System Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
System Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Hardware Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28
Instrument Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30
Notification Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Appearance Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Mobile Phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
Direct Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38
User Authentication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
User Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
Electronic Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40
Analysis Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40
Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40
Chapter 3 Run Manager. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Current Tray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Method Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Run Manager Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Run Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .44
About Run Table Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Edit a Menu Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Edit a Text Box or Edit Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Select Multiple Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47
Edit Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47
Move Selected Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47

Software User Guide Eksigent Control Software

September 2012 3 of 152
Contents

Auto-Complete Sample Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48

Choose Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Freeze Rows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
Freeze Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
Select a Vial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
Add Vials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
Start the Sample Run Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51
About the Sequential Option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52
About the As Available Option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52
About the Synchronized Multi-Channel Option . . . . . . . . . . . . . . . . . . . . . . . .52
About the Flush/Equilibrate when Idle Option . . . . . . . . . . . . . . . . . . . . . . . . .52
Stop the Sample Run Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52
Chapter 4 Peak Viewer Utility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Plot Dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Peak Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Analyze Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Edit Peak Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Show Peak Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Sort Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Select Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Copy Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Delete Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .56
Mark Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .56
Peak Viewer Sample Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .56
Run a Sample Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .56
Print a Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .56
Export a Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57
Customize Peak Attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57
Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57
Generate Charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .58
Generate Peak Trends . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .58
Generate Peak Trends using Custom Formulas . . . . . . . . . . . . . . . . . . . . . . .58
Modify the Plot Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59
File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61
Edit Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .62
View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .62
Peaks Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63
Plots Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65
Overlay Chromatograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68
Perform a Math Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Chapter 5 Autosampler Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Configure the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71
Chapter 6 LC Method Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Create an LC Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Edit an LC Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Summary Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Run Conditions Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75

Eksigent Control Software Software User Guide

4 of 152 September 2012
 Contents

Gradient Profile Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76

Gradient Table Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .78
Detector Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79
Chapter 7 Analysis Method Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Perform Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
Peak Detection Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
Insert a Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83
Quantitation Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83
Options Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .84
Peak Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
Capacity Factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86
Peak Asymmetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
Calculation Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
Chapter 8 Integration Time Events. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Peak Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Detection Threshold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Detection Threshold Asymmetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .92
Shoulder Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .92
Minimum Peak Width . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93
Minimum Peak Height . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93
Minimum Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .94
Integration Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .94
Negative Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .94
Peak Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95
Valley To Valley . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95
Front Skim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .96
Back Skim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .98
Manual Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .98
Forward Horizontal Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .99
Backward Horizontal Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .100
Lowest Point Horizontal Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .101
Reset Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .102
Reset Baseline At Valley . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103
Force Peak Start . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .104
Force Peak Stop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .104
Split Peak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
Merge Peak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
Force Result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .106
Manual Peak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .106
Reference Peak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107
Incompatible Events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .108
Chapter 9 Quantitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Peak Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .113
Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .118
Terms and Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .118
Types of Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .119
Types of Fits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121

Software User Guide Eksigent Control Software

September 2012 5 of 152
Contents

Linear Fit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121

Nonlinear Fits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121
Scaling Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .123
External Standard Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .124
Internal Standard Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .126
Automated Calibration Table Generation through the Run Manager . . . . . . . .127
Chapter 10 User Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
User Authentication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
Enable User Authentication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
User Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .130
Add or Remove Users and Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .131
Manage Electronic Signature Roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .132
Manage Electronic Signature Reasons . . . . . . . . . . . . . . . . . . . . . . . . . . . . .133
Manage User Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .134
Chapter 11 Electronic Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
View Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .141
About Electronic Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .142
Sign Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .143
Revoke Signatures on Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .144
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

Eksigent Control Software Software User Guide

6 of 152 September 2012
Installation
1
Install the Software
The application software and important instrument calibration values are supplied on disk. The
instructions presented in this chapter should be followed to install the software on the computer.

Note: This software should be installed by an individual with Administrator privileges.

1. Close all open applications.

2. Insert the software disk in the drive.
The current software version is shown. Refer to Figure 1-1.

Figure 1-1 Initial software setup dialog

Software User Guide Eksigent Control Software

September 2012 7 of 152
Installation

3. Click Next for license agreement dialog.

Figure 1-2 License agreement dialog

4. Click Next to specify the target installation directory.

Tip! Choose the default directory unless there is a conflict.

5. Click Next to select a desktop icon and a Quick Launch icon. Refer to Figure 1-3.

Figure 1-3 Icon creation dialog

Eksigent Control Software Software User Guide

8 of 152 September 2012
 Installation

6. Click Next to open the Ready to Install dialog. Refer to Figure 1-4.

Figure 1-4 Ready to install dialog

7. Click Install.
A status dialog indicates the progress of the installation.

Figure 1-5 Installing status dialog

After the software has been installed, the integrity of the installation can be verified
by running the Validate Installed Files utility. This utility is available from the Eksigent
Program menu.

Software User Guide Eksigent Control Software

September 2012 9 of 152
Installation

Note: This validation can be run at any time from the list of programs that is
accessed from the Programs menu. Refer to Figure 1-6

Figure 1-6 Programs associated with Eksigent software

When the validation utility is run, a status dialog indicates the progress of the
validation.

Figure 1-7 Installation Qualification progress bar

Configure the System

After the software is successfully installed, configure the HPLC system using the Instrument
Configuration dialog. This dialog is used to select which hardware components are installed, set
the communications protocol, and select certain system options. The performance parameters
set in this window are described in Instrument Configuration on page 30.
1. Connect the instrument to a serial port, or USB port if equipped, on the computer.
2. Turn on the HPLC instrument.
3. Run the Eksigent control software from the desktop icon.

Note: If the software does not detect the instrument, a warning message is
shown. Check that the instrument is turned on and that the serial cable is
properly connected.

4. Select Instrument Configuration from the System menu to open the Instrument
Configuration dialog. Refer to Figure 1-8.

Eksigent Control Software Software User Guide

10 of 152 September 2012
 Installation

Figure 1-8 Instrument Configuration dialog

5. Make any necessary changes. For more information, refer to Instrument
Configuration on page 30.

Note: If there is no communication between the computer and the

instrument, then the COM port entry should be changed.

6. Click OK to accept the new settings.

7. Restart the software.

Import Instrument Calibration Settings and

Configure Software Drivers
Software drivers allow the Eksigent software to be controlled by third party programs. The user
can select the appropriate drivers through the Driver Configuration Utility dialog that is accessed
from the Eksigent Program group in the Windows Start menu. The Driver Configuration Utility
also allows the user to import the previously exported or factory-defined system calibration
settings.

Software User Guide Eksigent Control Software

September 2012 11 of 152
Installation

Figure 1-9 Eksigent Driver Configuration Utility dialog

• Do one of the following:
• For installs on a new system or an attempt to restore a system to the original
factory-installed calibration settings, insert the disk with the original calibration
values and then click Calibration Disk.
• Click OK to complete software installation.

Eksigent Control Software Software User Guide

12 of 152 September 2012
Acquisition Window
2
The application software consists of three primary modules:
• The Acquisition window is used to establish operational parameters and monitor an
acquisition.
• The Run Manager is used to set up and queue a series of acquisitions.
• The Peak Viewer is used to view and analyze data after acquisition.
These three modules control the acquisition of each sample, manage individual sample
information, and process the resulting data for the configured LC device.
When the software is started, the Acquisition window (Figure 2-1) opens. All areas of the
software can be accessed from this screen, including the Run Manager and the Peak Viewer.

Note: When the Eksigent device is controlled by an external software application such
as the Analyst® software, the Run Manager is not available. This button becomes an LC
Method Editor button and enables the user to edit methods.

Figure 2-1 Acquisition window

Software User Guide Eksigent Control Software

September 2012 13 of 152
Acquisition Window

Components of the Acquisition Window

The Acquisition window shows the currently acquired sample data and provides access to a
broad range of device configuration and diagnostic information. The main screen has the
following sections:
• Status Area on page 14
• Control Buttons on page 15
• Spectral Absorbance Region on page 15
• Main Plot Region on page 16
• Peak Table (UV Detector Systems only) on page 16
• Contour Plot Region (UV Detector Systems only) on page 16

Status Area
The status area shows information about the current run, including the flow rate, run time, current
method, sample information, pump state, injection valve position, the location in the sequence,
and the file name used to save the data after the run is completed. Refer to Figure 2-2.

1
Figure 2-2 Status area

Customize the Status Area

• Right-click the status bars (item 1 in Figure 2-2) in the status area and then select an
item from the status area options. Refer to Figure 2-3.

Figure 2-3 Status information options

If a status bar is selected, it shows a graphical representation of the selected
parameters such as the current mobile phase flow rates (Qa and Qb), the total flow
rate (Qc), the internal flowmeter pressures (Pa and Pb), the column pressure (if

Eksigent Control Software Software User Guide

14 of 152 September 2012
 Acquisition Window

installed, Pc and Pd), and the pump power as a percentage of maximum pump
power for each channel.

Change the Flow Rate and Pressure

The units for flow rate and pressure can be changed by selecting the corresponding items from
the menu or by clicking the labels at the bottom of each status bar.
• Flow units can be shown in nL/min or µL/min.
• Pressure units can be shown in psi or bar.
The current column temperature is shown if a column heater is installed.

Control Buttons
Run Manager
The Run Manager button opens the Run Manager dialog, where sample and method information
is entered to create sample sequences. For more information, refer to Chapter 3.

Pause Button
When an acquisition is in progress, the Pause button maintains the conditions of the device at
their current values indefinitely. Clicking this button during a run maintains the elution conditions
continuing to acquire data. After being clicked, the Pause button changes to Resume and is used
to continue the LC method.

Stop Button
The Stop button stops the LC method and then stops the sequence table at its current position.
For multi-channel devices, only the currently active channel is stopped. The device channel is
placed into the Standby state and the pumps are turned off.

Extend Run Button

The Extend Run button provides a menu to extend or shorten the LC method run time. Run time
can be extended indefinitely, but cannot be shorted to less than the original method run time.

Acquisition Information Button

The Acquisition Information button opens a dialog that shows information about the sample run
and other acquisition information saved with the data file.

Direct Control Button

The Direct Control button provides a shortcut to the Direct Control dialog.

Spectral Absorbance Region

If the system is equipped with a UV Detector, the spectral absorbance region shows a real-time
UV absorbance spectrum. During a sample run, this region is continuously updated with the most
recently acquired spectrum. If the pointer is within the spectral contour plot region, the spectral
absorbance region shows the spectrum collected at the point in time nearest to the pointer.

Software User Guide Eksigent Control Software

September 2012 15 of 152
Acquisition Window

The vertical dashed lines in the spectral absorbance region indicate the absorbance wavelength
range used to calculate absorbance for the chromatogram. These values are initially defined in
the LC Method Editor. Refer to About Run Table Cells on page 46. The wavelength range can be
modified graphically by using the pointer to drag the dashed lines to a new wavelength range. To
modify only the upper or lower wavelength setting, hold the Ctrl key while dragging the relevant
dashed line.
The axes limits for the spectral absorbance region are defined by the upper and lower
wavelength ranges (X-axis) of the spectrometer and the current chromatogram axis limits 
(Y-axis).

Main Plot Region

The main plot region can show the UV absorbance signal of the detector as a function of time
(UV detector systems only), the mobile phase gradient profile, the measured flow rate, and the
system pressure. External detector information can also be shown using the external A/D signal
input.

Modify the Plot Scale

Use the following steps as required.
• Click the upper or lower X or Y-axis limits and then type a new value. It is possible to
graphically zoom into a specific range by dragging the pointer over the region of
interest.
A zoom window is drawn for reference and the zoom action occurs when the mouse
button is released. Right-click to open a menu containing Zoom Last and Zoom Out
functions.
• Click the X-axis label to change the X-axis time from minutes to seconds.
• Right-click and then select Add Integration Event to add integration timed events
graphically. The list of all available events are shown. Move the pointer and then
click the left mouse button to select the start and stop time.
• If peak results are present, move the pointer over the peak baseline to show a move
icon that can be used to manually adjust the peak baselines. Drag the baseline point
to a new location to show the Peak Detection Tab of the Analysis Method window
with a new Manual Baseline event added to the integration timed event table.

Peak Table (UV Detector Systems only)

Peak results are shown in the peak table. The table columns can be customized by selecting the
Choose Peak Table Columns option of the Analysis menu. If a corresponding column is selected,
peak names can be assigned and edited.

Contour Plot Region (UV Detector Systems only)

For systems equipped with a UV detector, the contour plot region shows spectral absorbance
data versus time over the entire spectrometer wavelength range. This spectral data appears
directly below the chromatogram window and has the same time X-axis range and units. The Y-
axis values are determined by the spectrometer wavelength range. The absorbance values in the
contour plot (Z-axis) are color-coded according to a user-selected color palette.

Eksigent Control Software Software User Guide

16 of 152 September 2012
 Acquisition Window

After data is collected, moving the pointer over the contour plot region updates the spectral
absorbance region with the absorbance spectrum at the indicated acquisition time.

File Menu
Table 2-1 lists the commands available from the File menu in the Acquisition window.
Table 2-1 File Menu
Command Function
Open Opens a previously stored data file (.txt,.dat) in the main acquisition
window. Only a single file can viewed at one time. The Peak Viewer utility
should be used to view multiple files or to open files while an acquisition
is in progress. Refer to Peaks Menu on page 63.
Save As Saves a data file to the hard disk in a .txt, .xls, .dat, or .cdf (AIA/ANDI)
format. A bitmap image of the spectral absorbance contour can also be
independently exported using this command.
Output Options Opens the Output Options dialog, allowing access to the file output
parameters. Refer to Output Options on page 17.
Peak Viewer Opens the Open dialog, allowing users to select a file or list of files. When
a file is selected, then the Peak Viewer dialog opens to allow users to
view each file. Refer to Peak Preview on page 19.
Print Preview Opens the Report dialog, refer to Print Preview on page 19.
Print Prints a report summarizing the current data, refer to Print on page 21.
Autosave Instructs the system to automatically save the data file at the end of an
analysis.
Autoprint Prints a report summarizing the current data at the end of a run.
Exit Opens the Close Program dialog.

Output Options
The Output Options dialog (Figure 2-4) is used to specify the preferred data file formats, paths,
and naming conventions to be used when the AutoSave option is selected.

Software User Guide Eksigent Control Software

September 2012 17 of 152
Acquisition Window

Figure 2-4 Output Options dialog

Output
Output folder: Used to indicate the default folder where Autosave data will be stored. Additional
sub-folders can be created with the output filename entry. If the folder does not exist, users are
prompted with a choice for creating that folder.
Output filename(s): Used to specify filename attributes for each data set after the run has
completed. Users can customize the file naming convention by using one or more tags. These
may include the method name, sample name, date, time, vial number, incremental counter, and
so on. The default filename format uses a dynamically created date subfolder and creates a
unique filename based on the time:
\<date>\ EK< channel>_<time>
Many other unique filenames can be generated from the various tags. Click Help for more
information on the available tags or use the list to insert new tags.
When the user creates a naming convention, an example filename is shown.
Prompt to save: Select to prompt users to name the data file at the completion of each run. This
is not recommended when there is more than one sample in the Run Manager. Tags that use
information from the Run Table are shown in the example filename as either blank or as the value
last used with that tag.
Autosave: Select to automatically generate a data file name and save the file in the folder
specified in the Output folder. If this command is not selected, the user is prompted to save the
data file after each sample run. The use of the Autosave option is recommended.
If a unique filename is not specified in the Output filename(s) edit box and Autosave is selected,
a unique filename is created if the current filename already exists in the specified folder.

Eksigent Control Software Software User Guide

18 of 152 September 2012
 Acquisition Window

Autosave Output Format

Use the Autosave Output Format region to specify which data file types should be automatically
created. File types include Text, ANDI, binary .dat, and a peak table (text format) that can be
appended.
• Text files contain the chromatogram, flow, and pressure data, and are tab-delimited.
Text files have the .txt file extensions.
• ANDI files contain a single chromatogram and AIA-defined information only. ANDI
files have the .cdf file extension.
• Binary .dat files contain system settings, flow, pressure data, and complete
absorbance spectral data for systems with spectrometers.
• The Appendable peak table format is a tab-delimited text file that contains sample
and peak information only. The file is named PeakTable.xls and is located in the
specified sample file folder. The information from subsequent sample runs is
appended to this file, so the analysis results of an entire sample set are created in a
single file for importing into spreadsheet or database applications.

Ownership Tags
Operator Name: The name of the person who is running the experiment or test that generated
the current dataset.
Dataset Origin: The name of the organization where the current dataset originated. Dataset
Origin information can include the organization's address, telephone number, e-mail nodes, and
the names of individual contributors, including the system operators, and any other appropriate
information.
Dataset Owner: The name of the owner of a proprietary dataset. The person or organization
named here is responsible for the accuracy of the information in this field. Data copyrights should
be indicated here.

Peak Preview
The Peak Preview function provides access to the Peak Viewer for loading and analyzing larger
sets of sample data. Refer to Peaks Menu on page 63.

Print Preview
The Print Preview function is used to preview the appearance of a report before it is printed. Print
previews are generated in the Report dialog (Figure 2-5). The Report window is shown with a
representation of the report for the currently loaded data.

Software User Guide Eksigent Control Software

September 2012 19 of 152
Acquisition Window

Figure 2-5 Print Preview dialog

Select between portrait and landscape mode for the orientation of the report.
To generate a PDF or HTML copy of this report, click either Export PDF or Export HTML.
• Double-click on the report to zoom in.
• Right-double-click on the report to zoom out.
• Use the horizontal and vertical scroll bars to scroll the report.
• Left click, hold, and drag on the report. The report scrolls in the direction that is
dragged. During this procedure, a hand graphic is used as the icon.
• Click the magnifying glass to toggle between two best-fit views (one best-fit to the
vertical and one best-fit to the horizontal).
• Click on the down-arrow to the right of the magnifying glass to select predefined
viewing styles and magnification. The available viewing styles are Whole Page,
Page Height, Two Pages, and Thumbnail. The available magnifications are 150,
100, 75, 50, and 25%.
• Click the printer icon to print the report. A Print dialog opens, allowing users to
modify the print settings.
To exit the print preview, close the window. The selected report format is used the next time the
Report window is opened.

Eksigent Control Software Software User Guide

20 of 152 September 2012
 Acquisition Window

Print
Click Print to print the report for the currently loaded data using the Print Preview or the Print
dialog. The report for the currently loaded data is sent to the default printer specified for that
computer. The most recently selected report format is used.

View Menu
Table 2-2 lists the commands available from the View menu in the Acquisition window.
Table 2-2 View Menu
Command Function
UV Detector Toolbox Opens the UV Detector dialog, which allows for manual control of the
detection settings. Refer to UV Detector Toolbox on page 21.
PeakPark ToolBox Opens the PeakPark toolbox, which allows for setting peak parking
options, refer to PeakPark ToolBox on page 23.
Smoothing Toolbox Opens the Smoothing window, which provides access to the post-
acquisition data spline values. Refer to PeakPark ToolBox on page 23.
System Logs Opens the System Logs sub-menu to access audit trails of system
messages, and warnings. Refer to System Logs on page 24.

UV Detector Toolbox
If the system includes a UV absorbance spectrometer, the UV Detector Toolbox can be used to
view the current UV detector settings and make adjustments as necessary.

Note: This window is typically used for diagnostic purposes, as each LC method
contains detector settings that are specific to that method. As a result, many of the
settings in this toolbox are not accessible during acquisition as they are being controlled
by the parameters specified in the LC method.

