Interfacing Guide

Interfacing Guide

Version 3.5
4 September, 2000

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Interfacing Guide

Interfacing Guide
The software described in this book is furnished under a license agreement and may
be used only in accordance with the terms of that agreement.

Copyright Notice

Micromass Ltd believes that the information in this publication is accurate. However
the information is subject to change without notice and should not be construed as a
contractual undertaking by Micromass Ltd. Despite the care which has been given to
the preparation of this publication, Micromass Ltd accepts no responsibility for any
loss or any other matter which may arise from any error or inaccuracy which may
inadvertently have been included.

Copyright (C) 1993-2000 Micromass Ltd. All Rights Reserved.

No part of this publication may be copied without the express written permission of
Micromass Ltd.

Trademarks

Micromass ® is a registered trade mark of Micromass Limited

(Reg. U.S. Pat. & Tm. Off.).

Windows is a trademark of Microsoft Corporation. Other product names mentioned

in this manual may be trademarks or registered trademarks of their respective
companies and are hereby acknowledged.

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Table of Contents
Importing 5
Copying Data 5
Import Worksheet 6
To Import a Worksheet 6
Creating Import Files 7
Access 97 7
Excel 8
Notepad 8
Import Data 8
To Import Data 8
Creating Import Files 9
Access 97 9
Excel 9
Notepad 9

Exporting 10
Export to LIMS File 10
Copying to and from the Windows NT Clipboard 13
Export SEQUEST file 15
OpenLynx Batch Files 16
Paragraphs 16
Batch Block 17
Plate Block 17
Sample Block 18
Fields 18
Comments 18
File Format 19
OpenLynx Browser 23
Sections 23
Fields 23
Comments 23
Tabulated Sections 24
Free Format Text Sections 24
File Section Descriptions 25
MetaboLynx Browser 34
Sections 34
Fields 34
Comments 34
Tabulated Sections 35
Free Format Text Sections 35
File Section Descriptions 36
ProteinLynx Browser 46
Sections 46
Fields 46
Tabulated Sections 46
File Section Descriptions 47
Bio-Rad File Descriptions 53

File Formats 56
Sample List 56
An Example Generic Sample List File 59

AutoLynx 60

Status.ini 62
File Format 63

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Index 69

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Conventions
The Interfacing Guide follows these typographic conventions

This Represents

bold Anything you must type exactly as it appears

italic Place holders for information you must provide. For example
if you are asked to type filename, you would type the actual
name for a file instead of the word shown in italic type.

ALL Directory names, filenames and acronyms.

CAPITALS

Keyboard Formats

Key combinations and key sequences appear in the following formats.

KEY1+KEY2 A plus sign (+) between key names means to press and hold
down the first key while you press the second key. For
example, "press ALT+ESC" means to press and hold down the
ALT key and press the ESC key. Then release both keys.

KEY1,KEY2 A comma sign (,) between key names means to press and
release the keys one after the other. For example, "press
ALT,F" means to press and release the ALT key and then press
the F key.

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About This Manual

This manual is designed to explain how data can be imported into and exported from
MassLynx for use in other applications. When you have read this manual you
should be able to -

• Import data from Excel, Access and Notepad.

• Export quantify data to LIMS systems.

• Read ProteinLynx, OpenLynx and MetaboLynx report files.

• Read Chromatogram and Spectrum text files.

This manual assumes that you have no previous knowledge of MassLynx. However
this manual does assume that you are familiar with using the Microsoft Windows
NT Graphical Environment and have the basic skills required to work with
Windows NT software.

If you have never used Microsoft Windows NT before we would suggest that you
spend a short time reading “Chapter 2 Learning the Basics” in the Microsoft
Windows NT Workstation Start Here guide supplied with your Windows NT
software.

This manual also assumes knowledge of Access, Excel, Notepad and LIMS systems.

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Importing
There are several ways of importing data into a Sample List:

• Copying and pasting data from text editors, Access and Excel.

• Import Worksheet.

• Import Data.

Copying Data
Data created in other Windows applications can be copied to the clipboard and
pasted into the Sample List editor.

1. Press the button or select New from the File menu. If the previous
Sample List has not been saved you will be prompted to save it. A Sample
List with one default row will be displayed.

2. Add rows and columns to the Sample List so that it matches the number of
rows and columns as the other Windows application. Note if this is not done
data may be lost.

3. Select the relevant area in the other Windows application and copy it.

4. In the Sample List editor, position the cursor on the cell at the top left corner
of the paste area and select Paste.

Notes:

If copying from a text editor e.g. Notepad fields must be tab delimited.

When copying from an Access database the last record is not pasted and will have to
be entered manually.

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Import Worksheet
Sample Lists can be created in a number of other packages and imported into
MassLynx. MassLynx V3.0 and V3.1 allowed OpenLynx batch files and
MassLynx V2.3 Sample List files to be imported. While these options are still
supported, there are now several other file types that have been added.

• ACCESS 97

• Tab and Comma delimited text files

• Excel 97 and Excel 5.0, 6.0 and 7.0 files

To Import a Worksheet

1. Choose Import Worksheet from the MassLynx File menu.

Figure 1 The Import Worksheet dialog

2. Locate the required file, or type in a file name, and press Open. Generic
Batch files created in OpenLynx are the default file types. Click on the
arrow, at the end of the Files of type box, to import a different file type.

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Creating Import Files

The following is a list of instructions on how to create files suitable for importing
into MassLynx.

For all types of file fields must have the same name as in the Sample List (see
Sample List on page 56) although they can be defined in any order. For Access 97
the data type must also match. The names correspond to the name in brackets on the
Customize Field Display dialog.

Access 97

When the table is created it must be called ANALYSIS.

It is recommended that the design view is used when creating a new table, this
allows you to define the data type of the field.

You must have the first column called Index as the primary key. Column headings
must match those shown on page 56. Other columns can be present but they will not
be imported into the Sample List.

n To define the data type as a double

1. Select Number from the drop down list box in the Data Type column.

2. On the general page, at the bottom left of the screen, click on Field Size and
select Double from the drop down list box.

n To save in access 97 format

The table can be saved as an access database by selecting Save from the File menu
and can be imported into MassLynx in this format. Tables can also be saved as tab
or comma delimited files for importing into MassLynx.

n To save in tab or comma delimited format

1. Select Save As/Export from the File menu, select the

To an External File or Database option and press OK.

2. Select the required directory from the browser displayed, select

Text files (*.txt;*.csv;*.tab;*.asc) from the Save as type drop down list box
and then press the Export button.

3. Make sure the Delimited option is selected and press the Next button.

4. Check the Include Field Names on First Row option, select the type of
delimiter to use and press the Next button.

5. Enter the name to save the file as and press the Finish button.

If files are saved as comma or tab delimited then they must be imported into
MassLynx as comma or tab delimited files.

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Excel

You must have the first column called Index, other column headings must match
those shown on page 56.