Software User Guide Eksigent Control Software

September 2012 21 of 152
Acquisition Window

Figure 2-6 UV Detector Toolbox dialog

For more information and descriptions of the parameters in this dialog, refer to Chapter 6.
Up to four independent chromatograms can be generated and displayed from the spectral data.
Only active chromatograms are editable here. The Chromatogram max is a chromatogram
generated using the wavelength at maximum absorbance for each point in time. Other
acquisition parameters, set in the method, are shown here.

Baseline Region
The Baseline region is used to indicate the parameters for collection of the baseline. If the Real-
time correction option is selected, users can indicate the Wavelength and Bandwidth.

Reference/Background
Use the Reference/Background options to turn on or off the Automatic background and reference
acquisition. If this option is selected, the detector background and reference signal are acquired
prior to every LC method acquisition. When the option is not selected, the Acquire reference and
Acquire background buttons can be used to manually acquire those signals. In this case, each
LC method acquisition starts immediately and the current background and reference information
(in memory) are used.
Detector Sync.
Use the Detector Sync. options to determine how to synchronize the detector acquisition. The
Sync. with injection start option indicates that the detector should start acquiring data (time = 0)
when the injection valve moves to the inject position. The Sync. with gradient start option

Eksigent Control Software Software User Guide

22 of 152 September 2012
 Acquisition Window

indicates that the detector should start acquiring data (time = 0) when the injection has
completed and the gradient (flow profile) begins. This mode is useful when comparing retention
time reproducibility with varying injection volumes (binary gradient LC methods with metered
injections.)

PeakPark ToolBox
Eksigent LC devices can rapidly reduce the total column flow rate to allow for extended MS/MS
analysis at a particular point in the chromatogram. This procedure, which is commonly called
peak parking, is controlled using the PeakPark ToolBox (Figure 2-7). Adjustments to the
composition of the flow profile are paused during the parked period and resume after parking is
discontinued. Peak parking is only enabled during an acquisition.

Figure 2-7 PeakPark ToolBox dialog

Set the Total LC Flow Rate

Do one of the following:
• Click Park Now during sample acquisition to rapidly set the total LC flow rate to the
value indicated in the Flowrate field. When this feature is selected, the button
changes to Unpark and it can be clicked again to resume the method condition at the
original flow rate.
• Alternatively, the LC device Park In external trigger signal can be used to initiate or
resume peak parking using an external device control. For example, a mass
spectrometer using contact closure control can be used.
The Flowrate field indicates the total pump flow rate during parking conditions. When peak
parking is activated, the pumps provide this flow rate while maintaining the current mobile phase
composition.
The Flowrate Reference option determines the reference method that is to be used to rapidly
stabilize the LC flow rate at the new lowered value.

Software User Guide Eksigent Control Software

September 2012 23 of 152
Acquisition Window

• The Column flow rate reference method uses the measured column pressure at the
start of the PeakPark operation to estimate the current column flow resistance. This
value, with the real-time measured column pressure is used during the peak-park
transition to stabilize the column at the new flow rate. This method is typically the
fastest method to attain the target peak-park flow rate values.
• The Mobile Phases flow rate reference method uses the flow rates measured
directly from the individual mobile phase (A and B) flowmeters while the pump flow
rates are decreasing. This method is typically slower to lower the total flow rate
through the column, but more accurately maintains the mobile phase mixture
fraction.
Timing check boxes can be used to ignore external triggers or peak-park for a fixed duration after
the initial trigger event. This option is useful when noisy trigger signals are present (from the
mass spectrometer) and ensures that the device will stay in park mode for a configurable
acquisition period.

Smoothing Toolbox
Use the Smoothing Toolbox (Figure 2-8) to apply a cubic spline fit to the chromatogram after
acquisition is completed. The error band defines the looseness of fit in Y units, where a larger
number applies more smoothing. The Smoothing Toolbox can be used with systems with a
spectrometer.

Figure 2-8 Smoothing Toolbox dialog

System Logs
Use the System Logs sub-menu to show a variety of log files, which are audit trails that record all
pertinent system information, including ordinary usage statistics, system warning messages, and
experiment status logs. Log files are designed to prevent malicious tampering with their contents
to make sure of the long-term validity of the system audit trail. Each log file is archived on a
regular basis.

Open the Log Dialog

• Click any of the available logs in the System Logs menu to open the Log dialog.

Eksigent Control Software Software User Guide

24 of 152 September 2012
 Acquisition Window

Figure 2-9 View instrument logs

A typical log (the Alerts log) is shown in Figure 2-10.

Figure 2-10 Alerts Log dialog

View a Log
• To view the contents of a log in the log window, click any available log in the left
column. The entries of that log are shown in the pane to the right.
• Alternatively, click Select Log to open the Open File dialog and then select a log
file.

Sort a Log
• To sort the log contents, click any column heading. The log entries are sorted based
on that column. Ascending sort is always used when the column is first clicked.
• To use descending sort, click the column heading again.
Log entries often appear in alternating lines of black and blue. The coloring scheme
is to help locate identical entries within a field. The color of the entries is based on
the column on which the sort is applied. For example, the log entries in Figure 2-10
are sorted based on date. Starting at the top, the color alternates when a different
value is detected. The first line is always black. On the second line, the date value is
different, so the color alternates to blue. On the third line, the date value is the same
as the second, so the color stays blue. On the fourth line, the date value changes
again, so the color alternates back to black. This pattern continues to the end of the
entries.
The Log Information field shows some basic information about the selected log,
including creation date, last modified date, and the file location of the log file.
• To exit the dialog, click OK.

Software User Guide Eksigent Control Software

September 2012 25 of 152
Acquisition Window

Export a Log
The contents of any log can be exported to a PDF file or to an Excel spreadsheet (.xls).
• Select an Export format in the Log Information field and then click Export.
• If the Excel option is selected, a Windows Export to dialog opens. Type a file
name for the log and then click Save.
• If the PDF option is selected, a PDF preview window opens. Use the Portrait
or Landscape buttons to change the page orientation. Click Save to open a
Save As dialog to save the PDF file. Use the page navigation arrows to
navigate through multiple-page PDF documents. Use the magnifying glass
icon to switch between two best-fit views of the document. To print the PDF,
click the printer icon.
The Alerts log (Figure 2-10) contains a list of any warnings and messages automatically
generated by the system but which do not need immediate attention. The Alerts Log dialog opens
automatically when a system check discloses a potential issue and shows the issue as an Alert
event. The log includes information such as the Login name of the current user, the date of each
occurrence of the Alert event, and a detailed description of the event.
The System log (Figure 2-11) contains a list of user actions that affect the device, such as
calibration options.

Figure 2-11 System Log dialog

The Sample Queue log (Figure 2-12) contains a list of samples that have been processed for
acquisition by the Run Manager. The column on the left side of the table indicates what action
has been taken on each sample.

Figure 2-12 Sample Queue Log dialog

Eksigent Control Software Software User Guide

26 of 152 September 2012
 Acquisition Window

The Channel01 log (Figure 2-13) contains a list of user actions that affect Channel 1 conditions,
such as flow rate. For multi-channel instruments, channel log information is available for each
additional channel.

Figure 2-13 Individual channel log dialog

System Menu
Table 2-3 lists the commands available from the System menu in the Acquisition window.
Table 2-3 System Menu
Command Function
Hardware Diagnostics Opens the Hardware Diagnostics dialog. Refer to Hardware
Diagnostics on page 28.
Instrument Opens the Instrument Configuration dialog. Refer to Instrument
Configuration Configuration on page 30.
Notification Options Opens the Notification Options dialog. Refer to Notification Options on
page 33.
Appearance Settings Opens the Appearance Settings dialog for customizing the data. Refer
to Appearance Settings on page 33.
Mobile Phases Opens the Mobile Phases dialog to describe the mobile-phases and
controlling the purge and flush functions. Refer to Mobile Phases on
page 36.
Direct Control Opens the Direct Control dialog, which allows for manual control of the
pumping system and injection valve. Refer to Direct Control on
page 38.
User Authentication Opens the User Logon dialog. Refer to Enable User Authentication on
page 129.
User Manager Opens the User Logon dialog, followed by the User Manager dialog.
Refer to User Manager on page 39.
Electronic Signatures Opens the Electronic Signatures dialog. Refer to Electronic Signatures
on page 40.

Software User Guide Eksigent Control Software

September 2012 27 of 152
Acquisition Window

Hardware Diagnostics
Use the options on the Hardware Diagnostics dialog (Figure 2-14) to calibrate the LC hardware,
examine instrument usage statistics, and perform automated diagnostic routines.
.

Figure 2-14 Hardware Diagnostics dialog

Users can select the Remind me to run diagnostic tests once a month check box to receive
monthly reminders.

Flow Calibration Tab

Use the Auto-Diagnose region to select any of the auto-diagnostics. The system sequences
through the selected diagnostics automatically when the user clicks Start Diagnostics.
• Re-Initialize Transducers is a calibration function that reads and sets the steady-
state, zero-pressure reading on the internal system transducers.
• Check For Leaks/Blockage is a diagnostic function that sequences the pumps at
different flow rates, determines whether pressures and flow rates reach expected
levels, and reports any problems. It is recommended to use a column or flow
restrictor at the device outlet. (Only available on ekspert™ systems.)
The Calibrate region is a calibration function that guides the user through the following steps:
• Calibrate Flowmeter shows the Flowmeter Calibration dialog (Figure 2-14), which
guides the user through flow calibration steps.
• Set Response slide bar allows the user to adjust how quickly the pump responds to
setpoint changes and flow disturbances. Sliding the bar to the right increases the
responsiveness. This setting affects flow control stability.

Eksigent Control Software Software User Guide

28 of 152 September 2012
 Acquisition Window

Usage Information
• Total Sample Injections shows the total number of injections performed. This number
is useful for tracking instrument usage. Click CLR to clear the counter.
• Total Flowmeter Usage shows the total number of hours of flowmeter usage. This
number is useful for tracking instrument usage. Click CLR to clear the counter.
• Filter Usage shows the volume of fluid that has passed through the cell guard filter.
Click CLR to clear the field when the filter is changed.

Calibration Values Tab

The Calibration Values tab is shown in Figure 2-15.

Figure 2-15 Calibration Values tab

Flow Region
The Flow region on the Calibration Values tab (Figure 2-15) shows fluid-independent and fluid-
dependent K values used for flow control. The actual K values may slightly change every few
seconds because they are calculated based on measured temperature.

Pressure Sensors
The Pressure Sensors region shows the pressure sensor calibration values.

PID Region
The PID region shows calibration values relating to the pump control parameters.

Software User Guide Eksigent Control Software

September 2012 29 of 152
Acquisition Window

Instrument Configuration
System Tab
Use the Instrument Configuration dialog to set hardware configuration options. Usually these are
set during the initial installation, but they may be set any time the system configuration changes.

Figure 2-16 Instrument Configuration dialog—System tab

Eksigent Device is used to configure the software for the appropriate Eksigent LC instrument.
COM Port allows the user to select the serial port used to connect to the LC instrument.
Injection Valve allows the user to configure the software for the presence or absence of an
injection valve. For most systems, this field should be set to Internal.
System shut-down is an option that shuts down power to critical electronic components after a
specified period of inactivity. The system shut down option allows the user to program a series of
unattended runs and, following successful completion, executes a method designed to reduce
the wear on the lamp, pump seals, pump check valves, and heater element.
Display flow profile setpoint values is an option to show setpoints for the flow rate values in
the status area of the main screen. If the check box is not selected (default), the measured flow
rate values are shown in the status area.
The Export Settings button is used to copy system settings to a file. This file can be used to
transfer instrument settings to another computer.

Device I/O Tab

The Device I/O tab is shown in Figure 2-17.

Eksigent Control Software Software User Guide

30 of 152 September 2012
 Acquisition Window

Figure 2-17 Instrument Configuration dialog—Device I/O tab

Signal Input Polarity

• Run Trig In active low is an option that triggers the start of a run when the Run
Trigger is brought low (TTL or contact closure). This option allows the use of an
external device, such as an autosampler, to trigger the start of a run. If no external
device is attached, this option should remain selected to avoid false signals.
• Park Trig In active low is an option that starts the Peak Parking feature when the
Park Trigger input is brought low (TTL or contact closure). This option allows the use
of an external detector to reduce the flow when a peak is detected to allow more time
to resolve the data. If no external device is attached, this option should remain
selected to avoid false signals.

Signal Output Polarity

• Ready Trig Out active low is an option that brings the Ready output contact low
(TTL or contact closure), when the device is waiting for the next sample. During a
run, the Ready output contact is held at TTL high (or contact open). Use this option
to signal an external device, such as an autosampler, that the LC pump is ready for
the next sample.
• Park Trig Out active low is an option that brings the Park output contact low (TTL or
contact closure) when the LC device is running in Peak Park mode.
• Gradient Trig Out active low is an option that brings the Gradient output contact
low (TTL or contact closure) when the LC device is running and a gradient is in
progress.

Software User Guide Eksigent Control Software

September 2012 31 of 152
Acquisition Window

Input A/D Range

Aux A/D Range radio buttons allow you to set the input signal range of an auxiliary analog device
as measured on the A/D converter of the device. The maximum dynamic range is ±10 V. Over-
voltage protection is provided up to 15 V.

Output D/A Range

Scale (mV/mAU) indicates the multiplier used on the chromatogram signal (systems with
spectrometers) to create the analog signal out of the device. This signal can be used in
conjunction with an external data acquisition system. The default value is 1 mAU/mV.
Offset (mV) indicates the offset added to the analog out signal specified above.

Advanced Tab
The Advanced Tab is shown in Figure 2-18.

Figure 2-18 Instrument Configuration dialog—Advanced tab

Flow Stabilization Limits

• Use the Stabilize flowrate option to program the system to start the pumps and
stabilize the column flow within a specified flow rate range before allowing the LC
method to begin. The LC method flow profile will not start until the column flow is
stabilized within the specified flow stabilization limit. It is recommended to program a
pre-run flush into each LC method to equilibrate the column. If an LC method is
started with the pumps off (no equilibration), the actual method start is delayed until
the stabilization criteria is met, which may result in timing incompatibilities with
external devices.

Eksigent Control Software Software User Guide

32 of 152 September 2012
 Acquisition Window

• Use the Stop device if pump power remains at 100% option to set a time duration
that will stop the pumps and data collection if pump power remains at 100% for a
specified period of time. Pump power can remain at 100% for unusually long
durations if pump flow-control logic is attempting to compensate for leaks or
blockages in the flow path.
• Use the Stop device if Pc exceeds option to set an output column pressure sensor
(Pc) value that will stop data collection if the outlet pressure exceeds a specified
limit. High values of Pc can indicate a clogged column, post-column filter, or flow cell.
• Use the Stop device if Pc is below option to set an output column pressure sensor
value that will stop data collection if the outlet pressure is below the specified limit. A
low Pc value may indicate that there is a leak, the fitting is loose, and so on.
• Use the Rapid-Inject pressure limit option to protect the system from over-pressure
during a Rapid Inject process. This value is usually lower than the absolute column
pressure limit. The system flow rate is reduced as the system pressure approaches
this limit and is maintained just below the designated limit until the injection is
complete. After injection, the flow rate returns to the value specified in the analytical
method.

Notification Options
Use the Notification Options dialog to set e-mail notification options.

E-mail Settings
For notification of various events via e-mail, select the Notify by E-mail option and then indicate
the address and server. The Test button is used to verify that communication has been
established.

Notification Events
• LC device error allows the user to choose to receive an e-mail if the LC device
reports an error.
• Autosampler error allows the user to choose to receive an e-mail if the autosampler
device reports an error.
• RunTable complete allows the user to choose to receive an e-mail when the
instrument has completed acquiring all samples specified in the Run Manager
sequence.

Notification Frequency
Use the Notification Frequency region to select whether to receive e-mail notifications
immediately, hourly, daily, or not at all.

Appearance Settings
The Appearance Settings dialog (Figure 2-19) allows the user to determine the attributes of data
plotted in the main window.

Software User Guide Eksigent Control Software

September 2012 33 of 152
Acquisition Window

Figure 2-19 Appearance Settings dialog

Table 2-4 Flow Data
Field Description
Qa (nL/min) Select to show the measured flow rate of mobile phase A in the
main window and then select a color.
Qb (nL/min) Select to show the measured flow rate of mobile phase B in the
main window and then select a color.
Qtotal (nL/min) Select to show the total flow in the main window and then select a
color.
Profile A (nL/ Select to show the gradient profile of mobile phase A in the main
min) window and then select a color.
Profile B (nL/ Select to show the gradient profile of mobile phase B in the main
min) window and then select a color.
%B Select to show the measured mixture % (from flow rate) of mobile
phase B in the main window and then select a color.

Table 2-5 Pressure

Field Description
Column (Pc, psi) Select to show the measured column pressure in the main
window and then select a color.
Amp A (Pa, psi) Select to show the measured internal pressure of mobile phase A
in the main window and then select a color.
Amp B (Pb, psi) Select to show the measured internal pressure of mobile phase B
in the main window and then select a color.

Eksigent Control Software Software User Guide

34 of 152 September 2012
 Acquisition Window

Table 2-6 Absorbance

Field Description
UV signal (mAU) Select to show the signal channel of the detector and then
select the color (systems with spectrometers).
UV reference Select to show the reference channel of the detector and then
select the color (systems with spectrometers).

A/D Channel
The Aux A/D (mV), scale X option allows the user to show the analog signal from an auxiliary
device and to select the color. The user can also designate a multiplier to be used to magnify the
analog signal plot. The offset value is a number added to the measured value.

Plot Axes
The Apply axes settings to all channels option allows the user to set the scale of the time axis to
vary automatically to fit the amount of data available to be shown.

More Options
Click More Options to open the Chart Options dialog. Select and order the columns for labeling
peaks on chromatograms, specifying plot colors, and so on that will be shown in the Main Plot
region.

Figure 2-20 Chart Options dialog—Peak Labels tab

Software User Guide Eksigent Control Software

September 2012 35 of 152
Acquisition Window

Figure 2-21 Chart Options dialog—Properties tab

Contours and Shading

Use the menu in the Contours and Shading region to select a color scheme for the spectral data.

Mobile Phases
Use the Mobile Phases dialog to configure the A and B operating fluids, document any additives,
and reset the usage counters. Accurate flow viscosity correction, flow rate measurement, and
flow stability depends upon correct identification of mobile phase fluid compositions in the Mobile
Phases dialog.

Eksigent Control Software Software User Guide

36 of 152 September 2012
 Acquisition Window

Figure 2-22 Mobile Phases dialog

Table 2-7 Mobile Phases
Field Description
Binary mixture Used to specify the mobile phase in each reservoir.
Comments/Modifiers Used to document mobile phase buffering additives,
dates, lot numbers, and other information relating to the
composition of mobile phase A and B.
Channel (upper right Indicates the LC device channel to which the current
corner) mobile phase settings are applied (multi-channel
systems only).
More button Expands the Mobile Phase dialog (Figure 2-7) to show
fields that allow the user to change parameters to
manually adjust the purge and flush functions.
Automatically purge check Initiates a sequence that thoroughly purges both A and
box B pumps following a change of mobile phase.
Automatically flush check Initiates a sequence that thoroughly flushes the fluid
box path from the pump through to the injection valve.
Create New Fluid Use this option to add a new mobile phase to the list.
The user is prompted to follow the flow meter calibration
sequence after the new fluid properties are entered.
Purge Settings Purge cycles specifies the number of pump volumes to
be purged with mobile phase following a mobile phase
change. Side A and Side B designate which pumps
should be purged following the mobile phase change.
Purge Now initiates an immediate purge of the pumps.

Software User Guide Eksigent Control Software

September 2012 37 of 152
Acquisition Window

Table 2-7 Mobile Phases (Continued)

Field Description
Flush Settings Total Volume specifies the volume and Flush Flowrate
specifies the flow rate of mobile phase that should be
used to flush the fluid path between the pump and the
injection valve following a mobile phase change. The
Flush Now button initiates an immediate flushing of the
pumps.
Cancel button Ignores any changes made to the mobile phase settings
and returns the user to the main screen.
OK button Exits the Mobile Phases dialog. If the mobile phases
have changed, an automatic purge or flush sequence
may be initiated according to the above settings.
Apply button Click Apply to set the new mobile phase values and
leave the window open.

Direct Control
The Direct Control dialog (Figure 2-23) allows users to start the pumps at a specific flow rate.
Direct control is useful for operations such as system flushing, equilibrating, and tuning an
electrospray interface.

Figure 2-23 Direct Control dialog

Table 2-8 Pump Direct Control
Field Description
Conserved Flow Specifies mobile phase composition and the total flow
rate.
Independent Flow Independently specifies the actual flow rate of each
individual mobile phase. The combined flow rate is
calculated and shown.

Eksigent Control Software Software User Guide

38 of 152 September 2012
 Acquisition Window

Table 2-8 Pump Direct Control (Continued)

Field Description
Monitor Baseline Enables data collection while in direct control mode.
When Start is clicked, an equivalent method (of 1 hour
duration) starts. The results are plotted real-time in the
main plot window. When the method ends or is stopped,
the data is saved in the relevant data file (if the Autosave
option has been selected).
Start button Initiates the specified pump direct control options. When
changing the settings, click Start again for changes to
take effect.
Stop button Stops the pumps.

Table 2-9 Valve Direct Control

Field Description
Load Position Changes the state of the internal valve to the Load
position. The header of the Valve Direct Control region
changes to reflect the current position of the valve.
Inject Position Changes the state of the internal valve to the Inject
position. The header of the Valve Direct Control region
changes to reflect the current position of the valve.

Table 2-10 Lamp Direct Control (UV systems only)

Field Description
On button Turns on the lamp. The header of the Lamp Direct
Control region changes to reflect the current state of the
lamp.
Off button Turns off the lamp.

Table 2-11 Column Oven/Heater (UV systems only)

Field Description
Setpoint Used for direct control of the column oven temperature.
This setting overrides the existing temperature setting.
Start Starts the heater.
Stop Stops the heater.

User Authentication
User authentication is used to set user access to the software. This allows applying varying
permissions to several users. For more information, refer to Chapter 9.

User Manager
The User Manager dialog is used to set different permissions for various users. It is described in
Chapter 10 and is only relevant if User Authentication is enabled.

Software User Guide Eksigent Control Software

September 2012 39 of 152
Acquisition Window

Electronic Signatures
Electronic Signatures are used to view, apply, and revoke electronic signatures from data files.
Refer to Chapter 11.

Analysis Menu
Table 2-12 lists the commands available from the Analysis menu in the Acquisition window.
Table 2-12 Analysis Menu
Command Function
Settings Opens the Analysis Settings dialog, which contains peak detection
parameters. Refer to Chapter 7.
Choose Peak Table Prompts the user to select which peak analysis parameters to display
Columns in the peak table that is shown after a chromatogram is analyzed.
UV Detector Signal Analyzes the UV data trace when an analysis is performed.
AUX A/D Signal Analyzes the A/D data trace when an analysis is performed.
Automatic Automatically analyzes data at the conclusion of each sample data
collection.
Re-Analyze Now Analyzes the chromatogram using the current analysis method settings
and show the results on the screen.
Remove Results Removes the analysis results (peak table) from the screen.

Use the Analysis menu to adjust the parameters that control the analysis process. These
parameters are used by the peak-finding algorithm when identifying, placing, and integrating the
peaks found in the chromatogram. The Analysis menu can also be configured to automatically
analyze a chromatogram after acquisition is complete.
Use the Analysis Settings dialog to set peak integration parameters. These settings determine
which peaks the integration routines recognize during peak finding.

Help Menu
Table 2-13 lists the commands available from the Help menu in the Acquisition window.
Table 2-13 Help Menu
Command Function
Help Opens the interactive help system.
Check for Updates Opens the default Internet browser and selects a web page to show the
latest version of software.
Email Tech Support Opens the default e-mail client software and fills in the address and
system information to be sent to Eksigent Technical Support.
www.eksigent.com Accesses the Eksigent website with the default Internet browser.
About Opens installed software and firmware versions.

Eksigent Control Software Software User Guide

40 of 152 September 2012
Run Manager
3
The Run Manager queues a series of samples and then acquires them using the specified
instrument methods. The sequence of samples can be saved as a file, recalled, run, copied, or
modified.

Figure 3-1 Run Manager dialog

Current Tray
The Current Tray (lower left corner of Figure 3-1) shows an image of the configured autosampler
tray type and indicates active sample vials and their states.
Vial state:
• Green: Sample is currently running.
• Blue: Valid method associated with this vial.
• Blue/Checked: The sample finished successfully.
• Red: An error occurred while running this vial or the sample was stopped.
• Yellow: Vial is selected.

Software User Guide Eksigent Control Software

September 2012 41 of 152
Run Manager

Autosampler
The Autosampler area indicates the currently selected (or active) tray and provides a text
description of the current autosampler action or status. The tray shown can be selected using the
arrow buttons next to the tray name in the Status area or by choosing a row in the table with the
desired tray.
For autosamplers with tray cooling, the tray temperature appears in the tray temperature area.
• The Pause button holds the autosampler in its current state or position. If an
autosampler method is running, the Pause button holds the method and stops the
autosampler in its current action.
• The Resume button allows the method to continue when the system has been
paused. This action is useful for changing sample trays while the autosampler is
running.

Method Definitions
Autosampler Methods: Opens the autosampler method editor that is used to create and edit
methods specifying the amount of sample to be drawn from the sample vial and the parameters
to be used for pre- or post-injection syringe cleaning. The editor shown depends on the type of
autosampler configured. CTC PAL Autosampler Control or NanoLC-AS1 Autosampler Control
editors are currently supported.
LC Methods: Opens a window for typing the parameters used for separating and detecting the
sample. This information includes flow rate, gradient profile, detection wavelength, and so on,
and is stored in a sample method. The method parameters available depend on the configuration
of the LC device. 1D LC methods and 2D methods are available.
Analysis Methods: Opens an Analysis Method Settings dialog that is used to set the peak
detection configuration parameters.

Run Manager Menus

Table 3-1 to Table 3-5 show the lists of the menus available on the Run Manager dialog. Each
menu contains a list of commands and sub-menus.
Table 3-1 File Menu
Command Function
Open Opens the selected Run Table sequence file.
Save Saves the current sequence as a run file.
Save As Saves the current sequence as a specific file.
Import Imports data into the Run Table from one of four different file types: a
proprietary file type for the grid which allows saving format information as
well as data, a comma-delimited text file, a tab-delimited text file, and an
Excel file.

Eksigent Control Software Software User Guide

42 of 152 September 2012
 Run Manager

Table 3-1 File Menu (Continued)

Command Function
Export Exports data from the table. Save the Run Table data in one of four
different file types: a proprietary file type for the grid which allows saving
format information as well as data, a comma-delimited text file, a tab-
delimited text file, and an Excel file.
Print Prints the contents of the table.
Exit Ends the current Run Table sequence and exits the Run Manager dialog.

Table 3-2 Edit Menu

Command Function
Cut Removes the current selection and copies it into the Windows clipboard.
Copy Copies the selected Run Table cells to the Windows clipboard.
Paste Pastes the cut or copied cells into the Run Table.
Delete Removes the contents of the currently selected Run Table cells.
Undo Restores the table to its state prior to the previous command.
Insert Row Inserts a single row at the currently selected Run Table row.
Insert Rows Opens a dialog used to insert a set number of rows into the Run Table.
Insert Copied Rows Copies rows from the Windows clipboard into the Run Table.
Reset Rows Clears the status of the selected rows.
Reset Table Resets the status for the entire Run Table. The user can restart the
queued sequence of events.
Erase Table Removes all entries from the Run Table.
Choose Columns Opens the Choose Columns dialog. This dialog is used to show, hide,
and move the available columns in the Run Table.

Table 3-3 View Menu

Command Function
Acquisition Window Opens the main Acquisition window with the chromatogram plot and
status area.

Table 3-4 Devices Menu

Command Function
LC Device Settings Opens the Instrument Configuration dialog, which allows configuration of
the LC device and setting the various configuration parameters of the
device. Refer to Figure 2-16 on page 30.
LC Wait for Contact Delays the start of the LC method until it receives an external contact
Closure closure signal. This allows the start of the acquisition to be synchronized
to an external signal.
Autosampler Type Used to select an autosampler or remove an autosampler.
Autosampler Device Opens the Autosampler Configuration dialog. Used to configure
Settings autosamplers that come with the instrument.

Software User Guide Eksigent Control Software

September 2012 43 of 152
Run Manager

Table 3-4 Devices Menu (Continued)

Command Function
Skip Missing Vials If selected, allows the table sequence to continue running if the
requested vial is missing from the autosampler tray. The sample row is
skipped and marked with an error. If not selected, an error occurs and the
sequence stops (no subsequent sample rows are processed).
Inject Ahead If selected, allows the autosampler to run ahead to the next line in the
table and start the next autosampler method before the current LC
method is complete. This is primarily useful for high-throughput
applications with short LC method durations
Spotter Type Used to select the Spotter device.
Spotter Device Used to modify the spotter device settings.
Settings
AutoNumber Spot Used to automatically control the location of spots to optimize plate
Position usage.

Table 3-5 Help Menu

Command Function
Help Opens the Help file.
About Opens the About dialog.

Run Table
The sample grid in the Run Table allows the user to link together an autosampler method, a
sample tray, a sample vial, an analysis method, sample method overrides, and sample
information such as injection amount, sample name, ID, type, and any other comments. Each
sample is represented by a single row.
Table 3-6 Run Manager Columns
Column Description
Seq. # The row number of the sample in sequence.
Run Indicates which samples are to be processed in the sequence.
(unchecked rows will be skipped).
Run Interval Time field for typing a sampling run interval. Time format is
hh:mm:ss. The specified time is the time between the start of each
acquisition. Blank values are treated as no interval.
Run Replicates Text field for specifying the number of replicates for each row in the
Run Table. Blank values are treated as a single run.
Autosampler Method Selects the autosampler method.
Autosampler Tray Selects the tray location of the sample vial or well.
Autosampler Vial Selects the vial to be sampled.
Autosampler Aspirate Specifies an override value for the aspirate volume in the
(µL) autosampler method. Leave blank to use the value specified in the
LC method.

Eksigent Control Software Software User Guide

44 of 152 September 2012
 Run Manager

Table 3-6 Run Manager Columns (Continued)

Column Description
Autosampler Dispense Specifies an override value for the dispense volume in the
(µL) autosampler method. Leave blank to use the value specified in the
LC method.
LC Method Selects the LC method for the LC device acquisition.
LC Flow Rate Specifies an override value for the total flow rate in the LC method.
Leave blank to use the value specified in the LC method.
LC Injection Vol. (nL) Specifies an override value for the injection volume (nL) in the LC
method. Leave blank to use the value specified in the LC method.
LC Channel Selects the LC channel for the LC device. Used for multi-channel
LC devices only. An asterisk (*) indicates any available channel may
be used. For high-throughput applications with identical columns on
each channel, this option allows the fastest processing of all the
samples in the list, as no specific channel is required to be available
for any particular sample
LC. Inj Type Selects an override value for the injection type used in the LC
method. Leave blank to use the value specified in the LC method.
LC Column Temp (°C) Specifies an override for the column temperature (°C) in the LC
method. Leave blank to use the value specified in the LC method.
Sample Name Text field for labeling the sample.
Sample Type Text field for describing the sample type.
Sample Amount Text field for typing the amount of sample.
Sample ID Text field for assigning an ID to the sample.
Analysis Method Selects the post-acquisition analysis method.
Spotter Plate # Selects the plate number for spotting deposition.
Spotter Time/Drop (ms) Frequency of spotting.
Spotter Time (min) Duration of the spotting operation.
Other Comments Text field for typing additional comments about the sample.
Other Status The current status of the sample row being acquired.
Other Flag Tag Text field for specifying a tag for use in generating the data file
name. Only use characters allowed for valid filenames.
Other Data File Name Text field that shows the data file name.

When an acquisition is in progress, the color of the sample row indicates the state of its progress:
• Light green: The sample is preparing to run (equilibrating).
• Dark green: The sample is running.
• Red: The sample has stopped.
• Yellow: An error occurred.
• Gray: The sample has completed.
After acquisition has been completed, the table can be set to the pre-run state using the Reset
Table button. The sequence begins with the first sample row the next time it is started.

Software User Guide Eksigent Control Software

September 2012 45 of 152
Run Manager

About Run Table Cells

The actions allowed in each cell in the Run Table are dependent on the column type.
Table 3-7 Cell Types and Descriptions
Cell type Description
Menu Selection is made from a list.
Edit Box Allows numbers and decimal points for floating point numbers.
Text Box Allows any character.

Cells in the table can be navigated with the arrow keys on the keyboard or by selecting cells with
the pointer.

Edit a Menu Cell

1. In the Acquisition window, click Run Manager.
2. Do one of the following:
• If a cell uses a menu, double-click the cell to open the menu.
• If the cell is already is open, then press Enter or press Space.
3. After an item in the menu is selected, the value is shown in the table.
4. Press Enter.

Figure 3-2 Activated cell with list box

Edit a Text Box or Edit Box

1. In the Acquisition window, click Run Manager.
2. Do one of the following:
• If a cell uses a text box or edit box, double-click the cell to activate it.
• If the cell already has focus, the edit box can be activated by typing numbers
or characters.
3. Press Enter.

Figure 3-3 Activated cell with text edit box

Cut, Copy, Paste, and Delete operations can be applied to any cell.

Eksigent Control Software Software User Guide

46 of 152 September 2012
 Run Manager

Select Multiple Cells

Use the following functions as required:
• In the Acquisition window, click Run Manager.
• To select any range of cells in the Run Table, drag an area to select it. Release
the mouse button to finish the cell selection.
• Drag the row label (Seq #) to select an entire row.

Figure 3-4 Run Manager multi-cell selection

• Hold Shift and then use the arrow keys to select a cell range.
• Click inside the Seq # column header to select the entire Run Table.
• Click Edit > Select All to select the entire Run Table. This feature works only
if any cell in the Run Table is highlighted.

Edit Cells
Use the following functions as required:
• In the Acquisition window, click Run Manager.
• After one or more rows are selected, right-click to open a menu to cut, copy,
paste, insert new rows, insert copied rows, insert series of rows, or delete
selected rows.
• Cut, Copy, and Delete operate on the selected rows. Paste puts copied or cut
rows into the currently active cell.
• Paste a single copied row into multiple rows by selecting the destination rows
prior to pasting.

Move Selected Cells

Use the following functions as required:
• In the Acquisition window, click Run Manager.
• A black border is visible around the cell selection. Move the pointer over the
selection border and an arrow icon with rectangle at the base appears. Drag
the border to move the selection to a new location within the Run Table grid.
• If the selected cell types do not match the cell types of the new location, an
icon indicates the operation is not allowed.
• This operation can be performed on entire rows by using the same method
after the entire row is selected.

Software User Guide Eksigent Control Software

September 2012 47 of 152
Run Manager

• Drag the row label (Seq #).

When an acquisition is in progress or if the sample row is being used in some
operation, the rows are locked for editing. If the rows are locked, they cannot be
moved or edited.

Auto-Complete Sample Lists

Create large sample lists by dragging a selection and then using the auto-complete function to
complete subsequent rows based on the previous values of the selection.
1. In the Acquisition window, click Run Manager.
2. After selecting cells, drag the small square in the selection border down the column.
• For most selections, the square is located at the bottom right of the selection
border.
• For entire row selections, the square is located at the bottom left of the
selection border.
Various types of auto-complete operations are available when auto-completing an
extend-dragged selection of column cells.
• Single cell: New cells repeat the first selection.
• Multiple text cells: New cells repeat the entire selection.
• Multiple numeric cells: An attempt is made to identify any trend in the
selection and the trend is extrapolated. For example, if the user selects two
cells containing 1 followed by 2, auto-complete will insert 3, 4, 5, and so on
into the following cells.
• Multiple list box cells (numeric & vials): Behave the same as numeric cells,
but the range is limited by the values in the list. Extending a selection beyond
the last number in the list box wraps the pattern back to the values at the
beginning of the list.

Choose Columns
1. In the Acquisition window, click Run Manager.
2. Right-click the column labels at the top of the table and then click Columns.

Eksigent Control Software Software User Guide

48 of 152 September 2012
 Run Manager

Figure 3-5 Choose Columns dialog

3. Do the following as required:
• To arrange columns, left-click on a column label and then drag the column to a
new location.
• To drag entire column categories, click the first row where the column
categories (for example, LC, Autosampler, and so on) are located and drag
whole categories of columns to a new location. To drag individual columns,
click on the second row label (for example, Tray, Vial) and drag individual
columns to new locations. When moving a column outside its category, the
category header is added above the relocated column.
• Resize columns by moving the pointer over the grid lines in the column labels.
A resize cursor icon indicates a drag operation that will set the column height
to a new size.
• Click column labels in the second row to sort columns (except for the Run
column that sorts by clicking on the column header in the first fixed row). A
direction arrow is shown indicating the direction of the sort.
• Perform hierarchical sorting by sorting the desired columns in the desired
order. If the Run Table sequence is running, a dialog opens before allowing
the sort operation.

Software User Guide Eksigent Control Software

September 2012 49 of 152
Run Manager

Freeze Rows
Freeze rows in the Run Table so that they remain in the visible area while the rest of the table
area is scrolled.
1. In the Acquisition window, click Run Manager.
2. To freeze rows at the top, move the pointer over the border between the fixed
column label rows and the scrollable area until the pointer changes to a lock mouse
cursor.
3. Left-click and then drag the border down any number of rows to freeze. Any
movement or scrolling in the grid area does not affect the frozen rows.

Freeze Columns
Freeze columns in the Run Table so that they remain in the visible area while the rest of the table
area is scrolled.
1. In the Acquisition window, click Run Manager.
2. To freeze columns at the left of the grid, move the pointer over the border between
the fixed column and the scrollable area until the pointer changes to a lock mouse
cursor.
3. Drag the border across any number of columns to freeze. Any movement or scrolling
in the grid area will not affect the frozen rows.

Select a Vial
1. In the Acquisition window, click Run Manager.
2. Click a vial in the tray image to select the vial for the current sample row. If the active
row in the sample table is valid, the vial numbers are updated to reflect the vial
number selected in the graphic.

Add Vials
1. To add many new samples to the sample table, drag the cursor on the tray to select
multiple vials.
A Vial Selection dialog (Figure 3-6) opens to indicate how the sample table rows will
be filled. The new rows duplicate the information of the row number indicated in the
Current Table Row text box, but include the newly inserted vial numbers. The default
entry is the currently selected row in the table.
2. Do one of the following:
• Click Insert rows to add the newly selected vials into the table beginning with
the currently active cell.
• Click Overwrite existing rows to add the entries starting at the currently
active table cell and then fill down over the existing entries.

Eksigent Control Software Software User Guide

50 of 152 September 2012
 Run Manager

Figure 3-6 Select vials in the current tray

Start the Sample Run Sequence

1. In the Acquisition window, click Run Manager.
2. Click Start to begin the sample sequence defined by the rows in the table.
When a sequence begins, current changes to the Run Table are validated and
saved.