Select the area containing the data to be imported, including the column headings,
and name the area ANALYSIS. To do this select Define from the Name option on
the Insert menu, type ANALYSIS and press OK.

Leave all cells in General format

For a text field containing only numeric data an apostrophe ( ‘ ) must be inserted in
front of the number.

If the file is to be saved as tab or comma delimited then Excel will only allow one
sheet to be saved. If the current workbook contains more than one worksheet then
each worksheet must be saved as a separate text file.

Notepad

You must have the first column called Index, other column headings must match
those shown on page 56.

Type in the field name/value and then a comma (or press tab for tab delimited files)
and enter the next value. End each line with a carriage return.

Text fields should be enclosed in quotes.

Import Data
Sample List data can be created in a number of other packages and imported into
MassLynx. The file types supported are:

• ACCESS 97

• Tab and Comma delimited text files

• Excel 97 and Excel 5.0, 6.0 and 7.0 files

To Import Data

1. In MassLynx ensure that the correct number of rows and columns is displayed.
If this is not done then data will be lost.

2. Choose Import Data from the MassLynx File menu.

3. Locate the required file, or type in a file name, and press Open. Excel 5.0 files
are the default file types. Click on the arrow, at the end of the Files of type
box, to import a different file type.

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Creating Import Files

The following is a list of instructions on how to create files suitable for importing
into MassLynx.

For all types of file

• Fields must not have column headings.

• Fields must be in the same order as they are to appear in the MassLynx Sample
List

Access 97

When the table is created it must be called ANALYSIS.

For Access 97 the data type of the column must match.

It is recommended that the design view is used when creating a new table, this
allows you to define the data type of the field.

To define the data type as a double see Import Worksheet above.

To save in tab or comma delimited format follow the instructions for

Import Worksheet above, except for step 4 where the Include Field Names on First
Row option should not be checked.

If files are saved as comma or tab delimited then they must be imported into
MassLynx as comma or tab delimited files.

Excel

Select the area containing the data to be imported, including the column headings,
and name the area ANALYSIS. To do this select Define from the Name option on
the Insert menu, type ANALYSIS and press OK.

Leave all cells in General format

For a text field containing only numeric data an apostrophe ( ‘ ) must be inserted in
front of the number.

If the file is to be saved as tab or comma delimited then Excel will only allow one
sheet to be saved. If the current workbook contains more than one worksheet then
each worksheet must be saved as a separate text file.

Notepad

Type in the field name/value and then a comma (or press tab for tab delimited files)
and enter the next value. End each line with a carriage return.

Text fields should be enclosed in quotes.

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Exporting
There are several ways of exporting data from MassLynx:

• Export to LIMS.

• Copying Chromatogram and Spectrum peak lists.

• Export SEQUEST file.

• OpenLynx Batch files.

• OpenLynx Browser files.

• ProteinLynx Browser files.

Export to LIMS File

Quantification results can be written to a text file for use with LIMS systems. This
can be performed automatically by selecting the Export Results to LIMS option on
the Quantify Samples dialog. The results can also be exported from the Quantify
window. Select Export to LIMS File from the File menu, select a file from the
browser displayed or enter the name of a new one and press Save. If the selected
file already exists, the user will be prompted to overwrite the existing file.

The file generated will consist of three areas; the Header Section , the
Samples Section and the Calibration section.

The Header Section

The header section contains the following four sections. Each shows the full path
name of the file generated by or used to create the report and the date and time that
the file was last modified. All fields are text.

• LIMS EXPORT FILE The LIMS file generated

• SAMPLELIST The Sample List file.

• QUANMETHOD The quantification method file.

• QUANCALIBRATION The quantify curve file.

e.g. LIMS EXPORT FILE:

C:\Masslynx\lims1
Tue Nov 10 11:33:10 1998

Compound Section header fields

The compound section will include an entry for each sample in the current sample
list. The header will contain the File Name, Sample ID and any text entered in the
SPARE_1 to SPARE_5 fields in the sample list.

E.g. ASSAY01,ID,,,,,

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Samples Section

For each sample there will be one entry for each compound named in the compound
box in the quantify method. Each entry will have the following fields, separated by
a comma. The data type column shows what type of field the data was exported
from.

Field Description Data Type

The compound number shown in the compound box in the quantification method. int

The text name of this compound. char

The scan at which the matching peak was found in the current sample datafile. Int

The retention time of the matching peak. Float

The relative retention time at which the matching peak was found. Float

The area of the matching peak. Float

The height of the matching peak. Float

The response of the sample for this compound. Float

The flags associated with the peak. Text

The concentration of compound recorded for this sample. Float

The blank subtracted concentration of the compound for this sample. Float

The chromatogram trace used to locate peaks for this compound. Char

The error between the expected concentration and the calculated concentration. Float

The ordinal number of the compound in the quantification method that is used as the Int
reference peak for this compound.

The area of the reference peak used for this compound for this sample. Float

The height of the reference peak Float

The retention time of the reference peak. float

The modification date of the peak used to quantify this compound for this sample. Text
This refers manual modification of the peak.

The modification time of the peak. Text

The modification text (modification comment) of the peak. Text

The MassLynx user who altered the peak. Text

The mass of the peak. Float

The retention time the peak was expected at for this compound. Float

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Field Description Data Type

The relative retention time the peak was expected at for this compound. Float

The user factor associated with this compound. Float

The user RF factor associated with this compound. Float

The start retention time of the detected peak Float

The end retention time of the detected peak Float

The Calibration Section

The calibration section will have a subsection for each calibration curve calculated
for the current quantification calibration. Each subsection will contain information
as displayed on the calibration graphs window. Where a line entry is inappropriate
it will not be entered in the report file.

• Correlation coefficient: or Coefficient of Determination:

• Response Factor: or Calibration Curve:

• Response Type:

• Curve Type:, Origin:, and Weighting:

E.g.

Compound 1 name: I. Std

Response Factor: 846.154

Response type: External Std, Area
Curve type: RF

Compound 2 name: Parent

Coefficient of Determination: 1
Calibration curve: 0.568051 * x + 0.0010347
Response type: Internal Std ( Ref 1 ), Area * ( IS Conc. / IS Area )
Curve type: Linear, Origin: Exclude, Weighting: 1/x, Axis trans: None

Compound 3 name: Metabolite

Coefficient of Determination: 1
Calibration curve: 0.336996 * x + -0.00516146
Response type: Internal Std ( Ref 1 ), Area * ( IS Conc. / IS Area )
Curve type: Linear, Origin: Exclude, Weighting: 1/x, Axis trans: None

All fields are text. It is possible to parse the correlation coefficients out, but their
format will depend on how the quantify methods are set up, so this will have to be
done on a per application basis.

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Copying to and from the Windows NT Clipboard

The Windows NT Clipboard provides temporary storage for information that is
being transferred between application programs (word processors, spreadsheets,
MassLynx etc.). You can use the Clipboard to move data out of the Chromatogram
and Spectrum windows as a text list. This data can then be pasted into reports
written with a Windows compatible word processor.

n To copy a chromatogram as a text list to the Clipboard

1. Display the required time range in a chromatogram window.

2. Press the Toolbar button or choose Copy Chromatogram List from the
Chromatogram Edit menu. The section of the chromatogram on display will
be transferred to the Clipboard as (time, intensity) pairs or (scan, intensity)
pairs depending on the horizontal axis setting.

3. To read the information into another application, choose Paste from the other
application’s Edit menu.

Copying the Chromatogram list to the clipboard gives the following format.

Retention Time or Scan Number Intensity

Retention Time or Scan Number Intensity
Retention Time or Scan Number Intensity
Retention Time or Scan Number Intensity

The retention time or scan/intensity pairs are separated by a tab.

n To copy integrated chromatogram peaks as a text list to the Clipboard

1. Display the required time range in a chromatogram window

2. Press the Toolbar button or choose Copy Detected Peaks from the
Chromatogram Edit menu. The chromatogram peaks on display will be
transferred to the Clipboard. The information transferred for each peak is the
peak top, height, area, start, end, start height and end height.

3. To read the information into another application, choose Paste from the other
application’s Edit menu.

Copying the Chromatogram list to the clipboard gives the following format.

Retention Peak Peak Peak Peak Peak Peak

Time Height Area Start RT End RT Start End
Intensity Intensity
Retention Peak Peak Peak Peak Peak Peak
Time Height Area Start RT End RT Start End
Intensity Intensity

The fields are separated by a tab.

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n To copy a spectrum as a text list to the Clipboard

1. Display the required mass range in a Spectrum window.

2. Press the Toolbar button or choose Copy Spectrum List from the
Spectrum Edit menu. The section of the spectrum on display will be
transferred to the Clipboard as (mass, intensity) pairs.

3. To read the information into another application, choose Paste from the other
application’s Edit menu.

Copying the Spectrum list to the clipboard gives the following format.

Mass Intensity
Mass Intensity
Mass Intensity
Mass Intensity

The mass/intensity pairs are separated by a tab.

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Export SEQUEST file

MassLynx has a facility to convert files into a format which can be used by the
“SEQUEST” program. The “SEQUEST” program correlates uninterpreted tandem
mass spectra of peptides with amino acid sequences from protein and nucleotide
databases. It is written by Jimmy Eng and John Yates (University of Washington).
Further details can be obtained via the Internet at
http://thompson.mbt.washington.edu/sequest.

n To Export a SEQUEST file

1. Display the relevant centered MS/MS data file select Export SEQUEST file
from the File menu.

Figure 2 Export SEQUEST dialog

2. The Precursor ion mass is picked up from the data file, if it was entered in
the Function Editor, otherwise type in a value.

3. The Precursor charge state defaults to 2, change this as required.

4. Enter any known sequence information in the Partial sequence info box.

5. File Path and Destination is the location and filename that the file will be
saved to. The file name is the original file name with the scan and function
numbers appended to it. To change the destination press the Browse button
and select a new destination from the dialog displayed, or type a new one in.

6. Press the OK button.

Note: this option is only enabled if BioLynx is installed.

The file produced is an ASCII text file with the following format.

Precursor mass Charge

Mass Intensity
Mass Intensity
Mass Intensity
Mass Intensity

The mass/intensity pairs are separated by a space.

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OpenLynx Batch Files

OpenLynx Batch files ( *.olb) are produced when samples are submitted from the
OpenLynx Login program. When created they are stored in the
Masslynx\Openlynx\BatchDB folder. When they have been acquired and processed
they are moved to the Masslynx\Openlynx\BatchDB\Processed folder.

Paragraphs

The file will hold section blocks of data called paragraphs. A file will have a
“Batch” paragraph and at least one “Plate” paragraph, followed by a paragraph for
each sample to be analysed. Where there is more than one plate in an analysis, there
will be a paragraph for each plate followed by sample paragraphs for each sample.

A paragraph will always start with the name of the section surrounded by square
parentheses on a line by itself. i.e. [SectionName].

e.g. [SectionName1]
....Data Item 1...
....Data Item 2…
[SectionName2]
….Data Item 1…
….Data Item 2…

A typical multi-plate analysis file would be arranged as follows

[Batch]
….Data Item 1…
….Data Item 2…
[Plate:1]
....Data Item 1...
....Data Item 2…

[Sample:1.1]
....Data Item 1...
....Data Item 2…

[Sample:1.n]
....Data Item 1...
....Data Item 2…
[Plate:2]
....Data Item 1...
....Data Item 2…
[Sample:2.1]
....Data Item 1...
....Data Item 2…
[Sample:2.n]
....Data Item 1...
....Data Item 2…
[Plate:m]
....Data Item 1...
....Data Item 2…

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[Sample:m.1]
....Data Item 1...
....Data Item 2…
[Sample:m.n]
....Data Item 1...
....Data Item 2…

Batch Block

The first paragraph in the file will contain information that is pertinent to the whole
batch.

MSMethod
MSTune
LCMethod
EconomyScheduling
PriorityScheduling
AnalysisTime
ProcessParameters
Process
UserName
BatchID
UserAddress
SampleReportEnable
NumberOfPlates

Plate Block

A file will contain a plate block for each plate which will contain information that is
pertinent to the whole plate rather than a specific well. Within this plate block will
be information concerning the plate description, plate ID and wells used. Where
samples are not being presented in a plate this block can be used to describe the
batch of samples loaded into an autosampler carousel.

JobCode
UserName
Rows
Columns
Track
NumberOfWells

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Sample Block

For each sample to be analysed there will be a sample block that contains well
position, and other information, specific to a certain sample.

Well
SampleDescription
Conditions
SampleID
MSDataName
SampleType
MSInjectionVolume
NumberOfMasses
Mass1
NumberOfFractions
NumberOfWaveLengths
NumberOfConcs
NumberOfFormulae
NumberOfFactors
NumberOfUserFields

Fields

Sections will have a group of fields, each field will be on one line. The field name
will be the first item on the line, followed by “=” and then the data item for that
field. The type of data will depend on the field type.

i.e. [SectionName]
FieldName1=Data1
FieldName2=Data2
...

e.g. [Plate:3]
JobCode=JB123456
NumberOfWells=96

Comments

A comment line is denoted by the first character being a semi-colon. A comment

line can be any where in a section. Multiple line comments must have a semi-colon
preceding each line.

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File Format

[Batch]

When creating files manually the fields marked an (M) must be defined, all other
fields are optional.

Field/Section Name Data Description

Type

NumberOfPlates (M) Integer Number of plates in analysis.

LabName Text Laboratory name.

MSMethod Text The name of the MS method to be used.

MSTune Text The name of the MS Tune file to be used. If not specified the
current instrument tuning parameters will be used.