Figure 3-7 Run Manager sequence selection

3. Select a run option: Sequential, As Available, or Synchronized Multi-Channel.
4. (Optional) Select Flush/Equilibrate when Idle to minimize the equilibration delay at
the start of each run. Refer to About the Flush/Equilibrate when Idle Option.

Tip! After all acquisitions are complete, to return the table to the initial
state, click Reset Table. The sequence begins with the first sample row the
next time it is started.

The Elapsed Time indicator shows the approximate time elapsed from when the Run
Table started. The Queued Time indicator shows the approximate time required to

Software User Guide Eksigent Control Software

September 2012 51 of 152
Run Manager

run all of the active samples in the Run Table. This time is an approximation based
on the LC methods only and does not include additional time required for
autosampler methods.

About the Sequential Option

The Sequential option is the only option available for single channel instruments. This option runs
the samples in the order they appear in the table, row by row. For example, the sequence starts
with row 1 and proceeds to row 2, row 3, and so on. After each row finishes, the next row begins.

About the As Available Option

The As Available option is available for multi-channeled devices. This option starts each row
when its assigned LC channel becomes available. A row does not start until all previous rows
with the assigned channel number are finished processing. For high-throughput applications, this
option allows the fastest processing of all the samples in the list.

About the Synchronized Multi-Channel Option

The Synchronized Multi-Channel option is available for multi-channeled devices. This option
requires that all channels of a device start simultaneously. As a consequence, the LC methods
on every channel must finish before the next series of samples begin synchronously.

About the Flush/Equilibrate when Idle Option

Flush/Equilibrate when Idle is an option that keeps the pumps running to minimize equilibration
delay at the start of each run. Selecting this option also makes sure that the column heater
equilibrates to the temperature specified in the method. This option applies only to LC methods
with pre-flush settings.

Stop the Sample Run Sequence

• Click Stop to end the Run Sequence.
If the table contains rows with samples that have been previously stopped during
acquisition, a prompt to start these samples again is shown each time the sample
table is started.

Eksigent Control Software Software User Guide

52 of 152 September 2012
Peak Viewer Utility
4
The Peak Viewer utility is used to view and analyze data after acquisition.

Plot Dialog
The Plot dialog can be configured to show one or multiple data sets simultaneously. For systems
with spectrometers, the chromatogram (UV absorbance data) is shown. All other systems show
the AUX A/D signal (for use with external detectors).

Peak Table
When the utility starts, the peak table indicates data source information related to the loaded data
files and any peak information stored in the data file (resulting from automated analysis following
the acquisition).
The peak table shows the current peak analysis results for each data set and can be used to edit
(remove) peak information directly. A sample report, peak statistics, and peak trends are also
accessible from the peak table.

Analyze Peaks
By default the analysis parameters stored in the data files are used for the peak analysis. If the
data has not been previously analyzed or if there are no peaks detected, the table is empty
except for the data source information. For more information, refer to Peak Detection Tab on
page 82.
1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.

Tip! The Peak Viewer can also be started directly from the installed
Program Group menu.

Software User Guide Eksigent Control Software

September 2012 53 of 152
Peak Viewer Utility

Figure 4-1 Peak Viewer utility

4. Do one of the following:
• To analyze all open files, select all files in the table and then click Find Peaks.
If no rows are selected in the table, a prompt indicates that all files will be
analyzed.
• To analyze specific files, select each file (by row) of interest and then click
Find Peaks. Only the selected files are processed.

Note: The results in the data file are not permanently changed. However,
the new peak attributes can be saved.

5. Select the files in the table and then click File > Save Changes.

Edit Peak Parameters

1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.
4. Click Settings.
The Analysis Settings Editor dialog opens. For more information refer to Chapter 7.
The new peak information is updated in the peak table, the plots, and the report.

Eksigent Control Software Software User Guide

54 of 152 September 2012
 Peak Viewer Utility

Show Peak Parameters

Update the contents of the table using the available peak parameters, including Retention Time,
Area,% Area, Plates, Height, Asymmetry, Base Width, and so on. After the parameters are
selected, the table is updated to show the relevant parameters.
1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.
4. Select a parameter from the Show menu.
5. (Optional) To customize the data source information, right-click, and then click
Annotations.

Sort Data
1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.
4. Click the relevant column header labeled with the peak number.
The rows are sorted in ascending or descending order in that column each time the
column heading is clicked.

Tip! To sort the information by peak area, select Show Area and then
click the relevant peak number at the top of the table.

Select Data
Data in the table can be selected in various ways:
• Drag across a range of cells.
• Click the row label (first column) to select entire rows.
• Hold the Shift key and then click a range of cells or rows.
• Hold the Ctrl key and then click multiple cells or rows in any order.

Copy Data
Any range of information in the table can be copied to the Windows clipboard.
1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.
4. Select the data, right-click, and then click Copy. The cell contents can be pasted into
any other application.

Software User Guide Eksigent Control Software

September 2012 55 of 152
Peak Viewer Utility

Delete Data
1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.
4. Select the peak in the table and then press the Delete key.

Mark Values
Peak information in the table can be color-coded to easily identify trends in the data.
• To mark the data, type a value in the Mark Values field and then select a sign
(greater than, less than, equal) to mark all values in the table that meet the specified
criteria. A slight color gradient is used to differentiate the range of values.

Peak Viewer Sample Report

Individual peak attributes can be edited by graphically editing the chromatogram, by deleting a
peak from the table, or by analyzing the data again. Any changes to the current peak information
cause the report to be automatically updated to reflect the results of the new analysis.

Run a Sample Report

At any time, a text sample report is available that includes a list of peak attributes for every
individual open data file.
1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.
4. Click the Sample Report tab above the peak table. It contains a section for each file
indicated by the data source information shown in the peak table and a set of peak
attributes for each peak in the file.

Figure 4-2 Peak Viewer Sample Report

5. (Optional) To copy the contents of the report to the Windows clipboard, select the
text, right-click, and then click Copy.

Print a Report
• To print the peak table, sample report, or statistics, click File > Print.

Eksigent Control Software Software User Guide

56 of 152 September 2012
 Peak Viewer Utility

Export a Report
• Click File > Export.

Customize Peak Attributes

1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.
4. Click Peaks > Annotations.
5. Click the Report Contents tab.

Statistics
Statistics are generated from all of the open files and for the peak attribute currently shown in the
peak table. The statistics table, shows displays the mean, median, relative standard deviation
(RSD), maximum, and minimum value generated for each peak number is at the top of the
Statistics tab. The chart below the table indicates the mean and the one and three sigma range
for the current peak attribute with the data source number on the abscissa.

Figure 4-3 Peak Viewer statistics

Software User Guide Eksigent Control Software

September 2012 57 of 152
Peak Viewer Utility

Generate Charts
A chart can be generated for each individual peak. The statistics table and chart are useful for
examining the reproducibility of any of the peak attributes within a set of data files. The table and
chart are regenerated following any modifications to the peak attributes in the table or
chromatograms.
1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.
4. Select the corresponding row in the statistics table.
In case of a numerical data source label, for example relative retention time, the
abscissa shows the actual numerical value.

Generate Peak Trends

When monitoring a process, dilution, or other related set of samples, it is useful to examine the
temporal trends of particular peaks or groups of peaks.
1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.
4. Select a peak attribute for all loaded sample files.
• The trend table at the top of the Trend tab gives the user the option to trend by
peak attribute, or by a custom formula.
• The chart in the lower left area shows the actual trend lines for each selected
peak
• The chart in the lower right area shows an overlay of all chromatograms.

Generate Peak Trends using Custom Formulas

1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.
4. Select the Custom Formula option and then type the formulas in the third column of
the trend table. For example, to create a trend which is the average of Peak 1 and
Peak 2 type:
½ (Peak1 + Peak2)
The value used for Peak1 is the currently selected peak attribute (for example, Area,
Retention Time, and so on) To apply the formula and show the result, check the box
in the first row. Users can also edit the name of the peak trend in the second row,
which is then shown as the legend.
The X-axis uses the currently select sample Annotation method.

Eksigent Control Software Software User Guide

58 of 152 September 2012
 Peak Viewer Utility

Tip! All charts and table entries can be copied to the clipboard by right-
clicking and selecting Copy.

Figure 4-4 Peak Viewer peak trends

Modify the Plot Area

The chromatogram or external detector signal for each data file is shown individually in the plot
area. The plot area can be modified to show multiple plots simultaneously.
1. In the Acquisition window, click File > Peak Viewer.
2. Browse to files either in the Eksigent data or text format.
3. Click Open to load the data into the Peak Viewer.
4. Click View > Tile and then select the number of plot windows to show.

Software User Guide Eksigent Control Software

September 2012 59 of 152
Peak Viewer Utility

5. Use the following functions as required:

Figure 4-5 Plot area options

• Right-click in the plot area and then click Copy to copy the contents of the plot
area to the Windows clipboard.
• If multiple chromatograms have been overlaid, the overlaid data can be
removed individually. Select a data set, right-click, and then click either
Remove > Overlay or Remove > Overlays.
• Individual peaks can be selected by moving the cursor close to or across the
peak area. To remove a peak from the peak table, select the peak. right-click,
and then click Remove > Peak.
• Right-click in the plot area and then click Add Integration Event to add
integration timed events graphically. After analyzing the chromatogram again,
the results are updated in the peak table, sample report, and statistics.
• Zoom in and out of a region of interest by dragging a region directly on the
plot. A rectangle is shown indicating the region of interest. Releasing the
cursor draws the plot using the new axis limits.
• Double-click the plot area to re-scale the plot to fit the entire data contents in
the plot window.
• Click the X-axis time units to toggle the axis units from seconds to minutes.
• The plot axes can be modified directly by clicking the X or Y axis limits
(maximum or minimum value) to open a text box that allows the user to type
the new axis limit values. The new limits take effect after pressing Enter.
• If peaks are present, moving the cursor over the peak baseline shows a move
icon that allows the user to manually adjust the peak baselines. Drag the
baseline point to a new location.
• The Autoscale properties available from this menu automatically adjust the
axis limits to show the entire data set based on maximum and minimum values
in the data set. Right-click in the plot area and then click Zoom Out or Zoom
Last to undo the previous zoom region or axis settings.
• Right-click in the plot area and then click Properties to change peak labels
and plot area display settings. Refer to Table 4-5.

Eksigent Control Software Software User Guide

60 of 152 September 2012
 Peak Viewer Utility

File Menu
Table 4-1 lists the commands available from the File menu.
Table 4-1 File Menu
Command Function
Open Used to load new data sets into the Peak Viewer. The existing peak
information and plots are removed and the new file data is used to
populate the peak viewer. No changes to the previously loaded data are
stored.
Add Files Used to add new data files to the current data set. The new data is added
to the end of the peak table (and plots windows).
Save Changes Used to save changes to the peak information for the open data files.
Modifications to the peak information are stored in the data files.
Only the selected files are updated. If no files are selected, a prompt to
save all files opens.
Export Used to export the current peak table, sample report, and statistics
information in various Windows file formats (Excel, tab-delimited text, and
so on).
Print Preview Used to preview the report before it is printed. The format of the report is
similar to the one generated in the Acquisition window. It contains file,
sample and method information, a plot of the chromatogram, and the set
of peak results is shown in the sample report.
Print Used to print the selected plots, current peak table, sample report,
statistics, and trends information on the default printer.
Print All Used to print all information for the data set, including the peak table, the
sample report, statistics, trends, and plots.
Monitoring Used to monitor samples in real time as they are completed from the Run
Table. When selected, the results of each sample are automatically
loaded into the Peak Viewer software, followed by an update of all charts,
trends, and reports. If not already open, it also loads the Run Manager
window, which allows users to queue and acquire a series of samples.
Monitor Folder As an alternative to monitoring the Run Table, this function observes a
specified folder for new files (in the text output format). After detecting a
new file, it is opened and analyzed automatically by the Peak Viewer
software, followed by an update of all charts and reports.
Skip First Sample Select this option to ignore data from the first sample acquired.
When selected, the first file after the user starts monitoring the Run Table
or a folder is skipped.
Exit Closes the Peak Viewer utility.

Software User Guide Eksigent Control Software

September 2012 61 of 152
Peak Viewer Utility

Edit Menu
Table 4-2 lists the commands available from the Edit menu.
Table 4-2 Edit Menu
Command Function
Copy Table Copies the selected section of the currently shown table to the clipboard.
Selection Sections of the peak table can be selected freely by dragging in the table
cells of interest. For the summary report and statistics table, click a row to
select the entire row.
Copy Plot Selection Copies the current selected plot to the clipboard. To select a plot, click the
desired plot or click anywhere in the peak table row for the data file.
Users can also select the plot, right-click, and then click Copy.
Select All Selects the entire table that is currently shown.

View Menu
Table 4-3 lists the commands available from the View menu.
Table 4-3 View Menu
Command Function
Full Screen Sets the plot area to show a single data set. The current active data file
(selected via plot window or peak table grid) is used to fill the entire plot
area. Full Screen is the default setting when the Peak Viewer utility starts.
Tile Rearranges the plot area to show multiple data sets in a tiled window
format. Use the right scroll-bar to scroll through the plots. Any data files
added to the data set are appended at the end. An example is shown in
Figure 4-6.

Eksigent Control Software Software User Guide

62 of 152 September 2012
 Peak Viewer Utility

Figure 4-6 Multiple chromatograms

Peaks Menu
Table 4-4 lists the commands available from the Peaks menu.
Table 4-4 Peaks Menu
Command Function
Analysis Settings Provides access to the Analysis Method Editor. Refer to Chapter 7. Users
can also click Settings to open the Analysis Method Editor.
Import Analysis Imports analysis settings from an existing analysis method file and
Settings applies the settings to each selected file.
If no files (rows) in the table are selected, a prompt to apply the settings
to all files opens.
Find Peaks Analyzes the current data set. Each selected file is processed in
sequence using the analysis settings stored in the file.
If no files (rows) in the table are selected, a prompt to process all files
opens.

Software User Guide Eksigent Control Software

September 2012 63 of 152
Peak Viewer Utility

Table 4-4 Peaks Menu (Continued)

Command Function
Update Calibration Used to update the quantitation analysis method currently in use. When
Table with Standards this option is selected, the analyst results from the currently selected data
are added to the quantitation list for standards in the method.
Use Smoothed Data Applies the analysis settings to the smoothed data instead of the original
data.
Annotations Opens the Annotations dialog, refer to Figure 4-7.
Display Peak Adds peak names as labels to the chromatogram plot (normally used with
Names quantitation, if peaks have been named).
Smoothing Tool Box Prompts the user with options to smooth (time domain and spline) the
chromatogram data. After selecting the smoothing parameters, a new
chromatogram is added to the plot and labeled as smoothed data. The
original data remains.
Baseline Noise Tool Prompts the user with options for calculating the baseline noise of the
chromatogram.
Filter Tool Box Prompts the user with options to filter (Kalman) the chromatogram data.
After selecting the parameters, new chromatograms are added to the plot
and labeled as filtered data. The original data remains.
Math on/between Prompts the user with options to perform basic math on or between
Data Sets different data sets. For example, subtracting a fixed offset in time or
absorbance from a data set, or subtracting one 'blank' chromatogram
from another (simple baseline correction).
Align Select to shift all chromatograms in time so that all chromatograms have
Chromatograms the same retention time for the first peak.
Report Comments Opens the Report Contents tab of the Annotations dialog, which contains
the list of peak attributes that can be shown in the sample report. Any
combination of peak attributes can be added to the report by selecting
the corresponding check boxes. Refer to Figure 4-8.
Peak Labels Opens the Peak Labels tab of the Annotations dialog, which contains the
list of peak attributes that can be shown as peak labels in the
chromatogram plots. The list is identical to the options in the Report
Contents tab.

Eksigent Control Software Software User Guide

64 of 152 September 2012
 Peak Viewer Utility

Figure 4-7 Plot Labels tab

Figure 4-8 Report Contents tab

Plots Menu
Table 4-5 lists the commands available from the Plots menu.
Table 4-5 Plots Menu
Command Function
Plot Series Use this option to choose the data source for the plot data (that is, UV
data, A/D data, column pressure, and so on).

Software User Guide Eksigent Control Software

September 2012 65 of 152
Peak Viewer Utility

Table 4-5 Plots Menu (Continued)

Command Function
Properties Opens the Chart Options dialog. The peak labels can be selected in the
Peak Labels tab so that any peak attribute can be labeled on the plot next
to each peak. Refer to Peak Label Options on page 67.
Overlay Selection Used to present two or more chromatograms on a common set of axes.
For more information, refer to Overlay Chromatograms on page 68.
Remove Overlays Used to remove all overlayed data when using 'overlay selection'. Only
the original data is displayed.
Make All Plots When selected, the Make All Plots Identical option causes all plots that
Identical are shown to have the same attributes. The axes limits, plot labels,
colors, and so on, are adjusted on all the plot windows to be identical to
the currently selected plot. While selected, any further actions to modify
the plot window affect all other plot windows that are shown. For
example, zooming in a region of one chromatogram also causes the axes
limits for all other chromatograms to be adjusted as well.
Autoscale All Plots Disables the Make All Plots Identical feature and automatically scales all
plot windows to fit the entire contents of their individual chromatograms. It
is possible that the resulting plot axes limits vary among each loaded
data file.

Eksigent Control Software Software User Guide

66 of 152 September 2012
 Peak Viewer Utility

Peak Label Options

Multiple peak attributes can be added to the label by selecting multiple check boxes. The
orientation of the labels can be changed by selecting a corresponding angle from the Orientation
menu. Refer to Figure 4-9.

Figure 4-9 Peak Labels tab

The colors used to draw the plot area and grid lines can also be adjusted in the Properties tab by
double-clicking the relevant color dialog. Refer to Figure 4-10.

Figure 4-10 Properties tab

Software User Guide Eksigent Control Software

September 2012 67 of 152
Peak Viewer Utility

Overlay Chromatograms
1. To overlay chromatograms, in the peak table, select the data file rows using one of
the following functions:
• Hold the Shift key and then select multiple sequential rows.
• Hold the Ctrl key and then select multiple rows in any order.
• Drag an area to select rows in a range.
2. Click Plots > Overlay Selection.
The topmost data file in the peak table selection is used as the active chromatogram
and the plot window is updated with overlays of the data from the selected data files.
Refer to Figure 4-11.

Tip! The overlays can be removed by selecting Remove Overlays.

Figure 4-11 Overlaying chromatogram data

Eksigent Control Software Software User Guide

68 of 152 September 2012
 Peak Viewer Utility

Perform a Math Operation

1. From the Peaks menu, click Math on/between Data Sets. Refer to Figure 4-12.

Figure 4-12 Math on/between Data Sets dialog

2. Click a data set in the Available Data list.
3. Click the upper arrow to move the data set to the Selected Source Data group.
4. Type an arithmetic operator in the Operator field and then either type a numerical
value or select another data set from the Available Data list and then press the
lower arrow. If using a data set, an additional offset can be applied by typing a non-
zero value in the Time Offset field.
5. Click Apply.
The plot window is updated to show the resulting data sets. If Re-Analyze Peaks is
selected, the software automatically analyzes the modified chromatograms.

Tip! Click Undo to restore the original data.

Software User Guide Eksigent Control Software

September 2012 69 of 152
Peak Viewer Utility

Eksigent Control Software Software User Guide

70 of 152 September 2012
Autosampler Control
5
Configure the Autosampler
• To configure the software to be controlled within the Run Manager, click Devices >
Autosampler Type > <customer autosampler type here>. Refer to Figure 5-1.