LCMethod Text The name of the acquisition Inlet method to be used.

InletPreRunMethod Text The name of the acquisition Inlet prerun method to be used. If
not specified no prerun is performed.

InletPostRunMethod Text The name of the acquisition Inlet postrun method to be used. If
not specified no postrun is performed.

InletSwitchMethod Text The name of the acquisition Inlet column switch method to be
used. If not specified no switch method is performed.

Process Text Path of External Program to be executed for sample processing.

Directory is not necessary if file exists in current directory.

ProcessParameters Text Path of Parameter File to be used by External Program.

EconomyScheduling Integer None zero if batch is to be run as a Night-Time task. Otherwise

will be scheduled normally.

PriorityScheduling Integer None zero if batch is to be run as a Priority task. Otherwise will
be scheduled normally.

AnalysisTime Float Time of analysis for each sample in the batch. Equals zero if no
time is specified.

BatchID Text Name of batch.

UserName Text Name of user submitting batch.

UserAddress Text E-mail address to send batch results to.

ReportScheme Text Name of the OpenLynx Browser report scheme to use when
formatting output results.

SampleReportEnable Boolean Indicates if per sample printing is required. 0 = False, 1 = True

HPLCMethod Text Path of HPLC method parameter override file if one exists.

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[Plate:N]

Where N = Plate Number

Field/Section Data Type Description

Name

PlateID Text Plate Identifier. A text description of the plate can be defined in
files created externally. This is not generated in files created
from the OpenLynx Login program.

PlatePosition Text The description of the plate position, as co-ordinates for plate
position in the autosampler bed.

1. X,Y.

2. Not used for a linear autosampler e.g. HP GC type.

Where X and Y are integers.

Origin Text The description of the start well position, as a pair of

co-ordinates for well position in plate, or an absolute position

WellAwellX(or wellXwellA ) e.g. A1

Where X is an integer and A is an alphabetical character.

Or

TL=Top Left, TR=Top Right, BL=Bottom Left, BR=Bottom

Right

JobCode Text Job or Batch Identifier.

UserName Text Name of operator performing analysis.

Rows (M) Integer Number of rows on plate

Columns (M) Integer Number of columns on plate

Track (M) Text R=Rows, C=Columns, RS=Rows Snake, CS=Columns Snake

NumberOfWells Integer Number of wells used in plate or vials in an autosampler tray

(M)

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[Sample:N:M]

Where N = Plate Number, M = Well Number

Field/Section Name Data Description

Type

Well (M) Text The description of the well position, as co-ordinates for well
position in plate, or an absolute position. There are two formats
for a Well. This field can be used to identify a vial position in a
non XY autosampler.

1. wellAwellY (or wellYwellA ) e.g. B6, 6B or 2,6.

2. Absolute rack position. e.g. 18

Where X and Y are integers and A is an alphabetical character.

SampleType Integer Sample type

0 = Unknown, 1 = Standard, 2 = QC and 3 = Blank.

NumberOfMasses Integer The number of masses defined.

Mass1 Float 1st mass to be used for targeting. This could be the mono-
isotopic mass or the mass with the greatest intensity, derived
from the formula’s isotope cluster. If the analysis being
performed by the MS requires an expected molecular weight
then this field is Mandatory unless a formula is supplied.

Mass2 Float 2nd Mass.

MassN Float Nth Mass.

NumberOfFraction Integer The number of fractions defined. Only one fraction mass is
Triggers currently supported by MassLynx.

Fraction1 Float 1St Mass to be monitored by Fraction Collection system.

Fraction2 Float Second Fraction Mass. Not currently used.

FractionN Float Nth Fraction Mass

NumberOfFormulae Integer The number of formulae defined.

Formula1 Text The 1st chemical composition, if used.

Formula2 Text The 2nd chemical composition

FormulaN Text The Nth chemical composition

NumberOfWavelengths Integer The number of wavelengths defined.

Wavelength1 Text The 1st wavelength, if used.

Wavelength2 Text The 2nd wavelength

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Field/Section Name Data Description

Type

WavelengthN Text The Nth wavelength

NumberOfConcs Integer The number of concentrations defined.

Conc1 Text The 1st concentration, if used.

Conc2 Text The 2nd concentration

ConcN Text The Nth concentration

NumberOfFactors Integer The number of user factors defined.

Factor1 Float 1St User Factor if required. MassLynx currently only supports 1
User Factor.

Factor2 Float The 2nd User Factor. Not currently used.

FactorN Float Nth User Factor. Not currently used.

SampleID Text Sample Identifier

SampleDescription Text Sample Description

Conditions Test Sample conditions

MSDataName Text The name of the MS data file to be processed and/or created.

MSInjectionVolume Float The amount of sample to inject, for an MS analysis.

NumberOfUserFields Integer The number of user fields defined.

User1 Text 1St User Field, if required.

User2 Text The 2nd User Field.

UserN Text Nth User Field.

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OpenLynx Browser
Sections

The file will hold section blocks of data. The start of a section block will always
start with the name of the section surrounded by square parentheses on a line by
itself. i.e. [SectionName].

The main body of the data will be enclosed by a pair of braces, the opening and
closing braces will be the only characters on their respective lines.

i.e. [SectionName]
{
....Data...
}

Section blocks can have section blocks embedded in them, in some cases multiple
instances of sections with the same name can be allowed, depending on the type of
data.

e.g. [SectionName1]
{
....Data...
[SectionName2]
{
....Data...
}
}

Fields

Sections will have a group of fields, each field will be on one line. The field name
will be the first item on the line, followed by a list of TAB separated data items for
that field. The type of data will depend on the field type.

i.e. [SectionName]
{
FieldName1 Data1
FieldName2 Data2_1Data2_2
...
}

Comments

A comment line is denoted by the first character being a semi-colon. A comment

line can be any where in a section. Multiple line comments have a semi-colon
preceding each line.

Page 23
Interfacing Guide

Tabulated Sections

Some sections can be considered to be a table, or list, of fields of the same type.
Tabulated sections do not have any field names to describe the data but will
normally have a comment line describing the names of the fields.

e.g. [TableSection]
{
;Field1 Field2
Data1_1Data1_2
Data2_1Data2_2
...
}

Free Format Text Sections

The information in these sections contains free format text which may stretch over
several lines. A line will be terminated with a <carriage return><linefeed> pair.

Page 24
 Interfacing Guide

File Section Descriptions

SAMPLE

Field/Section Name Data Type Description

Sample Integer The number of the sample in the batch.

Well Text The description of the well position, as a pair of co-ordinates for
plate position in rack and well position in plate, or an absolute
position. There are three formats for Well.

1. plateX,plateY:wellX,wellY

2. plateX,plateY:wellAwell1 (or well1wellA )

3. Absolute rack position.

Where X and Y are integers and A is an alphabetical character.

FileName Text The MassLynx NT MS data file name.

SampleType Integer Sample type: Unknown = 0, Standard = 1, QC = 2 or Blank = 3.