Figure 5-1 Selecting the AS1 autosampler

After the autosampler hardware is selected, the Run Manager attempts to
communicate with the device using the default settings. Refer to the hardware user
guide for more information on configuring the device and creating device methods.

Software User Guide Eksigent Control Software

September 2012 71 of 152
Autosampler Control

Eksigent Control Software Software User Guide

72 of 152 September 2012
LC Method Editor
6
LC Methods are created and edited using the LC Method Editor. The LC Method Settings dialog
contains a Selected Method region and, depending on the system, Summary, Run Conditions,
Gradient Profile, Gradient Table, and Detection tabs. For more information, refer to the
application-specific method creation documentation included with the hardware.

Note: Depending on the configuration of the LC device, it may not be equipped with an
absorbance detector.

Create an LC Method
1. In the Acquisition window, click Run Manager.
2. In the Run Manager dialog, click LC Methods.
3. Type a name in the Name field.
4. Use the information in the following sections to create the LC method.
5. Click Save.

Edit an LC Method
1. In the Acquisition window, click Run Manager.
2. In the Run Manager dialog, click LC Methods.
3. Select a method in the Name field.
4. Use the information in the following sections to create the LC method.
5. Click Save.

Summary Tab
The Summary tab is used to type descriptive information about the column used for a particular
run (Figure 6-1). In addition, it summarizes the information from the other tabs in the LC Method
Settings dialog. The Sample Injection, Flow Profile, and Detection fields show information about
system conditions and are not editable.

Software User Guide Eksigent Control Software

September 2012 73 of 152
LC Method Editor

Figure 6-1 LC Method Settings dialog—Summary tab

Selected Method
Shows the name of the LC method. The user can select an existing method to view or edit or the
user can type a new name.

Method Identification
Used to type comments or to assign an identification number to the LC method.

Column Information
(Optional) Contains fields that can be used to describe the column used for a run.
• Manufacturer: The name of the manufacturer of the column used for the LC
method.
• Type: The description of column used in the current run. An example might be C18,
CN, and so on.
• Serial Number: The serial number of the column used with the method.
• particle size: The particle size of the column stationary phase.
• diameter: The column inner diameter.
• length: The length of the column used with the LC method.

Detection
For devices that include a spectrometer, the Detection region shows the details of detection data
collected during the run. Information includes data rate, wavelength range, and data file size.

Eksigent Control Software Software User Guide

74 of 152 September 2012
 LC Method Editor

Run Conditions Tab

Information in the Run Conditions tab is used to specify pre-run, sample injection, and post-run
conditions (Figure 6-2). The size of the sample injection and the temperature of the run are
determined here.

Figure 6-2 LC Method Settings dialog—Run Conditions tab

Pre-Run
• Flush column for _ minutes using _% initial flowrate conditions: Select this
check box to equilibrate the column prior to the run for a defined duration and flow
rate using the method initial mobile phase composition. The specified duration is the
minimum time that the column equilibrates before acquisition begins. If the specified
duration elapses and the acquisition has not started (for example, column
temperature has not stabilized), the device equilibrates indefinitely.
• Stabilize column temperature at _ºC prior to injecting sample and beginning
Flow Profile: For systems with column heaters, select this check box to set the
temperature (ºC) for the column heater. Acquisition does not start until the column
reaches within 0.1ºC the specified temperature.

Sample Injection
Select a sample injection mode.
• None: The sample valve does not actuate during the acquisition.
• Standard: The sample valve switches to the Inject position when the acquisition
begins and then switches to the Load position when the acquisition ends. As a result,
the sample loop remains in the flow path during the acquisition.

Software User Guide Eksigent Control Software

September 2012 75 of 152
LC Method Editor

• Metered: Offers the flexibility to vary the injection volume. The valve is switched to
the Inject position when the acquisition starts and the specified volume of sample is
metered to the column by the LC pumps at the specified conditions. After the
specified volume is injected, the sample valve switches to the Load position so the
sample loop is removed from the flow path during the acquisition.
• Rapid: Operates similarly to Metered injection mode option, but the LC pumps
steadily increase the flow rate during the injection (maintaining the initial mixture
fraction) to quickly meter a larger sample volume.

Post-Run
Select this check box to rinse the column after the run is complete for a defined duration and flow
rate using the method ending mobile phase composition.

Gradient Profile Tab

Use the Gradient Profile tab (Figure 6-3) to graphically show and program mobile phase
composition changes for the acquisition.

Figure 6-3 LC Method Settings dialog—Gradient Profile tab

Flow Mode
• Conserved flow: Select this option to maintain a constant total flow rate for the
entire duration of the acquisition while varying mobile phase composition.
• Independent flow: Select this option to specify the independent flow rates of each
mobile phase.

Eksigent Control Software Software User Guide

76 of 152 September 2012
 LC Method Editor

Profile Editor
Insert values at different points in time to create a mobile phase composition profile. Select A or B
from the option box or click the profile on the graphic to edit either the A pump or B pump flow
profile.
• Runtime: The total analysis time specified in minutes.
• Total flowrate: The combined flow rate of both A and B mobile phases. This value is
maintained constantly for the duration of the LC method run.

Note: Total flow rate is not shown for Independent Flow Mode.

• point: The point selector scrolls through the programmed points of the profile.

Programmable Events
For device firmware versions X.39 or greater, events are supported by the LC Method Editor
using the Gradient Profile tab.

Program an Event
• In the Gradient Profile tab, right-click in the chart area to show the Event menu, from
which one of 12 possible events may be selected (Figure 6-4). Up to 32 Events can
be inserted into the method. The event is inserted at the time located in the X axis
where the right-click was performed. The event may be moved by dragging the
cursor over the event flag icon.

Figure 6-4 Programmable events

Software User Guide Eksigent Control Software

September 2012 77 of 152
LC Method Editor

Delete an Event
• To delete an event, right-click the event flag icon.

Display Event Information

• Show event information after it is inserted by moving the cursor over the flag icon. A
tooltip describing the event type is shown.

Gradient Table Tab

The tabular representation of the Gradient Profile is shown on the Gradient Table tab (Figure 6-
5). Data describing the LC method flow profile can be typed in the Gradient Table. As with the
Gradient Profile tab (Figure 6-4), the total flow rate is not shown in the Gradient Table tab when
the Independent Flow Mode is selected.

Figure 6-5 LC Method Settings dialog—Gradient Table tab

Select a flow profile event from the Event menu in the Event column. Any events added in the
table are also reflected in the Gradient Profile tab. Use the arrow and X to insert or remove rows
in the table.
The Flow Mode region is used to select between conserved flow and independent flow modes.
• Conserved flow: Select this option to maintain a constant total flow rate for the
entire duration of the acquisition while varying mobile phase composition.
• Independent flow: Select this option to specify the independent flow rates of each
mobile phase.

Eksigent Control Software Software User Guide

78 of 152 September 2012
 LC Method Editor

Note: Total flow rate is not shown for Independent Flow Mode.

Detector Tab
The Detector tab is available for instruments that include a spectrometer (Figure 6-6). This tab is
used to set up the spectral range that defines the main chromatogram, as well as the rate at
which spectra are acquired.

Figure 6-6 LC Method Settings dialog—Detector tab

Data Acquisition
• Approximate acquisition rate in Hz: Specifies the data acquisition rate used to
collect the absorbance signal. For instruments equipped with an absorption
spectrometer, an entire absorption spectrum is measured at each time point.
• Average reference/background acq’ns: Specifies the number of data points
averaged together to calculate the spectrometer dark current and reference signals
prior to initiating acquisition. The default value is four.

Detector Wavelength Range

The wavelength used to define the range of spectral information that is collected during the
acquisition.
• Lower limit: The minimum lower limit value is 200 nm.
• Upper limit: The maximum upper limit value is 380 nm.

Software User Guide Eksigent Control Software

September 2012 79 of 152
LC Method Editor

Chromatogram
The Chromatogram region is used to indicate which mode of spectrometer acquisition (Signal
Type) to use. Absorbance is the default selection as it is typically used for HPLC detection.
However, for diagnostic purposes, the user can select either Transmission or Detector counts for
monitoring system performance.

Absorbance
Defines the parameters used to show the single wavelength chromatogram in the Acquisition
window. Two fields specify the spectral window wavelength range by defining a center
wavelength and a spectral band height.
• Wavelength: Corresponds to the center wavelength of the spectral window. It can
be set to within 1 nm of the specified detector wavelength range (for example, 201-
C379 nm) as long as the bandwidth setting keeps the spectral window within this
range.
• Bandwidth: Adjusted to set the wavelength range used to generate the
chromatogram. Wider bandwidth can be used to reduce baseline noise, but large
bandwidths can compromise detector response linearity. The bandwidth value is
limited by the acquisition wavelength range. For example, if the wavelength is set to
205 nm, the bandwidth can be no greater than 10 nm. The minimal bandwidth setting
is 1 nm.

Mode
Select between Single beam and Dual beam modes of operation.
• Single beam: The detector uses a detector reference signal acquired at the start of
the acquisition for the entire chromatogram.
• Dual beam: The reference signal is continuously measured with an independent
spectrometer. In both cases the reference signal uses the center wavelength and
bandwidth specified.
• Realtime baseline correction: Select the check box to enable real time baseline
correction. In this case a region of the spectrum, typically on the red (high
wavelength) end, is used to normalize the rest of the spectrum. This is useful for
removing a refractive index front that may occur on injection.
If the Realtime baseline correction check box is selected, then type values in the
Monitor baseline and Bandwidth fields. These fields together determine the spectral
window used to normalize the rest of the spectrum. Using typical values of 360 nm
for the monitor baseline and 20 nm for the bandwidth would have the effect of
dividing all other wavelengths in the spectrum by the average normalized intensity
between 350 to 370 nm. This normalization occurs at each time point in the run. The
spectral window defined by the monitor baseline and bandwidth must fit within the
specified range of the detector (200 to 380 nm).

Eksigent Control Software Software User Guide

80 of 152 September 2012
Analysis Method Editor
7
The analysis module automatically analyzes chromatograms. The significant feature of this
module is the automatic peak detection algorithm that locates likely peaks and performs peak
integration to extract the peak area and a set of physical peak properties such as retention time,
peak height, and width.
The automatic peak detection algorithm is based on the first derivative, which is calculated from
the chromatogram. Following peak detection, the algorithm determines the start and end time for
each peak that define the default integration interval. Baselines are constructed that pass
through the absorbance level at the start and end of the respective integration interval.
Subsequent peak integration determines the area between the baseline and absorbance values
of each peak.
The analysis module default settings are adequate for the analysis of simple chromatograms.
More complex chromatograms may require more careful treatment of the data, or special
techniques to integrate specific peaks or group of peaks. This is achieved by using a set of
integration timed events. They are provided to optimize peak detection and to customize peak
integration. Integration timed events can be added to a method either graphically in the
Acquisition window or in the Analysis Method Editor window.
In addition to the automatic peak detection algorithm, quantitation and peak identification can be
performed. Quantitation is the process of calculating concentrations of chemical compounds in
solutions using a calibration table of known compounds and their corresponding retention times.
At any time, clicking the Find peaks now! button to test the analysis method settings on the
currently active chromatogram data in the main plot window. The analysis results are shown
immediately.

Perform Analysis
1. In the Acquisition window, click Run Manager.
2. In the Run Manager dialog, click File > Peak Viewer.
3. In the Peak Viewer dialog, click open a data file.
4. In the Peak Viewer dialog, click Peaks > Analysis Settings.
The Analysis Method dialog (Figure 7-1) is divided into three tabs: Peak Detection,
Quantitation, and Options.
5. In the Analysis Method Settings dialog, open a method.

Software User Guide Eksigent Control Software

September 2012 81 of 152
Analysis Method Editor

Figure 7-1 Analysis Method Settings dialog—Peak Detection tab

6. Do one of the following:
• Use the information in the following sections to edit the existing method and
then click Find Peaks Now!.
• Click Find Peaks Now!.
7. If required, save the method.

Peak Detection Tab

The Peak Detection tab shown in Figure 7-1 contains the integration timed events table. A typical
integration timed event consists of a start and stop time indicating the time interval for which it
applies and a parameter which may specify a threshold value (for example, Detection Threshold)
or a more specific integration technique (for example, Tangent for Front or Back Skim). Events
may be added or removed except for the first four rows that contain entries for the Detection
Threshold, the Detection Threshold Asymmetry, the Minimum Peak Height, and the Minimum
Peak Width. Parameter values for these events may be adjusted and overwritten by subsequent
events of the same type. However, they are required by the peak detection algorithm during the
entire duration of the chromatogram. The analysis module provides a set of default values for
these events that have proven to work well for simple chromatograms and that may provide a
good starting point for the development of more complex analysis methods. For more
information, refer to Chapter 8.

Eksigent Control Software Software User Guide

82 of 152 September 2012
 Analysis Method Editor

Insert a Table
Do one of the following:
• Click the arrow to the right of the calibration table to open the Insert New Table Entry
dialog (Figure 7-2).
• On the Analysis Method Settings dialog, click Advanced > Insert New Table
Entry.

Figure 7-2 Insert New Table Entry dialog

Quantitation Tab
The Quantitation tab shown in Figure 7-3 consists of two parts: the calibration table and the
calibration curve window. The calibration table contains all the necessary information to
determine the concentration of unknown chemical compounds as well as sample specific
information.

Software User Guide Eksigent Control Software

September 2012 83 of 152
Analysis Method Editor

Figure 7-3 Analysis Method Settings dialog—Quantitation tab

Response: Select the response to be used for solving for unknown concentrations and
generating calibration curves.
Peak Windows: Shows the options for peak identification. For more information, refer to Peak
Identification on page 113.
Adding Standards: Shows the options for updating the calibration table for automatic
calibration. For more information, refer to Chapter 10.
• New calibrants will replace previous values: Allows for one replicate per level.
Each new replicate will replace the last replicate.
• New calibrants are appended to previous values: Allows for multiple replicates.
• Average previous replicates: Performs a rolling average of replicates if the
response of the column drifts with time. Rolling averages replace the oldest replicate
with the latest replicate to account for any changes in response.
• Average previous _ replicates: The number typed in the field indicates the number
of previous replicates to average.

Options Tab
The Options tab shown in Figure 7-4 contains the settings for peak identification and quantitation.
Refer to Chapter 9. This option is normally only used for UV systems.

Eksigent Control Software Software User Guide

84 of 152 September 2012
 Analysis Method Editor

Figure 7-4 Analysis Method Settings dialog—Options tab

Peak Results
Analyzing a chromatogram leads to a set of results for each identified peak. The results include
qualitative and quantitative properties that characterize the peak location and shape, the column
performance, and the amount of substance that created the peak. Peak results are shown in the
peak table in the Acquisition window. For more information, refer to Chapter 2.
The table columns can be customized using the Choose Peak Table Columns options on the
Analysis menu in the Acquisition window. The items that can be selected are shown in Table 7-1.
Table 7-1 Choose Peak Columns
Peak type Description
Peak Name The name of the peak as typed in the peak table.
Peak Number The peak number is assigned in ascending order according to the
retention time.
Retention Time (min) Position of the maximum peak absorbance, determined from a
quadratic curve fitted to peak data points around the absolute
maximum.
Peak Height (mAu) The maximum absorbance of a peak, determined from baseline-
corrected absorbance values.
Percent of Total Height Percentage from the sum of all peak heights.
(%)

Software User Guide Eksigent Control Software

September 2012 85 of 152
Analysis Method Editor

Table 7-1 Choose Peak Columns (Continued)

Peak type Description
Area (mAu.s) The area between the baseline and the absorbance data from the
beginning to the end of the peak.
Percent of Total Area Percentage from the sum of all areas.
(%)
Base Width (sec) The area between the baseline and the absorbance data from the
beginning to the end of the peak.
Width at 5% Peak width determined at 5 percent of the peak height.
Width at 10% Peak width determined at 10 percent of the peak height.
Width at 50% Peak width determined at 50 percent of the peak height.
Asymmetry at 50% The ratio of front to back width at 50 percent of the peak height.
Asymmetry at 10% The ratio of front to back width at 10 percent of the peak height.
Asymmetry at 5% The ratio of front to back width at 5 percent of the peak height.
Tailing Factor Ratio of total width to twice the front width at 5 percent of the peak
height.
Number of Plates (N) Number of theoretical plates based on different methods* [USP, DAB,
JP, EMG].
Number of Plates per Number of theoretical plates per meter based on different methods*
meter (N/m) [USP, DAB, JP, EMG].
Resolution Resolution between the peak of interest and the peak preceding it
based on different methods* [USP, DAB, JP, EMG].
Signal to Noise Signal to Noise Ratio.
Capacity Factor Ratio of time spent by substance in stationary phase to time spent by
substance in mobile phase.
Relative Retention Relative retention measured with respect to an unretained compound.

*The available calculation methods are United States Pharmacopoeia (USP), German Pharmaco-
poeia (DAB), Japanese Pharmacopoeia (JP), and the method based on the Exponential Modified
Gaussian (EMG) model.

Capacity Factor
The capacity factor of a peak with retention time is calculated according to the formula in
Figure 7-5 where item 1 is the retention time of an unretained or reference peak.

Figure 7-5 Capacity factor formula

The relative retention is calculated using the formula in Figure 7-6.

Eksigent Control Software Software User Guide

86 of 152 September 2012
 Analysis Method Editor

Figure 7-6 Relative retention formula

Reference peaks are defined by the corresponding integration timed event. For more
information, refer to Chapter 8.

Peak Asymmetry
Asymmetric peak shapes are characterized by different values for the front half width f and back,
or tail, half width b. As a quantitative measure of the peak asymmetry, the analysis module
provides values for the Asymmetry A
A=b/f
at 5, 10, and 50 percent of the peak height, and the Tailing Factor T which is calculated at 5
percent of the peak height:
T= (b+f)/2f

Figure 7-7 Asymmetric Peak with front width (f) and back width (b) indicated at 5, 10, and
50% of the peak height

Calculation Methods
The peak results include column performance parameters based on four different calculation
methods.

Software User Guide Eksigent Control Software

September 2012 87 of 152
Analysis Method Editor

United States Pharmacopoeia (USP) Calculation Method

Number of Plates N:

t = Retention time of peak

W = Base width determined by tangent method (Figure 7-8)

Figure 7-8 Tangent Method: The Base Width is Determined by the Intersection of the two
Tangents at the Inflection Points with the Peak Baseline
Resolution (R) between a peak of interest (peak 2) and the preceding peak (peak 1):

Where:
t1,2 = Retention time of peak 1 and peak 2
W1,2 = Base width of peak 1 and peak 2 determined by tangent method

German Pharmacopoeia (DAB) Calculation Method

Number of Plates N:

t = Retention time of peak

W50% = Width of peak at 50% peak height
Resolution (R) between a peak of interest (peak 2) and the preceding peak (peak 1):

Where:
t1,2 = Retention time of peak 1 (2)
W1(2), 50 = Width of peak 1(2) at 50% peak height

Eksigent Control Software Software User Guide

88 of 152 September 2012
 Analysis Method Editor

Japanese Pharmacopoeia (JP) Calculation Method

Number of Plates N:

t = Retention time of peak

W50% = Width of peak at 50% peak height
Resolution (R) between a peak of interest (peak 2) and the preceding peak (peak 1):

Where:
t1 ,2= Retention time of peak 1 and peak 2
W1 ,2 = Width of peak 1 and peak 2 at 50% peak height

Exponential Modified Gaussian (EMG) Calculation Method

Number of Plates N:

Where:
t = Retention time of peak
W10% = Width at 10% peak height
f10% = Front width of peak at 10% peak height
b10% = Back width of peak at 10% peak height
Resolution (R) between a peak of interest (peak 2) and the preceding peak (peak 1):

With:
t1,2 = Retention time of peak 1 and 2
W1 ,2= Width of peak 1 and peak 2 at 10% peak height

Software User Guide Eksigent Control Software

September 2012 89 of 152
Analysis Method Editor

Eksigent Control Software Software User Guide

90 of 152 September 2012
Integration Time Events
8
Analyzing a chromatogram is controlled by integration timed events. These events are provided
to improve peak detection and to customize integration of particular peaks or groups of peaks.
Integration timed events fall in two categories: Peak detection and peak integration.
Peak Detection events control the peak location algorithm and determine if a feature in a
chromatogram should be reported as a peak. These include:
• Detection Threshold
• Detection Threshold Asymmetry
• Shoulder Detection
• Minimum Peak Width
• Minimum Peak Height
• Minimum Area
• Integration Off
• Negative Peaks
Peak Integration events control the peak integration by manipulating the baseline and the
analysis of fused peaks. These include:
• Valley To Valley
• Front/Back Skim
• Manual Baseline
• Forward/Backward Horizontal Baseline
• Lowest Point Horizontal Baseline
• Reset Baseline
• Reset Baseline At Valley
• Force Peak Start/Stop
• Split/Merge Peak
• Force Result
• Manual Peak
• Reference Peak

Peak Detection

Detection Threshold
The Detection Threshold is applied to identify and locate peaks in a chromatogram. A non-zero
value is required by the software for the duration of the chromatogram. The threshold value is
specified as a percentage with respect to the highest value of the first derivative computed for the

Software User Guide Eksigent Control Software

September 2012 91 of 152
Integration Time Events

entire chromatogram. A high value suppresses the detection of very slowly rising features and
small peaks, while a low value increases the number of small peaks that are reported. The
default threshold value is 1%.
Table 8-1 Event Parameters
Event Description
parameters
Start Time Start using the specified value for the Detection Threshold.
Stop Time Stop using the specified value for the Detection Threshold.
Parameter Detection threshold.

Detection Threshold Asymmetry

Most chromatographic peaks exhibit asymmetric shapes, characterized by slower falling tails.
This phenomenon is taken into account by the peak detection algorithm via the Detection
Threshold Asymmetry which relaxes the detection threshold in the tail region of a potential peak.
The threshold value is specified as a percentage indicating which fraction of the Detection
Threshold is applied to detect the back of a peak. A non-zero value is required by the software for
the entire duration of the chromatogram. The default threshold value is 20%.
Table 8-2 Event Parameters
Event Description
parameters
Start Time Start using the specified value for the Detection Threshold Asymmetry.
Stop Time Stop using the specified value for the Detection Threshold Asymmetry.
Parameter Detection Threshold Asymmetry.

Shoulder Detection
Shoulders occur when two peaks are so close that no valley is formed in-between (for example,
Figure 8-1). The Shoulder Detection event enables the detection of shoulders attached to larger
peaks in a chromatogram. The shoulder detection algorithm is based on the second derivative.
The parameter indicates the sensitivity of the algorithm and is specified as a percentage with
respect to the highest value of the second derivative calculated for the entire chromatogram. A
higher value decreases shoulder sensitivity, while lower values increase the sensitivity to
shoulder peaks. A zero value indicates that shoulder detection is turned off. Shoulder detection
changes peak boundaries and the integrated areas of parent peaks.
Table 8-3 Event Parameters
Event Description
parameters
Start Time Start using Shoulder Detection.
Stop Time Stop using Shoulder Detection.
Parameter Shoulder Detection Sensitivity.

Eksigent Control Software Software User Guide

92 of 152 September 2012
 Integration Time Events

Figure 8-1 Fused peaks without shoulder detection enabled

Figure 8-2 Fused peaks with shoulder detection enabled

Minimum Peak Width

The Minimum Peak Width event sets a lower limit for the smallest width of a feature that is
reported as a true peak by the detection algorithm. A positive value is required by the software for
the entire duration of the chromatogram. The width is specified in seconds. The default value is
one second.
Table 8-4 Event Parameters
Event Description
parameters
Start Time Start using the specified value for the Minimum Peak Width.
Stop Time Stop using the specified value for the Minimum Peak Width.
Parameter Minimum Peak Width.

Minimum Peak Height

The Minimum Peak Height event sets a lower limit for the smallest peak height above the
baseline. Features in the chromatogram with heights below this limit are not reported as peaks.
The height is specified in units of mAU. The default value is zero.

Software User Guide Eksigent Control Software

September 2012 93 of 152
Integration Time Events

Table 8-5 Event Parameters

Event Description
parameters
Start Time Start using the specified value for the Minimum Peak Height.
Stop Time Stop using the specified value for the Minimum Peak Height.
Parameter Minimum Peak Height.

Minimum Area
The Minimum Area event sets a lower limit for the area that defines a peak. Features in a
chromatogram that lead to areas below this limit are not reported as peaks. A positive value is
required by the software. The area is specified in units of mAU. The default value is zero.
Table 8-6 Event Parameters
Event Description
parameters
Start Time Start using the specified value for the Minimum Peak Area.
Stop Time Stop using the specified value for the Minimum Peak Area.
Parameter Minimum Peak Area.

Integration Off
The Integration Off event disables peak detection and peak integration during the specified time
interval.
Table 8-7 Event Parameters
Event Description
parameters
Start Time Start disabling peak detection and integration.
Stop Time Stop disabling peak detection and integration.

Negative Peaks
The Negative Peaks event can be applied to integrate portions of the chromatogram that are
below the baseline (for example, Figure 8-3). As a consequence, features that appear as deep
valleys are reported as true peaks.
Table 8-8 Event Parameters
Event Description
parameters
Start Time Start detection of negative peaks.
Stop Time Stop detection of negative peaks.

Eksigent Control Software Software User Guide

94 of 152 September 2012
 Integration Time Events

Figure 8-3 Default baseline without negative peaks enabled

Figure 8-4 Baseline with negative peaks enabled between 5.5 and 8 minutes

Peak Integration

Valley To Valley
The Valley To Valley event is applied to groups of fused peaks. By default, a common baseline is
drawn for all fused peaks, with each peak separated by a vertical drop line. During a Valley To
Valley event the baseline is constructed by connecting the valleys between individual peaks.
Table 8-9 Event Parameters
Event Description
parameters
Start Time Start using Valley To Valley.
Stop Time Stop using Valley To Valley.

Software User Guide Eksigent Control Software

September 2012 95 of 152
Integration Time Events

Figure 8-5 Default baseline for a series of fused peaks

Figure 8-6 Baseline after Valley to Valley event

Front Skim
The Front Skim event is applied to resolve one or more small child peaks or shoulder peaks
attached to the front of a larger parent peak. To construct the baseline of the child peak, the
following options are available:
• Tangent skim leads to a straight baseline for the child peaks.
• Gaussian skim leads to a Gaussian curve for the baseline of the child peaks.
• Exponential skim leads to an exponential curve for the baseline of the child peaks.
Table 8-10 Event Parameters
Event Description
parameters
Start Time Start of the first child peak.
Stop Time Stop of the parent peak.
Parameter Tangent, Gaussian, or Exponential.

Eksigent Control Software Software User Guide

96 of 152 September 2012
 Integration Time Events

Figure 8-7 Default integration of fused peaks using vertical drop lines

Figure 8-8 Front Skim event with tangent baseline

Figure 8-9 Front Skim event with exponential baseline

Software User Guide Eksigent Control Software

September 2012 97 of 152
Integration Time Events

Figure 8-10 Front Skim event with Gaussian baseline

Back Skim
The Back Skim event is applied to resolve one or more small child peaks or shoulder peaks
attached to the back of a larger parent peak. To construct the baseline of the child peak the
following options are available:
• Tangent skim leads to a straight baseline for the child peaks.
• Gaussian skim leads to a Gaussian curve for the baseline of the child peaks.
• Exponential skim leads to an exponential curve for the baseline of the child peaks.
Table 8-11 Event Parameters
Event Description
parameters
Start Time Start of the parent peak.
Stop Time Stop of the last child peak.
Parameter Tangent, Gaussian, or Exponential.

Manual Baseline
The Manual Baseline event is applied to change a baseline of a peak without changing the
integration parameters. By default a baseline is constructed based on the peak boundaries as
they arise for a single isolated peak or in a group of fused peaks. A manual baseline is drawn
without changing the baseline of other peaks in the chromatogram. It is constructed by
connecting the data point at the specified start time with the data point at the specified stop time.
If the specified start time of the manual baseline is earlier than the start of the original baseline,
the original start time is maintained. Similarly, if the specified stop time of the manual baseline is
later than the original stop of the baseline, the original stop time is maintained.
Table 8-12 Event Parameters
Event Description
parameters
Start Time Start of Manual Baseline.
Stop Time Stop of Manual Baseline.

Eksigent Control Software Software User Guide

98 of 152 September 2012
 Integration Time Events

Figure 8-11 Default baseline

Figure 8-12 Manual baseline between 4.65 and 5.3 minutes

Forward Horizontal Baseline

The Forward Horizontal Baseline event forces a horizontal baseline in a forward direction. The
baseline is constructed by drawing a horizontal line from the data point which corresponds to the
start of the original baseline to the specified stop time. If the specified stop time is later than the
stop of the original baseline, the original stop time is maintained.
Table 8-13 Event Parameters
Event Description
parameters
Start Time Start of forward Horizontal Baseline.
Stop Time Stop of forward Horizontal Baseline.

Software User Guide Eksigent Control Software

September 2012 99 of 152
Integration Time Events

Figure 8-13 Default baseline

Figure 8-14 Forward Horizontal Baseline event between 4.5 and 7.2 minutes

Backward Horizontal Baseline

The Backward Horizontal Baseline event forces a horizontal baseline in a backward direction.
The baseline is constructed by drawing a horizontal line starting from the data point which
corresponds to the stop of the original baseline to the specified start time. If the specified start
time is earlier than the start of the original baseline, the original start time is maintained.
Table 8-14 Event Parameters
Event Description
parameters
Start Time Start of Backward Horizontal Baseline.
Stop Time Stop of Backward Horizontal Baseline.

Eksigent Control Software Software User Guide

100 of 152 September 2012
 Integration Time Events

Figure 8-15 Default baseline

Figure 8-16 Baseline after backward Horizontal Baseline Event between 4.3 and
5.75 minutes

Lowest Point Horizontal Baseline

The Lowest Point Horizontal Baseline event creates a horizontal baseline that intersects with the
absorbance minimum between the start and stop time of the event. The start and stop time of the
original baseline is maintained.
Table 8-15 Event Parameters
Event Description
parameters
Start Time Start of Lowest Point Horizontal Baseline.
Stop Time Stop of Lowest Point Horizontal Baseline.

Software User Guide Eksigent Control Software

September 2012 101 of 152
Integration Time Events

Figure 8-17 Default baseline

Figure 8-18 Baseline after Lowest Point Horizontal Baseline event between 3.9 and
9.5 minutes

Reset Baseline
The Reset Baseline event resets the baseline at the data point that corresponds to the specified
start time of the event.
Table 8-16 Event Parameters
Event Description
parameters
Start Time Start of Reset Baseline.

Figure 8-19 Default baseline

Eksigent Control Software Software User Guide

102 of 152 September 2012
 Integration Time Events

Figure 8-20 Reset Baseline event at 8.63 minutes

Reset Baseline At Valley

The Reset Baseline At Valley event generates a baseline reset at the next valley detected after
the specified start time.
Table 8-17 Event Parameters
Event Description
parameters
Start Time Start of Reset Baseline At Valley.

Figure 8-21 Default baseline

Figure 8-22 Baseline after Reset Baseline At Valley event

Software User Guide Eksigent Control Software

September 2012 103 of 152
Integration Time Events

Force Peak Start

The Force Peak Start event is applied to force the start of the baseline at the specified start time.
If the start of the event is earlier than the start of the original baseline, the event has no effect.
Table 8-18 Event Parameters
Event Description
parameters
Start Time Start of the peak.

Figure 8-23 Default baseline

Figure 8-24 Baseline after Force Peak Start event at 8.75 minutes

Force Peak Stop

The Force Peak Stop event is applied to force the stop of the baseline at the specified stop time.
If the stop of the event is later than the stop of the original baseline, the event has no effect.
Table 8-19 Event Parameters
Event Description
parameters
Start Time Stop of the peak.

Eksigent Control Software Software User Guide

104 of 152 September 2012
 Integration Time Events

Figure 8-25 Baseline for peak in Figure 8-23 after Force Peak Stop event at 9 minutes

Split Peak
The Split Peak event divides a peak by inserting a perpendicular drop-line at the specified start
time of the event. The feature to the left and right of the drop line are reported as two separated
peaks. If the start time is not within the peak boundaries of a detected peak, the event is ignored.
Table 8-20 Event Parameters
Event Description
parameters
Start Time Indicate when to split a peak.

Figure 8-26 Split Peak Event at 5 minutes

Merge Peak
The Merge Peak event reports the series of peaks between the start and stop of the event as one
peak. The retention time of the merged peaks is determined by the highest peak in the series. If
only one peak is detected between the start and stop time the event is ignored.
Table 8-21 Event Parameters
Event Description
parameters
Start Time Start of Merge Peak.
Stop Time Stop of Merge Peak.

Software User Guide Eksigent Control Software

September 2012 105 of 152
Integration Time Events

Figure 8-27 Default baseline

Figure 8-28 Baseline of merged peaks

Force Result
The Force Result event reports results for a peak in the specified time interval even if no peak
was detected. The event is useful for monitoring peaks that are expected to emerge within a
certain time interval during a series of runs.
Table 8-22 Event Parameters
Event Description
Parameters
Start Time Start of Force Result.
Stop Time Stop of Force Result.

Manual Peak
The Manual Peak event defines a feature in a chromatogram as a peak that was previously not
detected. The event is used to force integration without changing other integration parameters for
a specific region of the chromatogram.
Table 8-23 Event Parameters
Event Description
parameters
Start Time Start of Manual Peak.

Eksigent Control Software Software User Guide

106 of 152 September 2012
 Integration Time Events

Table 8-23 Event Parameters (Continued)

Event Description
parameters
Stop Time Stop of Manual Peak.

Figure 8-29 Default baseline

Figure 8-30 Manual peak event between 9 and 17 minutes

Reference Peak
The Reference Peak event defines the peak which is used to calculate the capacity factor and
relative retention. If no peak is detected in the time window defined by the start and stop of the
event, the Capacity Factor and the Relative Retention is set to zero. If more than one peak is
detected the retention time of the first peak is used in the calculation. Only one Reference Peak
event can be typed into the integration timed event table.
Table 8-24 Event Parameters
Event Description
parameters
Start Time Start of the reference peak time window.
Stop Time Stop of the reference peak time window.

Software User Guide Eksigent Control Software

September 2012 107 of 152
Integration Time Events

Incompatible Events
The analysis module restricts the simultaneous use of certain timed integration event
combinations. It is not possible to type an event in the integration timed event table if conflicts
arise with existing events. Conflicts are determined by checking for an overlap between two
events or, in the case of an event with only a start or stop time, if it is contained within a time
interval defined by another event.

Note: If an event is listed as conflicting with itself it cannot be applied a second time
within the range for which it already exists.

Note: If an event that is listed as not conflicting with itself is typed multiple times, the
parameter (for example, Detection Threshold) that was typed last is applied during the
overlapping time intervals.

Table 8-25 Incompatible events

Event Incompatible event
Shoulder Detection Negative Peaks
Integration Off Force Result
Negative Peaks Shoulder Detection
Negative Peaks
Valley To Valley
Front Skim
Back Skim
Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Manual Peak
Manual Baseline Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Force Peak Start
Force Peak Stop

Eksigent Control Software Software User Guide

108 of 152 September 2012
 Integration Time Events

Table 8-25 Incompatible events (Continued)

Event Incompatible event
Forward Horizontal Manual Baseline
Baseline Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Back Skim
Front Skim
Manual Peak
Backward Horizontal Manual Baseline
Baseline Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Back Skim
Front Skim
Manual Peak
Lowest Point Horizontal Manual Baseline
Baseline Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Back Skim
Front Skim
Manual Peak

Software User Guide Eksigent Control Software

September 2012 109 of 152
Integration Time Events

Table 8-25 Incompatible events (Continued)

Event Incompatible event
Reset Baseline Manual Baseline
Backward Horizontal Baseline
Forward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Back Skim
Front Skim
Manual Peak
Reset Baseline At Manual Baseline
Valley Backward Horizontal Baseline
Forward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Back Skim
Front Skim
Manual Peak
Back Skim Back Skim
Front Skim
Backward Horizontal Baseline
Forward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Manual Peak
Valley To Valley Forward Horizontal Baseline
Backward Horizontal Baseline
Lowest Point Horizontal Baseline
Reset Baseline
Reset Baseline At Valley
Valley To Valley
Manual Peak
Merge Peak Manual Peak

Eksigent Control Software Software User Guide

110 of 152 September 2012
 Integration Time Events

Table 8-25 Incompatible events (Continued)

Event Incompatible event
Split Peak Manual Peak
Force Peak Start Manual Baseline
Manual Peak
Force Peak Stop Manual Baseline
Manual Peak
Force Result Integration Off
Manual Peak

Software User Guide Eksigent Control Software

September 2012 111 of 152
Integration Time Events

Eksigent Control Software Software User Guide

112 of 152 September 2012
Quantitation
9
Quantitation is the process of calculating the concentration of chemical compounds in samples
from the peak areas or peak heights. Quantitation requires peak identification and calibration.
Peak Identification: Indicates the presence of a compound on the basis of its retention time.
Calibration: A method that determines the relationship between the amount of a compound and
its measured response.
The Quantitation module allows users to calculate the amount of an unknown component from
the measured peak height or area. The type of calculation performed depends on the type of
standard. Two types of standards are available: External Standard (ESTD) and Internal Standard
(ISTD).

Peak Identification
Peak Identification is an integral part of quantitation. A peak cannot be quantified unless it is
identified. The identification must have the following information in the calibration table:
Name and Retention Time: The user must supply a name for each retention time in the
calibration table for identification.
Retention Time Window: The retention time window accounts for the variability of retention
times by providing an upper and lower bound for the search. Two types are available to the user.
• Absolute: The upper and lower bounds are user defined.
• Relative: The window is calculated as a percentage.

Peak Identification Rules: More than one peak can be located within the defined retention time
window. The identified peak is chosen from one of five possible rules.
Rule 1—First Peak: The First Peak matching the criteria is found. Refer to Figure 9-1.

Software User Guide Eksigent Control Software

September 2012 113 of 152
Quantitation

Figure 9-1 First peak is found

Rule 2—Nearest: Finds the peak located closest to the center of the window. Refer to Figure 9-
2.

Eksigent Control Software Software User Guide

114 of 152 September 2012
 Quantitation

Figure 9-2 Center peak is chosen

Rule 3—Height: The peak with the largest height is found. Refer to Figure 9-3.

Software User Guide Eksigent Control Software

September 2012 115 of 152
Quantitation

Figure 9-3 Largest peak is found

Rule 4—Last: The last peak is found. Refer to Figure 9-4.

Eksigent Control Software Software User Guide

116 of 152 September 2012
 Quantitation

Figure 9-4 Third peak is found (the last peak in the window)
Rule 5—Best Match: Finds the peak with the most similar area relative to the indicated
specification in the calibration table.