SampleID Text MassLynx Sample List input field.

SampleDescription Text MassLynx Sample List input field.

Date Text Date that MS data file was acquired.

Time Text Time that MS data file was acquired.

JobCode Text MassLynx Sample List input field.

TaskCode Text MassLynx Sample List input field.

UserName Text Current MassLynx user name.

LabName Text Laboratory name.

Instrument Text Instrument name.

Conditions Text MassLynx Sample List input field.

Submitter Text MassLynx Sample List input field.

Plate Text Description of micro-titre plate, if applicable. See below for

detailed description.

INLET Section Description of compound for testing.

PARAMETERS

COMPOUND Section Description of compound for testing.

FRACTION Section Results of any FractionLynx fraction collection.

FUNCTION Section MS function data and test results. There will be one
FUNCTION section per MassLynx MS and DAD data
functions.

ANALOG Section Analogue chromatographic data.

Page 25
Interfacing Guide

PLATE FIELD

For samples acquired using a Gilson or Waters 2700 autosampler the following
information will be written to the file, otherwise this field will be blank.

Version Number ( two digits )

Origin Location ( TL - top left, TR - top right, BL - bottom left, BR - bottom right )

Priority ( XY - x coordinate before y coordinate, YX - y coordinate before

x coordinate )

Reference scheme ( LN - letter number, NL - number letter, NN - number number,

LL - letter letter, SC - sequential continuous, SD sequential discontinuous )

1:Number Of Rows
2:Number Of Columns
3:Row Spacing
4:Column Spacing
5:Row Offset
6:Column Offset
7:Which Rows Offset ( O or E )
8:Which Columns Offset ( O or E )
9:Plate Width
10:Plate Height
11:Vial/Well Depth
12:Vial/Well Diameter
13:Vial One X
14:Vial One Y

Note that all spacings, etc are given to 0.1 of a mm.

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 Interfacing Guide

e.g.

01,TL,XY,LN,1:8,2:12,3:120.0,4:120.0,5:0.0,6:0.0,7:O,8:O,9:1250.0,10:870.0,11:4
00.0,12:90.0,13:80.0,14:130.0

Which means:

Version = 01.
Origin Location = top left.
Priority = x coordinate before y coordinate.
Reference scheme = Letter Number.
1:Number Of Rows = 8.
2:Number Of Columns = 12.
3:Row Spacing = 12mm.
4:Column Spacing = 12mm.
5:Row Offset = 0.0mm.
6:Column Offset = 0.0mm.
7:Which Rows Offset ( O or E ) = Odd numbers, but because Row Offset = 0, this
has no effect .
8:Which Columns Offset ( O or E ) = Odd numbers, but because Column Offset = 0,
this has no effect.
9:Plate Width = 125mm.
10:Plate Height = 87mm.
11:Vial/Well Depth = 40mm.
12:Vial/Well Diameter = 9mm.
13:Vial One X = 8.0mm.
14:Vial One Y = 13.0mm.

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Interfacing Guide

COMPOUND

Field Name Data Type Description

Mono Mass Float The mass used for targeting. This could be the mono-isotopic
mass or the mass with the greatest intensity, derived from the
formula’s isotope cluster.

Formula Text The chemical composition, if entered.

Name Text The name of the compound. Unused at present.

FRACTION

Field Name Data Type Description

Mass Float The mass collected.

Org. Target Float The original mass minus any adducts.

Ion Mode Text The ionisation mode used to collect the fraction.

Start Time Float The time at which the fraction collection started.

End Time Float The time at which the fraction collection ended.

Start Site Text The name of the site at which the fraction collection started.

No. Of Tubes Integer The number of tubes the fraction was collected in.

INLET PARAMETERS

This is a free format text section.

FUNCTION

Field/Section Name Data Type Description

Function Integer The MassLynx MS data function number.

IonMode Text The type of ionisation mode e.g. AP+.

Type Text The type of MS scan function e.g. MS for full scan.

Description Text A brief description of the MS scan function.

SPECTRUM Section MS data and results of testing. There can be more than
one SPECTRUM section in a function.

CHROMATOGRAM Section Chromatographic data. There can be more than one

CHROMATOGRAM section in a function.

Page 28
 Interfacing Guide

SPECTRUM

Field/Section Data Type Description

Name

ProcDesc Text Description of processing performed on spectrum. E.g. Combine

(54:56-(38:39+74:75))

Process Integer The number of the MassLynx saved mass spectrum. Only present
if the processed spectrum was saved with data file.

State Text The result of testing the quality of the mass spectral data.

Peak ID Integer Spectrum Peak Identification number.

Peak Ref Integer Peak Reference Number.

Time Float The retention time of the mass spectrum.

TIC Float Total Ion Current, the sum of all the peak intensities in the
spectrum.

BPI Float The intensity of the base peak in the mass spectrum.

BPM Float The mass of the base peak in the mass spectrum.

Continuum Text TRUE if the spectrum is stored in continuum format. Otherwise

FALSE.

Saved Text TRUE if the processed spectrum was saved with the data file.
Otherwise FALSE.

MASSES Section Section describing the results of testing, and finding significant
masses. This includes all adducts.

RESULTS Section Section describing the results of the targeting of the expected
compound. Masses from the same compound are combined into
one item.

MS Section Section that holds all the mass/intensity pairs, for this mass
spectrum.

SEARCH Section Section holding the results of a library search on this spectrum.
This section will not be created if no search exists.

Page 29
Interfacing Guide

MASSES

Field Name Data Type Description

Mass Float The input mass.

Exp. Mass Float The expected mass due to adduction.

Obs. Mass Float The mass that was actually observed.

% BPI Float The intensity of the mass peak as a percentage of the base peak
intensity.

Int. Abs Float The absolute intensity of the MS peak.

RESULTS

Field Name Data Type Description

Mass Float The input mass.

Found Boolean 1 if any of the possible adduct ions have been found for this
compound, otherwise 0

% BPI Float The sum of the percentage intensities for the compound.

% Purity Float A measure of the contribution of this compound to the spectrum as

percentage of the TIC. This includes all MS peaks associated with
this compound.

Confirmed Boolean False if any of the confirmation tests made failed. If not specified
regarded as being True.

Status Text Description of confirmation failure. Not present if confirmed =

TRUE

MS

Field Name Data Type Description

Mass Float Observed mass of peak.

% BPI Float Intensity of peak as a percentage of the base peak.

Page 30
 Interfacing Guide

ELEMENTAL

Contains results of elemental calculations if defined, otherwise this section does not
appear.

Field Name Data Type Description

Mass Float Actual observed mass for which elemental composition was
searched.

Calc. Mass Float Calculated mass of reported formula

mDa Float Difference between observed mass and calculated mass in

milli-daltons

PPM Float Difference between observed mass and calculated mass in parts per
million

DBE Float Double Bond Equivalence.