Software User Guide Eksigent Control Software

September 2012 117 of 152
Quantitation

Figure 9-5 Middle peak is chosen because its area is closest to 1100 mA2 (the peak area
in the calibration table was 1100 mA2)

Calibration
Calibration is based on the principle that a relationship exists between the amount of a chemical
compound and its measured detector response. The relationship (calibration curve) can be linear
or nonlinear and the calibration curves are stored in the calibration table.

Terms and Definitions

Response Factor: Ratio of the amount to the response

Amount Ratio: Ratio of the ESTD amount to the ISTD amount

Eksigent Control Software Software User Guide

118 of 152 September 2012
 Quantitation

Response Ratio: Ratio of the ESTD response to the ISTD response

Multiplication Factor: A correction factor that is used to convert units (for example, conversion
factor for grams to kilograms is 1000)
Dilution Factor: A correction factor that accounts for serial dilution

Types of Calibration
A calibration curve is characterized by the number of levels (for example, different amounts of
analyte in each sample). Each level can have of one or more replicates. The calibration curve is
generated from averaging the replicate amounts and response for each level.
• Single Level Calibration: A calibration that uses a single point. It assumes the
response is linear throughout the entire concentration range and the curve passes
through the origin. For an example of a single level calibration, refer to Figure 9-6.

Software User Guide Eksigent Control Software

September 2012 119 of 152
Quantitation

Figure 9-6 Single level calibration curve

• Multi-Level Calibration: A calibration that uses more than one calibrant. For an
example of a multi-level calibration, refer to Figure 9-7.

Eksigent Control Software Software User Guide

120 of 152 September 2012
 Quantitation

Figure 9-7 Multi-level calibration curve

Types of Fits

Linear Fit
A linear response follows the Beer-Lambert Law. The response of a chemical compound is
directly proportional to the amount of that compound. The following equation is used:
aX + b = Y
Where:
X = amount (ESTD), amount ratio (ISTD)
Y = response (ESTD), response ratio (ISTD)
a = slope
b = Y-intercept

Nonlinear Fits
If the response is nonlinear, the Quantitation module provides two polynomial fits: quadratic and
cubic.

Software User Guide Eksigent Control Software

September 2012 121 of 152
Quantitation

Quadratic Fit
Quadratic: Minimum of three calibration levels
Y = aX2 + bX + c
Where:
X = amount (ESTD), amount ratio (ISTD)
Y = response (ESTD), response ratio (ISTD)
a = coefficient 1
b = coefficient 2
c = Y-intercept

Cubic Fit
Cubic: Minimum of four calibration levels
Y = aX3 + bX2 + cX + d
Where:
X = amount (ESTD), amount ratio (ISTD)
Y = response (ESTD), response ratio (ISTD)
a = coefficient 1
b = coefficient 2
c = coefficient 3
d = Y-intercept

Calibration Range
For quantitation with nonlinear fits, the Quantitation routine module will provide concentrations for
unknowns that are bound by the lower/upper limits of the amounts for calibration curves.

Note: Ideally, the equation generated should include the origin (for example, the Y-
intercept = 0, detector has zero response when the compound is not present). The user
has the option to force the fit through zero.

Correlation Coefficient
The correlation coefficient measures how well a polynomial fit matches the data. As the
coefficient approaches one, the curve is a better representation of the data.
0 ==> No fit
1 ==> Perfect fit

Weighting Factor
A weighting can be applied to each point in a calibration curve. The choice of weighting factor
determines the importance of a data point within a given data range. For example, a weight of 1/
amount places more emphasis on points with a smaller amount.

Eksigent Control Software Software User Guide

122 of 152 September 2012
 Quantitation

Table 9-1 Weighting Factors

Weight Description
None equal weights for all points
1/X² 1/amount²
1/X 1/amount
X amount
X² amount²
1/Y 1/Response
Y Response
Y² Response²

Scaling Factors
The quantitation module includes the ability to scale the X-axis of the calibration curves. For a list
of available scale factors, refer to Table 9-2.
Table 9-2 Scale Factors
Scale Factor
None
1/Amount
ln(Amount)
1/ln(Amount)
Sqrt(Amount)
Amount²
1/ResponseFactor
1/ResponseFactor²
ln(ResponseFactor)
1/ln(ResponseFactor)
Sqrt(ResponseFactor)
ResponseFactor²
Log(Amount)
1/Log(Amount)
Log(ResponseFactor)
1/Log(ResponseFactor)

Software User Guide Eksigent Control Software

September 2012 123 of 152
Quantitation

Calibration Table
The calibration table contains all of the necessary information to perform Quantitation. The
following information is required to create the table:
• The retention time for each named peak.
• Amounts for each peak.
• Response for each peak.
Each row of the table corresponds to a given compound. For a description of each column, refer
to Table 9-3.

Note: The user can bypass calibration and perform peak identification by supplying the
retention time for a named peak.

Table 9-3 Calibration Table Columns

Column Description
Peak Name Name of the peak.
RT Retention Time of the peak.
Width Width of identification window. Visible only if absolute windows are used.
Amount Amount for a level.
Area Area of the peak.
Height Height of the peak.
Multiplication Factor Factor used to convert the units of the amount.
Dilution Factor Factor used for serial dilution.
Used Determines if the point is used in the curve fit.
ISTD Check box indicating if the compound is an ISTD.
Associated ISTD Name of the ISTD associated with ESTD—blank if the peak is an ISTD.
ISTD Amount Amount of the Associated ISTD—blank if the peak is an ISTD.
ISTD Area Area of the Associated ISTD—blank if the peak is an ISTD.
Response Accuracy The ratio of calculated response plus the measured response, multiplied
by 100.
ISTD Ratio Ratio of ESTD amount/ISTD amount.
Sample Name Name of the sample.
Sample ID ID of the sample.
Date Date the sample was acquired.
User Name Name of the user.
Filename Name and location of the file.

External Standard Calculation

For ESTD calculations, the calibration curve is generated by examining a single analyte from a
solution or serial dilution. The calibration standards and unknown samples are analyzed under

Eksigent Control Software Software User Guide

124 of 152 September 2012
 Quantitation

the same conditions. Because the response is sensitive to changes in concentration, care must
be taken to make sure that the injection volume cannot vary.
The amount is calculated by solving the equation from its calibration curve using the response of
the unknown sample. Figure 9-8 shows a single-level calibration using the height as the
response.

Figure 9-8 Calibration curve for a linear response (Height)

The equation for the curve and the response of the unknown sample is required for calculation.
If an unknown sample has a peak area of 19.5 units, the amount is calculated as follows:
For a linear response,

Where:
a = the slope with units of Response/Amount.
The example equation is

Software User Guide Eksigent Control Software

September 2012 125 of 152
Quantitation

Rearranging and solving for the unknown sample leads to:

Internal Standard Calculation

An ISTD sample is prepared by adding a standard to the solution. The internal standard and the
analyte should have similar chemical properties and retention times. An ISTD calculation
eliminates the error from differing injection volumes because the ratio of the responses is used.
An ideal ISTD calculation uses the same amount of internal standard for each level of a multi-
level calibration. The Quantitation module allows the user to use different internal amounts for
each level if needed. Figure 9-9 shows the calibration curve for a multi-level ISTD calibration
using the peak area as the response.

Figure 9-9 Multi-level ISTD calibration curve

The equation of the calibration curve, the amount of internal standard in the unknown sample,
and the response ratio are necessary for the calculation.

Eksigent Control Software Software User Guide

126 of 152 September 2012
 Quantitation

For a linear response ratio,

Where:
a = the ratio:

b = the Y– intercept.
Rearranging the equation leads to:

And multiplying by the amount of internal standard

Automated Calibration Table Generation through

the Run Manager
The Run Manager dialog allows the user to automatically update calibration tables. An analysis
method file, the standard amounts (ESTD/ISTD), and the type of sample are required for
automation. Figure 9-10 shows the Run Table used for generating an automated two-level ISTD
calibration.

Software User Guide Eksigent Control Software

September 2012 127 of 152
Quantitation

Figure 9-10 Run table to generate a two-level ISTD calibration table

Automatic Quantitation allows for a maximum of five calibration standards. The amounts should
be listed in order of retention time, where amount 1 has the shortest retention time and amount 5
has the longest retention time. There are two types of samples: standard and unknown.
• If an unknown sample is selected, the analysis calculates the unknown amount from
the calibration table of the chosen analysis method file. For internal standard
calculations, the internal standard concentration must be typed into the calibration
table.
• If a standard sample is selected, the calibration table is updated according to the
analysis method file. It is important the user note the following:
• The analysis method file is updated with each run. The calibration table
generated for run 4 contains data from run 2, but the calibration table for run 2
does not contain any data from run 4.
• Each sample file generated contains a copy of the calibration table generated
for that run. The only file with the complete calibration table is the analysis
method.
The analysis method contains information about how the calibration table is generated. The
adding standards frame contained in the Options tab of the Analysis Method Settings dialog
(Figure 9-10) allows the user to choose how the standards are added to the table.

Eksigent Control Software Software User Guide

128 of 152 September 2012
User Manager
10
Eksigent software comes with system administration functions that enable a system
administrator to configure user and group privileges to maximize security and efficiency of the
system. A Windows network or local administrator can use the User Manager dialog to assign
user and group privileges to various features within the software. Proper user configuration
effectively turns the software into a closed system where user authentication is required. In this
environment, user actions can be clearly defined and carefully monitored.

User Authentication
By default, the user authentication features are not available when the software is installed. This
is an open system configuration, where every user who has access to the computer has full
access to the software. After user authentication has been enabled, all users are required to log
on to access the software.
The software automatically queries both the domain controller and the local computer for a list of
available users. These user accounts are defined on the primary domain controller or on the local
computer, but the privileges that these users have are defined in the software. Any Windows user
can access the software using the same accounts, assuming the right privileges have been
granted to the user.

Enable User Authentication

1. On the Acquisition window, click System > User Authentication.
If this feature is accessed for the first time, or if the User Authentication is not
enabled, a User Logon dialog opens.

Figure 10-1 User Logon dialog

2. Select a log on option.
3. Type a user name and the password.

Software User Guide Eksigent Control Software

September 2012 129 of 152
User Manager

If a valid system administrator user name and password combination is supplied for
the domain or the computer, the User Authentication dialog opens. Refer to
Figure 10-2.

Figure 10-2 User Authentication dialog for administrators

4. Select the Require User Authentication check box.
5. Click OK.
6. Restart the software to activate the user authentication.
7. (Optional) To cancel the log on at any time, click Cancel on the User Logon dialog.
If User Authentication is selected, the User Logon dialog opens when anyone starts
the software.
8. If the user is a system administrator, or if the user has Start and Exit software rights,
the software starts as usual. Otherwise, an Eksigent Security dialog opens. Refer to
Figure 10-3.

Figure 10-3 User does not have software start and exit rights

User Manager
The specific system functions that are controlled by the User Manager dialog include:
• Adding and removing Windows users and groups.
• Granting system privileges to Windows users and groups.
• Defining electronic signature roles.
• Defining electronic signature reasons.
The action that occurs is dependent on whether User Authentication has been enabled and the
assigned user privileges.
• If User Authentication is enabled, and the user is logged on as a system
administrator or a user with User Administration privileges on software startup, the
user can access the User Manager dialog.

Eksigent Control Software Software User Guide

130 of 152 September 2012
 User Manager

• If User Authentication is enabled and the user is not logged on as a system

administrator or a user with User Administration privileges on software startup, this
feature not available on the main menu.
• If User Authentication is not enabled, the user is prompted to establish system
administration credentials before getting access to the User Manager dialog. The
User Logon dialog opens. Refer to Figure 10-1.

Figure 10-4 User Manager dialog

Add or Remove Users and Groups

The list of users and groups that are permitted to use the application program appears in the
Current Members for <computer> region of the User Manager dialog. The User Manager dialog
supports both local users and network users and groups.
1. On the Acquisition window, click System > User Manager.
2. To view the local users that are permitted to use the application program, select the
computer name from the Show members for list (Figure 10-4).
The list of added users is shown in the Current Members for <computer> region.
3. To view the network users and groups that are added, select the domain name.
The list of added network users and groups is shown in the same area. If no users
appear, then no users have been added. If the computer is not on a network domain,
then the only available item in the Show members for the menu is the computer
name. In this environment, only local users can be added to the software.
4. To add and remove local or network users, make sure that the respective computer
or domain is shown in the User Manager dialog, and then click Add/Remove.

Software User Guide Eksigent Control Software

September 2012 131 of 152
User Manager

Figure 10-5 Add Members dialog

The Available Members region on the left shows all available users or groups that
exist on the domain or the computer and who have not been added to use the
software. The Added Members region on the right shows all users or groups that
have already been added.

Tip! Click Cancel at any time in the Add Members dialog to exit without
making any changes

5. To add a member, select the member to be added in the Available Members region
and then click the right arrow. This member name appears in the Added Members
region.
6. To remove a member, select the member to remove in the Added Members region
and then click the left arrow. This member name appears in the Available Members
region. When you are satisfied with the membership arrangement, click OK to
confirm the changes and return to the User Manager dialog. The members shown
are the same as those that specified in the Added Members list.

Manage Electronic Signature Roles

Electronic signature roles can be assigned to each user who has been added to the software.
The names of the roles will appear in the Electronic Signature Roles region in the User Manager
dialog. Refer to Figure 10-4. By default, five levels of electronic signature roles are used, and the
names of the roles are predefined for each level in the software. The roles are arranged so that
the role with the highest level of authority is placed at the top, and the role with the lowest level of
authority is placed at the bottom.
1. On the Acquisition window, click System > User Manager.
2. To change the number of levels used or the names of the roles, click Modify in the
Electronic Signature Roles region.

Eksigent Control Software Software User Guide

132 of 152 September 2012
 User Manager

The Electronic Signature Roles dialog opens.

Figure 10-6 Electronic Signature Roles dialog

Tip! Click Cancel at any time in the Electronic Signature Roles dialog to
exit without making any changes

3. To change the name of any of the roles, type a new role name in the text box for that
role.
4. To change the number of active roles, select a number between 1 and 5 in the
Number of Levels list. When reducing the number of roles, the highest signature
roles are deactivated first.
For example, choosing 3 makes the top two levels of electronic signature roles
unavailable, indicating that these two roles are not active, and only the bottom three
roles can be assigned to a user. If any users had previously been assigned to
Operations Manager or QA Manager, their role now defaults to Lab Manager, the
highest role available at this point.
5. Click OK.

Manage Electronic Signature Reasons

Electronic signature reasons are defined in the Electronic Signature Reasons region of the User
Manager dialog. Refer to Figure 10-4. By default, five electronic signature reasons are pre-
defined when the software is installed. Add, modify, or delete any electronic signature reason at
any time.
1. On the Acquisition window, click System > User Manager.
2. To add a new electronic signature reason, click Add in the Electronic Signature
Reasons region.

Figure 10-7 UserManager dialog

3. On the UserManager dialog, type a reason and then click OK.

Software User Guide Eksigent Control Software

September 2012 133 of 152
User Manager

This new reason is shown in the Electronic Signature Reasons region.

4. To modify an existing reason, select the reason in the Electronic Signature
Reasons region.
5. Click Edit.
The UserManager dialog opens. The reason selected appears in this dialog.
6. Edit the reason and then click OK.
7. To delete an existing reason, select the reason in the Electronic Signature Reasons
region and then click Delete.
8. Click Yes to proceed with deleting the reason.

Manage User Permissions

After a user or group has been added to the software, the system administrator can assign the
correct system privileges to this user or group.
1. On the Acquisition window, click System > User Manager.
2. Select the user name and then click Permissions.
The system administrator always has full access to the software and, therefore,
permissions do not need to be set for the system administrator. For any other user,
the General tab of the Member Permissions dialog opens.

Figure 10-8 Member Permissions dialog—General tab

The Member Permissions dialog includes five tabs: General, Runmanager, Data,
Diagnostics, and Other. Each tab contains permission settings that regulate user
actions in the portion of the software specified in the tab title. User permissions only
take effect when User Authentication is enabled. When User Authentication is not
enabled, all users have full access to every feature of the software and assigning
user permissions in this environment has no effect.

Eksigent Control Software Software User Guide

134 of 152 September 2012
 User Manager

General Tab
By default, all members automatically have permission to the Start/Exit Software feature when
they are added to the system. All other permissions on the General tab are not automatically
assigned. To give a member a particular permission on this tab, select the check box.
• Start/Exit Software: Gives a user the right to log in to the software when it is
opened. A user can also exit the software in the main program under File > Exit. A
user cannot log in to the software without this right.
• UV Detector Toolbox: Allows a user to open the UV Detector Toolbox from the
menu option View > UV Detector Toolbox in the Acquisition window. This menu
option is not available if a user does not have this right. For more information, refer to
UV Detector Toolbox on page 21.
• Peak Park Toolbox: Allows a user to open the PeakPark Toolbox from the menu
option View > PeakPark Toolbox in the Acquisition window. This menu option is not
available if a user does not have this right. For more information, refer to PeakPark
ToolBox on page 23.
• System Logs: Allows a user to view any of the available system logs from the menu
option View > System Logs in the Acquisition window. This menu option is not
available if a user does not have this right. For more information, refer to System
Logs on page 24.
• Analysis Settings: Allows a user to access the Analysis Settings dialog from the
menu option Analysis > Settings in the Acquisition window and Analysis Methods
in the Run Manager dialog. These controls are not available if a user does not have
this right. For more information, refer to Chapter 7.
• Notification Options: Allows a user to access the Notification Options dialog from
the menu option System > Notification Options in the main program. This menu
option is not available if a user does not have this right. For more information, refer to
Notification Options on page 33.
• Appearance: Allows a user to access the Appearance Settings dialog from the
menu option System > Appearance Settings in the Acquisition window. This
menu option is not available if a user does not have this right. For more information,
refer to Appearance Settings on page 33.
• Mobile Phases: Allows a user to access the Mobile Phases dialog from the menu
option System > Mobile Phases in the Acquisition window. This menu option is not
available if a user dos not have this right. For more information, refer to Mobile
Phases on page 36.
• Direct Control: Allows a user to access the Direct Control dialog from the menu
option System > Direct Control in the Acquisition window. This menu option is not
available if a user does not have this right. For more information, refer to Direct
Control on page 38.
• Check for Updates: Allows a user to check for software updates from the Eksigent
web site from the menu option Help > Check for Updates in the Acquisition
window. This menu option is not available if a user does not have this right.
To select or clear all permissions on this tab, click Check All or Uncheck All.

Software User Guide Eksigent Control Software

September 2012 135 of 152
User Manager

Runmanager Tab
This tab contains a slider on the left side that determines the user access level for the Run
Manager dialog. The access levels which range from least access to most access are: None,
Low, Medium, High, and Full. By default, all members have access level None in the Run
Manager dialog when they are added to the system.

Figure 10-9 Member Permissions dialog—Runmanager Tab

The Runmanager tab in Figure 10-9 shows a user with an access level of Full. This user has full
access permissions in the Run Manager dialog. To set the permission level of a user, move the
slider to the appropriate level.
For a summary of the basic intent for each access level, refer to Table 10-1.
Table 10-1 Run Manager Permissions for Each Access Level
Permission None Low Medium High Full
Open the Run Manager
dialog    
Start and Stop Runs   
Modify the Run Table  
Save Changes to the Run
Table 

None: Users cannot open the Run Manager dialog. The Run Manager button in the main
program is not available.
Low: Users can open the Run Manager dialog by clicking the Run Manager button in the main
program. The user can also exit the Run Manager dialog. In the File menu, the user can open,
export, and print pre-defined Run Tables.

Eksigent Control Software Software User Guide

136 of 152 September 2012
 User Manager

Low permission users can also do the following:

• Copy Run Table contents to an external medium such as Excel.
• Switch to the Acquisition window.
• View the contents of the Run Table by using the scroll bars and resizing the column.
• Access the Help menu.
Medium: Medium permissions include all actions available under Low. In addition, the user can
start and stop runs by clicking Start or Stop. Medium permission users can also select or clear the
Flush/Equilibrate When Idle selection box.
High: High permissions include all of the actions available under Medium. In addition, the user
can import content into the Run Table from the File menu. The user has access to all commands
in the Edit menu to modify the Run Table and has full direct access to modify the Run Table. The
High permissions user can also use the tray graphic in the Current Tray frame to modify the Run
Table.
Full: Full permissions include all actions available under High. In addition, the user can save new
or modified Run Tables by using the Save or Save As options on the File menu.
The access permissions controls for some features of the Run Manager dialog are not located in
the Runmanager tab of the Member Permissions dialog. These features include items in the
Device menu and buttons in the Method Definitions dialog. The right to access the Analysis
Methods button is controlled on the General tab, as described previously in this section. The
access to the remaining controls is defined on the Other tab. For more information, refer to Other
Tab on page 140.

Data Tab
The Data tab of the Member Permissions dialog (Figure 10-10) manages permissions to access
data in the main program and the application of electronic signatures. This tab also uses a slider
to determine the user level for data access. The access levels, from least access to most access,
are: None, Low, Medium Low, Medium, Medium High, High, and Full. By default, all members
have data access level None when they are added to the system.

Figure 10-10 Member Permissions dialog—Data tab

The figure shows a user with a data access level of None. To set the data permission level of a
user, move the slider to the appropriate level.

Software User Guide Eksigent Control Software

September 2012 137 of 152
User Manager

Table 10-2 outlines the privileges granted to each data access level.
Table 10-2 Run Manager Permissions for Each Access Level
Permission None Low Medium Medium Medium High Full
Low High
Open Data      
Toggle Auto-Print     
Save Data     
Toggle Auto-Save   
Apply E-Signatures  
Revoke E-
Signatures 

All controls for data access are found in the File menu in the Acquisition window. The electronic
signatures are applied in the Electronic Signatures dialog.
• Open Data: Enables the Open command in the File menu in the Acquisition dialog.
• Toggle Auto-Print: Enables the Auto-Print command in the File menu in the main
Acquisition window.
• Save Data: Enables the items Save As and Output Options in the File menu of the
Acquisition window.
• Toggle Auto-Save: Enables the Autosave command in the File menu of the
Acquisition dialog.
• Apply E-Signatures: Allows a user to apply electronic signatures in the Electronic
Signatures dialog.
• Revoke E-Signatures: Allows a user to revoke electronic signatures in the
Electronic Signatures dialog.
The Electronic Signature Role of the user can also be set in the Data tab. The E-Signature Role
menu is only enabled when the user has a Data level of Apply E-Signatures or Revoke E-
Signatures. By default, all users have the lowest level of E-Signature role when they are added to
the system. Select a role appropriate for the user by using the menu. For more information, refer
to Chapter 11.

Eksigent Control Software Software User Guide

138 of 152 September 2012
 User Manager

Diagnostics Tab
The Diagnostics tab of the Member Permissions dialog (Figure 10-11) is used to manage
permissions for the Hardware Diagnostics dialog. For more information, refer to Hardware
Diagnostics on page 28. Permissions are assigned by selecting the appropriate check box. By
default, all members have no permissions in the Hardware Diagnostics dialog when they are
added to the system.

Figure 10-11 Member Permissions dialog—Diagnostics tab

• Initialize Transducers: Enables the Re-Initialize Transducers check box.
• Leak Check: Enables the Check For Leaks/Blockage check box.
• Flow Stability Check: Enables the Check Flow Stability check box.
• Flow Meter Calibration: Enables the Calibrate Flowmeter button.
• Auto Tune: Enables the Auto Tune Controllers button and the Pump Time Response
slider.
• Reset Usage Statistics: Enables the CLR buttons in the Usage Information region.
• Optical Diagnostics: Enables the Optical Diagnostics tab.
To select or clear all permissions on this tab, click Check All or Uncheck All.

Software User Guide Eksigent Control Software

September 2012 139 of 152
User Manager

Other Tab
The Other tab of the Member Permissions dialog (Figure 10-12) contains the remaining
permissions. Permissions are assigned by selecting the appropriate check box. By default, no
permissions on the Other tab are granted when members are added to the system.

Figure 10-12 Member Permissions dialog—Other tab

The User Administration permission option assigns a non-system administrator the right to
access User Authentication and the User Manager dialog. Use this permission to assign
administrative privileges to a user for the software, but not administrative privileges for the
Windows operating system. A user with this right is able to control user membership and manage
user permissions. This option should be used carefully.
• Modify/Save Instrument Configuration: Enables the LC Device Settings and LC
Wait for Contact Closure commands on the Devices menu of the Run Manager
dialog.
• Modify/Save Instrument Methods: Enables the LC Methods button on the Run
Manager dialog.
• Modify/Save AutoSampler Configuration: Enables the Autosampler Type,
Autosampler Device Settings, and Skip Missing Vials options on the Devices menu
of the Run Manager.
• Modify/Save AutoSampler Methods: Enables the Autosampler Methods option on
the Run Manager dialog.
Click OK to confirm all permission changes for a user, or click Cancel to exit without saving
changes.

Eksigent Control Software Software User Guide

140 of 152 September 2012
Electronic Signatures
11
The Electronic Signatures dialog is used to view, apply, and revoke electronic signatures for data
files. There are several items included in any particular electronic signature, including the name
and signature role of the signer, the date and reason of the signature, any additional comments
about the signature that the user may have, and the revoke date if the signature is revoked.

Figure 11-1 Electronic Signatures dialog

View Data Files

1. In the Acquisition window, click System > Electronic Signatures.
2. To locate data files to view, use the Explorer region. When the folders are expanded,
only data files and other folders, if any, are shown.
3. To view the data files in any particular folder, click the folder in the Explorer region.
4. To sort data files, click the column heading of the parameter. The size of the columns
can be adjusted.
5. To view the signatures for any particular data file, click any data file with the pencil-
notepad icon in the Data Files region, and all the signatures for that file are shown in
the Signatures region. Signature items are shown with a paper-pencil icon. If the
icon has a red X marked through it, the signature has been revoked.

Software User Guide Eksigent Control Software

September 2012 141 of 152
Electronic Signatures

6. To view a signature in detail, select the signature in the Signatures region and then
click View. The signature is shown in a separate Signature dialog (Figure 11-2). This
is useful if a signature contains long comments.

Figure 11-2 Individual electronic Signature dialog

About Electronic Signatures

The Electronic Signatures dialog is composed of three regions: the Explorer region on the left,
the Data Files region on the top right, and the Signatures region on the bottom right. The size of
the regions and associated columns can be adjusted.

Explorer
When the folders are expanded, only data files and other folders, if any, are shown. If any data
files exist in a particular folder, the files are shown in the Data Files region. A data file with a blank
notepad icon indicates that the file contains no signatures, while a data file with a pencil-notepad
icon indicates that the file contains at least one signature.

Data Files
The Data Files region contains three columns: File Name, Creation Date, and Last Modified. The
File Name column contains the name of the data file, the Creation Date column contains the date
that the data file was created, and the Last Modified column contains the date that the data file
was last modified. Data files can be sorted in the Data Files region by any of these three
parameters.

Eksigent Control Software Software User Guide

142 of 152 September 2012
 Electronic Signatures

Signatures
The Signatures region contains six columns that are the parts of an electronic signature saved to
file.
• Signer is the Windows user name of the user signing the document.
• Date is the date when the document was signed.
• Role is the signature role of the user signing the document.
• Reason is the reason for the signature.
• Revoke Date is the date a signature was revoked.
• Comments where optional comments can be typed.
For signatures that are not revoked, the revoke date field indicates active instead of a date. The
signatures can be sorted in the Signatures region by any of these parameters. To do so, click on
the column heading of the parameter.

Sign Data Files

Only a system administrator or a user with the Apply E-Signatures right can apply electronic
signatures to a data file. For more information, refer to Chapter 10.
Users must log on and then establish the proper document signing rights before they can
proceed. Users are only asked to establish their credentials once within the one session of using
the Electronic Signatures dialog. If this dialog is exited and then typed, user credentials will have
to be established again.
1. In the Acquisition window, click System > Electronic Signatures.
2. Locate the required files.
3. Do one of the following:
• To sign one data file, select the file in the Data Files region and then click Add
Signature or double-click on the Data File.
• To select multiple files, drag the mouse across all required files, press Shift
and then select a range of files, or press Ctrl to select each file individually,
and then click Add Signature. The User Logon dialog opens. For more
information, refer to Figure 11-1.
4. Log on as a system administrator or a user with the Apply E-Signatures right.
If the user logged on successfully, the Sign Document dialog opens.

Software User Guide Eksigent Control Software

September 2012 143 of 152
Electronic Signatures

Figure 11-3 Sign Document dialog

5. In the Your Information region, verify that the Username and the Role are accurate.
For more information, refer to Manage Electronic Signature Roles on page 132.
A list of filenames that is shown in the You are signing these files field. This list
should include all the files that were selected to sign in the Data Files region of the
Electronic Signatures dialog.
When the signature is applied, all these documents are stamped with that signature.
The Signature Reason list contains a list of available signature reasons. Select a
reason before signing a document. The reasons are defined in Manage Electronic
Signature Reasons on page 133.
6. (Optional) Type any comments in the Optional Comments field.
7. To sign the document, click Sign. If a signature reason was not selected, the user is
prompted to select one. The Signature Reason list automatically expands.
If signing the document was successful, the Sign Document dialog closes and the
Electronic Signatures dialog opens. Click the signed data file to confirm that the
signature was applied. The applied signature is shown in the Signatures region.

Revoke Signatures on Data Files

Only a system administrator or a user with the Revoke E-Signatures right can revoke electronic
signatures to a data file.
1. In the Acquisition window, click System > Electronic Signatures.
2. Locate the required files.
3. To revoke an electronic signature, select the signature in the Signatures region, and
then click Revoke.

Eksigent Control Software Software User Guide

144 of 152 September 2012
 Electronic Signatures

If the user’s credentials have been established, then the user does not need to log
on. If the user’s credentials have not been established, then the logon prompt
(Figure 11-1) opens.
4. Type a valid user account that is either a system administrator or a user with the
Revoke E-Signatures right. If the user account is neither of these, the user cannot
revoke a signature.
When revoking signatures, remember that once a signature is revoked, it cannot be
activated. Signatures can only be revoked one at a time. There are no controls to
revoke multiple signatures simultaneously. Also users can only revoke their own
signatures. No user can revoke any other user signatures.

Software User Guide Eksigent Control Software

September 2012 145 of 152
Electronic Signatures

Eksigent Control Software Software User Guide

146 of 152 September 2012
Index

values, location 7
Calibration Disk button 12
A calibration functions 28
A/D channel, Appearance Settings 35 calibration table
Acquisition Window Quantitation tab 83
components 14 requirements for creating 124
overview 13 Calibration Values tab 29
acquisition, progress of 45 capacity factor, defined 86
Add Integration Event 16 Channel 1 log 27
adding users and groups 131 charts, generating 58
Advanced tab, Acquisition Window 32 Check For Leaks/Blockage 28
Alerts log 25 chromatograms
Amount Ratio 118 analyzing 40
Analysis methods defined 42 integration timed events 91
analysis module, overview 81 LC Method Editor 80
Analysis Settings Editor 54 overlaying 68
analyze peaks 53 Column Flow Rate Reference Method 24
ANDI files 19 column heaters 75
Appendable Peak Table Format 19 column pressure 14, 24, 33, 34
attributes, data 33 commands
Auto-Complete Command, Run Manager 48 Auto-Complete, Run Manager 48
Automatic background, turning on or off 22 configuring
automatic peak detection algorithm, described drivers 11
81 HPLC system 10
automatically purge 37 Plot window 53
autosampler methods system 10
defined 42 contour plot region 15
Run Table 44 Copy Plot Selection 62
Autosave correlation coefficient, described 122
File menu 17 creating
format 19 charts 58
using 17 LC methods 73
cubic spline fit, applying 24
B current mobile phase flow rates 14
Current Tray 41
Back Skim event 98
custom formula 58
Backward Horizontal Baseline 100
customize
C peak tables 16
calculation methods 86 D
calibration
data acquisition, LC Method Editor 79
curves, storage of 118
data files
curves, types 119
locating 141
described 118
revoking signatures 144
range 122
sample reports 56
terms 118

Software User Guide Eksigent Control Software

September 2012 147 of 152
Index

signing 143 Shoulder Detection 92

viewing signatures 141 Split Peak 105
data, setting attributes 33 Valley To Valley 95
detection threshold asymmetry, overview 92 events Manual Peak 106
detection threshold, overview 91 Explorer, electronic signatures 142
Detector Wavelength Range 79 Exponential Modified Gaussian (EMG) Calcu-
Device I/O tab, signal polarity 30 lation Method 89
devices Exponential skim 98
Run Manager 43, 71 Export Settings Button 30
Diagnostics tab 139 Extend Run Icon 15
Direct Control dialog box 38 External Standard Calculation, described 124
directory, location of software 8
drivers, configuring 11 F
Dual beam operation 80 File menu
Run Manager 42
E filter usage 29
editing Find Peaks 53
LC methods 73 fits, types of 121
Elapsed Time indicator 51 Flow Calibration tab 28
electronic signatures Flow Metering and Control region 28
defined 40 Flow Profile 78
reasons 130 Flow Stabilization Limits 32
roles 130 Flow Table tab 78
showing Electronic Signatures window 141 Flowmeter Calibration dialog box 28
system administrator rights 143 Flowrate field 23
Electronic Signatures window Flowrate reference option 23
components 142 Force Peak Start 104
use 141 Force Peak Stop 104
e-mail Force Result 106
notification options 33 Forward Horizontal Baseline 99
settings 33 Front Skim 96
enabling user authentication 129
events G
conflicting 108 Gaussian skim 98
Force Peak Start 104 General tab, member permissions 134
Force Peak Stop 104 German Pharmacopoeia (DAB) Calculation
Force Result 106 Method 88
Front Skim 96
incompatible events 108 H
LC methods 77 hardware configuration options, setting 30
Manual Baseline 98
Merge Peak 105 I
Minimum Area 94 ignore external triggers 24
Minimum Peak Height 93 incompatible events 108
Minimum Peak Width 93 Inject Ahead 44
Negative Peaks 94 Input A/D Range 32
Reference Peak 107 Insert New Table Entry 83
Reset Baseline 102 Instrument Configuration dialog box 10
Reset Baseline at Valley 103 Instrument Configuration window 30

Eksigent Control Software Software User Guide

148 of 152 September 2012
 Index

Integration Off 94
integration timed events, chromatograms 91 N
internal flowmeter pressures 14 Negative Peaks 94
Internal Standard Calculation, described 126 nonlinear fits 121
notification events 33
J notification frequency 33
Japanese Pharmacopoeia (JP) Calculation Notification Options 27
Method 89
O
L Options tab, peak identification 84
lamp, direct control 39 Other tab 140
LC Channel 45 Output D/A Range 32
LC methods Output Folder field 18
creating 73 output options 17
data acquisition 79 overlaid data, removing 60
defined 42 overlaying, chromatograms 68
editing 73 Ownership Tags 19
Mode 80
Run Manager 42 P
LC Wait for Contact Closure 43 Pause button 15
linear fit 121 PDF
log files 24 printing 20
Lowest Point Horizontal Baseline 101 report 20
peak asymmetry 87
M peak detection events, defined 91
Main Plot Region, modifying the plot scale 16 Peak Detection tab, overview 82
Make All Plots Identical 66 peak detection, disabling 94
Managing Electronic Signature Roles 132 peak identification
Managing User Permissions 134 described 113
Manual Baseline 98 Options tab 84
Manual Peak 106 peak integration events, defined 91
menus peak integration parameters, setting 40
File 42, 61 peak integration, disabling 94
Peak Viewer 61 peak label options 67
Run Manager 42 Peak Park Toolbox, overview 23
View menu 21, 62 Peak Preview
Merge Peak 105 File menu 61
Minimum Area 94 function 19
Minimum Peak Height 93 overview 19
Minimum Peak Width 93 Peak Preview function 19
mobile phases 37, 76 peak results
Mode, LC Method Editor 80 calculation methods 87
Monitor Folder 61 peak shapes, defined 87
monitoring peak trends 58 peak table
moving multiple cells 47 annotations 55
Multi-Level Calibration 120 customizing 16
multiple plots, showing 59 overview 53
Multiplication Factor 119 peak trends
generating 58

Software User Guide Eksigent Control Software

September 2012 149 of 152
Index

monitoring 58 Automated Calibration Table Generation

Peak Viewer utility 127
described 13, 53 described 13
menus 61 devices 43, 71
peak-park for a fixed duration 24 menus 42
peaks, monitoring peak trends 58 overview 41
PID region, Calibration Values tab 29 sample tray status 41
Plot window, configuring 53 Sequential option 52
plots Run Replicates 44
areas 59 Run Sequence 52
Plots menu 65 Run Table
printing editing 44
PDF 20 files 42
preview function 19 LC Channel 45
programmable events, LC Method Editor 77 navigation 46
Prompt to save 18
properties, Plots menu 66 S
pump power 15, 33 Sample Queue log 26
pumps, direct control 38 Sample report 56
sample status 41
Q scaling factors, described 123
quadratic fit 122 security, setting 129
quantitation selecting
automatic 128 multiple cells 47
defined 113 vials 50
Quantitation tab, overview 83 Seq. # 44
Queued Time indicator 51 Sequential option, Run Manager 52
Quick Launch icon 8 settings
data attributes 33
R email 33
reference acquisition 22 Shoulder Detection 92
Reference Peak 107 showing multiple plots 59
Reference/Background options 22 Signal Input Polarity 31
Re-Initialize Transducers 28 Signal Output Polarity 31
removing signatures, viewing 142
overlaid data 60 Single beam operation 80
Users and Groups 131 Single Level Calibration 119
Report Comments 64 Smoothing Toolbox 21
Report window 19 spectrometer
reports Detection region 74
HTML 20 Split Peak 105
PDF 20 Spotter Device Settings 44
Reset Baseline 102 Spotter Time 45
Reset Baseline at Valley 103 Spotter Time/Drop (ms) 45
Response Factor 118 statistics, generating 57
Response Ratio 119 status, sample 41
Run Conditions tab, overview 75 Stop button 15
Run Interval 44 Sync. with Gradient Start option 23
Run Manager Sync. with Injection start option 22

Eksigent Control Software Software User Guide

150 of 152 September 2012
 Index

System Configuration log 26 usage information 29

System menu 28 user
System Shut Down 30 authentication 39, 129
System tab 30 permission 39
user authentication 129
T User Authentication Window 130
Tangent skim 98 User Logon dialog box 130
Tile 59 User Manager overview 129
total flow rate 14, 24, 38 user permissions, managing 134
Total Flowmeter Usage 29 UV Detector Toolbox, overview 21
Total Sample Injections 29
Trend tab 58 V
Valley To Valley 95
U valve, direct control 39
United States Pharmacopoeia (USP) Calcula- vials, selecting 50
tion Method 88 View menu 21, 62
unknown chemical compounds, determining
83 W
usage counters, resetting 36 weighting factor, described 122

Software User Guide Eksigent Control Software

September 2012 151 of 152
Index

Eksigent Control Software Software User Guide

152 of 152 September 2012