Formula Text Representation of calculated chemical formula. E.g. C19 H14 O2

SEARCH

Contains Spectrum library search results if library search was defined, otherwise this
section does not appear.

Field Name Data Type Description

Library Text Name of library in which the search was made.

HIT Section Contains information about a library hit. There can be several or no
hits for each search

HIT

Field Name Data Type Description

Entry Integer Library entry number hit was made against.

For Integer Forward search match value. Value between 0 and 1000.

Rev Integer Reverse search match value. Value between 0 and 1000.

Name Text Library entry name

F1 Float Library entry general purpose filter 1 value.

F2 Float Library entry general purpose filter 2 value.

Mass Float Library entry mass value.

Page 31
Interfacing Guide

CHROMATOGRAM

Field/Section Data Type Description

Name

TraceNumber Integer Number of chromatogram trace.

Description Text The description of the chromatogram type.

ProcDesc Text Description of processing performed on chromatogram. E.g.

Smooth (Mn, 2x2)

MaxIntensity Float The absolute intensity of the point with maximum intensity in the
chromatographic data.

TRACE Section A section that holds the chromatographic data.

PEAK Section Section(s) that hold information about peak(s) detected in the
chromatogram.

TRACE

Field Name Data Type Description

Time Float The time of the chromatographic point.

Int. %Max Float Intensity of the chromatographic point as a percentage of the

maximum intensity.

Page 32
 Interfacing Guide

PEAK

Field Name Data Type Description

Peak ID Integer Peak Identification number.

Peak Ref Integer Peak Reference Number.

Time Float Peak retention time in decimal minutes.

Peak Float + Float Peak start and end retention times in decimal minutes. Two floats
separated by a TAB character.

Intensity Float + Float Peak baseline start and end intensity. Two floats separated by a
TAB character.

Height Float Detected peak height.

AreaAbs Float Detected peak area.

Area %BP Float Detected peak area as percentage of the largest peak in the
chromatogram.

Area %Total Float Detected peak area as percentage of the sum of all the peak areas in
the chromatogram.

Width Float Peak width in decimal minutes.

RT Index Float Retention time index for peak. Field only output if RT Index has
been calculated.

RT LogP Float Retention time LogP for peak. Field only output if RT LogP has
been calculated.

Calc Conc Float Calculated concentration for peak. Field only output if calculated.

Calc Amount Float Calculated amount for peak. Field only output if calculated.

ANALOG

Field/Section Data Type Description

Name

Number Integer The number of the MassLynx analog channel.

Description Text The description of the analog data source.

MaxIntensity Float The absolute intensity of the point with maximum intensity in the
analog channel data.

TRACE Section A section that holds the chromatographic data. See description
above.

PEAK Section Section(s) that hold information about peak(s) detected in the
chromatogram. See description above.

Page 33
Interfacing Guide

MetaboLynx Browser
Sections

The file will hold section blocks of data. The start of a section block will always
start with the name of the section surrounded by square parentheses on a line by
itself. i.e. [SectionName].

The main body of the data will be enclosed by a pair of braces, the opening and
closing braces will be the only characters on their respective lines.

i.e. [SectionName]
{
....Data...
}

Section blocks can have section blocks embedded in them, in some cases multiple
instances of sections with the same name can be allowed, depending on the type of
data.

e.g. [SectionName1]
{
....Data...
[SectionName2]
{
....Data...
}
}

Fields

Sections will have a group of fields, each field will be on one line. The field name
will be the first item on the line, followed by a list of TAB separated data items for
that field. The type of data will depend on the field type.

i.e. [SectionName]
{
FieldName1 Data1
FieldName2 Data2_1Data2_2
...
}

Comments

A comment line is denoted by the first character being a semi-colon. A comment

line can be any where in a section. Multiple line comments have a semi-colon
preceding each line.

Page 34
 Interfacing Guide

Tabulated Sections

Some sections can be considered to be a table, or list, of fields of the same type.
Tabulated sections do not have any field names to describe the data but will
normally have a comment line describing the names of the fields.

e.g. [TableSection]
{
;Field1 Field2
Data1_1Data1_2
Data2_1Data2_2
...
}

Free Format Text Sections

The information in these sections contains free format text which may stretch over
several lines. A line will be terminated with a <carriage return><linefeed> pair.

Page 35
Interfacing Guide

File Section Descriptions

SAMPLE

Field/Section Name Data Description

Type

Sample Integer The number of the sample in the batch.

ProcessParameters Text MassLynx Sample List input field. Name of the MEP file used to
process the data.

InjectionVolume Float MassLynx Sample List input field. Volume of sample injected, in
micro-litres.

InletFileName Text MassLynx Sample List input field. Name of the Inlet Parameters
file used to acquire the data.

MSMethodFileName Text MassLynx Sample List input field. Name of the Method File used
to acquire the data.

MSTuneFileName Text MassLynx Sample List input field. Name of the Instrument Tune
File used for the data acquisition.

Well Text The description of the well position, as a pair of co-ordinates for
plate position in rack and well position in plate, or an absolute
position. There are three formats for Well.

1. plateX,plateY:wellX,wellY

2. plateX,plateY:wellAwell1 (or well1wellA )

3. Absolute rack position.

Where X and Y are integers and A is an alphabetical character.

FileName Text The MassLynx NT MS data file name.

SampleType Text QC = Control Sample, Analyte = metabolised sample.

SampleID Text MassLynx Sample List input field.

SampleDescription Text MassLynx Sample List input field.

Date Text Date that MS data file was acquired.

Time Text Time that MS data file was acquired.

JobCode Text MassLynx Sample List input field.

TaskCode Text MassLynx Sample List input field.

UserName Text Current MassLynx user name.

LabName Text Laboratory name.

Page 36
 Interfacing Guide

Field/Section Name Data Description

Type

Instrument Text Instrument name.

Conditions Text MassLynx Sample List input field.

Submitter Text MassLynx Sample List input field.

Plate Text Description of micro-titre plate, if applicable. See below for

detailed description.

COMPOUND Section Description of parent drug(s); the masses taken from the
MassLynx Sample List.

FUNCTION Section MS function data and test results. There will be one FUNCTION
section per MassLynx MS and DAD data functions.

ANALOG Section Analogue chromatographic data.

EXPECTED Section Description of metabolites searched for.

METABOLITES

UNEXPECTED Section Description of potential metabolites found as a result of

METABOLITES comparing the sample with a control.

PLATE FIELD

For samples acquired using a Gilson or Waters 2700 autosampler the following
information will be written to the file, otherwise this field will be blank.

Version Number ( two digits )

Origin Location ( TL - top left, TR - top right, BL - bottom left, BR - bottom right )

Priority ( XY - x coordinate before y coordinate, YX - y coordinate before

x coordinate )

Reference scheme ( LN - letter number, NL - number letter, NN - number number,

LL - letter letter, SC - sequential continuous, SD sequential discontinuous )

1:Number Of Rows
2:Number Of Columns
3:Row Spacing
4:Column Spacing
5:Row Offset
6:Column Offset
7:Which Rows Offset ( O or E )
8:Which Columns Offset ( O or E )
9:Plate Width
10:Plate Height

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Interfacing Guide

11:Vial/Well Depth
12:Vial/Well Diameter
13:Vial One X
14:Vial One Y

Note that all spacings, etc are given to 0.1 of a mm.

e.g.

01,TL,XY,LN,1:8,2:12,3:120.0,4:120.0,5:0.0,6:0.0,7:O,8:O,9:1250.0,10:870.0,11:4
00.0,12:90.0,13:80.0,14:130.0

Which means:

Version = 01.
Origin Location = top left.
Priority = x coordinate before y coordinate.
Reference scheme = Letter Number.
1:Number Of Rows = 8.
2:Number Of Columns = 12.
3:Row Spacing = 12mm.
4:Column Spacing = 12mm.
5:Row Offset = 0.0mm.
6:Column Offset = 0.0mm.
7:Which Rows Offset ( O or E ) = Odd numbers, but because Row Offset = 0, this
has no effect .
8:Which Columns Offset ( O or E ) = Odd numbers, but because Column Offset = 0,
this has no effect.
9:Plate Width = 125mm.
10:Plate Height = 87mm.
11:Vial/Well Depth = 40mm.
12:Vial/Well Diameter = 9mm.
13:Vial One X = 8.0mm.
14:Vial One Y = 13.0mm.

Page 38
 Interfacing Guide

COMPOUND

Field Name Data Type Description

Mono Mass Float The parent drug used for targeting. This could be the
monoisotopic mass or the mass with the greatest intensity,
derived from the formula’s isotope cluster.

Formula Text The chemical composition, if entered.

FUNCTION

Field/Section Name Data Type Description

Function Integer The MassLynx MS data function number.

IonMode Text The type of ionisation mode e.g. AP+.

Type Text The type of MS scan function e.g. MS for full scan.

Description Text A brief description of the MS scan function.

ScanCycleTime Float The scan cycle time in seconds i.e. the scan duration + the
inter-scan delay time.

InterScanDelay Float The inter-scan delay in seconds.

SPECTRUM Section MS data and results of testing. There can be more than
one SPECTRUM section in a function.

CHROMATOGRAM Section Chromatographic data. There can be more than one

CHROMATOGRAM section in a function.

Page 39
Interfacing Guide

SPECTRUM

Field/Section Data Type Description

Name

ProcDesc Text Description of processing performed on spectrum. E.g. Combine

(54:56-(38:39+74:75))

Process Integer The number of the MassLynx saved mass spectrum. Only present
if the processed spectrum was saved with data file.

State Text The result of testing the quality of the mass spectral data.

Peak ID Integer Spectrum Peak Identification number.

Peak Ref Integer Peak Reference Number.

Peak Cluster ID Integer If this peak is considered to be the same as another peak (according
to Setup parameter Min Peak Separation) then this is the number of
the cluster containing this and all other similar peaks. A value of –1
indicates that this peak is considered separate from all others.

Control Peak ID Integer If the sample is an analyte and this spectrum matches one in the
control, then the Peak ID of the control spectrum is written to this
field. Only present if this spectrum has a matching control
spectrum.

Time Float The retention time of the mass spectrum.

TIC Float Total Ion Current, the sum of all the peak intensities in the
spectrum.

BPI Float The intensity of the base peak in the mass spectrum.

BPM Float The mass of the base peak in the mass spectrum.

Continuum Text TRUE if the spectrum is stored in continuum format. Otherwise

FALSE.

Saved Text TRUE if the processed spectrum was saved with the data file.
Otherwise FALSE.

MASSES Section Section describing the results of testing, and finding significant
masses. This includes all adducts.

RESULTS Section Section describing the results of the targeting of the expected
compound. Masses from the same compound are combined into
one item.

MS Section Section that holds all the mass/intensity pairs, for this mass
spectrum.

Page 40
 Interfacing Guide

MASSES

Field Name Data Type Description

Mass Float The input mass.

Exp. Mass Float The expected mass due to adduction.

Obs. Mass Float The mass that was actually observed.

% BPI Float The intensity of the mass peak as a percentage of the base peak
intensity.

Int. Abs Float The absolute intensity of the MS peak.

RESULTS

Field Name Data Type Description

Mass Float The input mass.

Found Boolean 1 if any of the possible adduct ions have been found for this
compound, otherwise 0.

% BPI Float The sum of the percentage intensities for the compound.

% Purity Float A measure of the contribution of this compound to the spectrum as

percentage of the TIC. This includes all MS peaks associated with
this compound.

Confirmed Boolean False if any of the confirmation tests made failed. If not specified
regarded as being True.

Status Text Description of confirmation failure. Not present if confirmed =

TRUE

MS

Field Name Data Type Description

Mass Float Observed mass of peak.

% BPI Float Intensity of peak as a percentage of the base peak.

Page 41
Interfacing Guide

ELEMENTAL

Contains results of elemental calculations if defined, otherwise this section does not
appear.

Field Name Data Type Description

Mass Float Actual observed mass for which elemental composition was
searched.

Calc. Mass Float Calculated mass of reported formula

Mda Float Difference between observed mass and calculated mass in

milli-daltons

PPM Float Difference between observed mass and calculated mass in parts per
million

DBE Float Double Bond Equivalence.

Formula Text Representation of calculated chemical formula. E.g. C19 H14 O2

CHROMATOGRAM

Field/Section Data Type Description

Name

TraceNumber Integer Number of chromatogram trace.

Description Text The description of the chromatogram type.

ProcDesc Text Description of processing performed on chromatogram. E.g.

Smooth (Mn, 2x2)

MaxIntensity Float The absolute intensity of the point with maximum intensity in the
chromatographic data.

TraceNumberIn Integer The number of the chromatogram trace relative to the start of the
Function function.

TRACE Section A section that holds the chromatographic data.

PEAK Section Section(s) that hold information about peak(s) detected in the
chromatogram.

Page 42
 Interfacing Guide

TRACE

Field Name Data Type Description

Time Float The time of the chromatographic point.

Int. %Max Float Intensity of the chromatographic point as a percentage of the

maximum intensity.

PEAK

Field Name Data Type Description

Peak ID Integer Peak Identification number.

Peak Ref Integer Peak Reference Number.

Peak Cluster ID Integer If this peak is considered to be the same as another peak (according
to Setup parameter Min Peak Separation) then this is the number of
the cluster containing this and all other similar peaks. A value of –1
indicates that this peak is considered separate from all others.

Time Float Peak retention time in decimal minutes.

Peak Float + Float Peak start and end retention times in decimal minutes. Two floats
separated by a TAB character.

Intensity Float + Float Peak baseline start and end intensity. Two floats separated by a
TAB character.

Height Float Detected peak height.

AreaAbs Float Detected peak area.

Area %BP Float The peak area as a percentage of the largest peak in the sample in
which a metabolite was detected. If no metabolite found = 0.

Area %Total Float The peak area as a percentage of the total area of all peaks in the
sample in which a metabolite was detected. If no metabolite found
= 0.

Width Float Peak width in decimal minutes.

Page 43
Interfacing Guide

ANALOG

Field/Section Data Type Description

Name

Number Integer The number of the MassLynx analog channel.

Description Text The description of the analog data source.

MaxIntensity Float The absolute intensity of the point with maximum intensity in the
analog channel data.

TRACE Section A section that holds the chromatographic data. See above.

PEAK Section Section(s) that hold information about peak(s) detected in the
chromatogram. See above.

EXPECTED METABOLITES

This is a tabulated section.

Field Name Data Type Description

Compound Float The number of the compound that this metabolite is associated with,
starting from zero.

Precursor Float Mass to be searched for, the sum of the compound and metabolite.

Metabolite Float Mass of the metabolite, as specified on the MetaboLynx Setup

Metabolites page. It is the mass difference between the Compound
Mass and the Precursor.

Found Boolean 1 indicates mass was found, 0 not found.

Formula Text The formula of the metabolite if known. Absolute formula if the
parent mass was specified as a formula (e.g. C18H24O2) or relative
formula if parent mass was specified as a mass (e.g. +CO2). If the
metabolite is not recognised the formula is 0.

ChroTrace Integer list This field is a comma-separated list of chromatogram traces searched
when looking for this mass; the trace numbers start from 1.

Peak Text list If the mass was found, this field is a comma-separated list of
chromatogram peak numbers in which the mass was found. Each
peak is identified by a string of text containing four forward slash
separated numbers in the following format:

peak-number/function-number/trace-number/mass-found

where the first 3 numbers are integers, the fourth a float.

If the mass was not found, this field is 0.

MetName Text Descriptive name of the metabolite

Page 44
 Interfacing Guide

UNEXPECTED METABOLITES

This is a tabulated section.

Field Name Data Type Description

Compound Float The number of the compound that this metabolite is associated
with, starting from zero.

Precursor Float Mass to be searched for, the sum of the compound and metabolite.

Metabolite Float Mass of the metabolite, as specified on the MetaboLynx Setup

Metabolites page. It is the mass difference between the Compound
Mass and the Precursor.

Found Boolean 1 indicates mass was found, 0 not found.

Formula Text The formula of the metabolite if known. Absolute formula if the
parent mass was specified as a formula (e.g. C18H24O2) or relative
formula if parent mass was specified as a mass (e.g. +CO2). If the
metabolite is not recognised the formula is 0.

ChroTrace Integer list This field is a comma-separated list of chromatogram traces

searched when looking for this mass; the trace numbers start from
1.

Peak Text list If the mass was found, this field is a comma-separated list of
chromatogram peak numbers in which the mass was found. Each
peak is identified by a string of text containing four forward slash
separated numbers in the following format:

peak-number/function-number/trace-number/mass-found

where the first 3 numbers are integers, the fourth a float.

If the mass was not found, this field is 0.

MetName Text Descriptive name of the metabolite

Page 45
Interfacing Guide

ProteinLynx Browser
Sections

The file will hold section blocks of data. The start of a section block will always
start with the name of the section surrounded by square parentheses on a line by
itself. i.e. [SectionName].

The main body of the data will be enclosed by a pair of braces, the opening and
closing braces will be the only characters on their respective lines.

e.g. [SectionName]
{
....Data...
}

Section blocks can have section blocks embedded in them, in some cases multiple
instances of sections with the same name can be allowed, depending on the type of
data.

e.g. [SectionName1]
{
....Data...
[SectionName2]
{
....Data...
}
}

Fields

Sections will have a group of fields, each field will be on one line. The field name
will be the first item on the line, followed by a list of TAB separated data items for
that field. The type of data will depend on the field type.

i.e. [SectionName]
{
FieldName1 Data1
FieldName2 Data2_1Data2_2
...
}

Tabulated Sections

Some sections can be considered to be a table, or list, of fields of the same type.
Tabulated sections do not require any field names to describe the data.

e.g. [TableSection]
{
;Field1 Field2
Data1_1Data1_2
Data2_1Data2_2
...
}

Page 46
 Interfacing Guide

File Section Descriptions

SAMPLE

Note: The fields may not appear in the same order as the table below and some
empty fields will not appear at all.

Field/Section Name Data Type Description

Sample Integer The number of the sample in the batch.

Well Text The description of the well position, as a pair of co-ordinates for
plate position in rack and well position in plate, or an absolute
position. There are three formats for Well.

1. wellX,wellY
2. wellAwell1 (or well1wellA )
3. Absolute rack position.

Where X and Y are integers and A is an alphabetical character.

Data_File_Name Text The MassLynx NT MS data file name.

Sample_ID Text MassLynx Sample ID.

Sample_Description Text MassLynx Sample description.

Spare1 Text User definable spare.

Spare2 Text User definable spare.

Spare3 Text User definable spare.

Spare4 Text User definable spare.

Spare5 Text User definable spare.

Date Text Date that MS data file was acquired.

Time Text Time that MS data file was acquired.

Job_Code Text MassLynx Sample List Jobcode field.

Task_Code Text MassLynx Sample List Taskcode field.

User_Name Text Current MassLynx user name.

Instrument Text Instrument name.

Plate Text Description of micro-titre plate, if applicable.

MS_File Text The MassLynx MS data file name.

Process_Parameters Text The MassLynx process parameter file name.

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Interfacing Guide

Field/Section Name Data Type Description

FUNCTION Section MS function data and results. There will be one FUNCTION
section per MassLynx MS data functions.

FUNCTION

Field/Section Name Data Description

Type

Function Integer The MassLynx MS data function number.

IonMode Text The type of ionisation mode e.g. AP+.

Type Text The type of MS scan function e.g. MS for full scan.

Description Text A brief description of the MS scan function.

PROCESS_PARAMETERS Section MS process parameter data and results. There will only be
one PROCESS_PARAMETERS section in a FUNCTION.

SEARCH_PARAMETERS Section MS search parameter data. There will only be one

SEARCH_PARAMETERS section in a FUNCTION.

SEARCH_RESULTS Section MS search results. There will only be one

SEARCH_RESULTS section in a FUNCTION.

SPECTRUM Section MS raw spectrum data. There will only be one SPECTRUM
in a function. Note: Only present for Maldi data.

PEAKLIST Section MSMS raw spectrum data. There will only be one
PEAKLIST in a function. Note: Only present for MSMS
data.

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PROCESS_PARAMETERS

Field Name Data Type Description

Do_Process Boolean 1 if processing has been performed, otherwise 0.

Combine_Mode Text Spectrum combine mode.

DoBackgroundSubtract Boolean 1 if background subtraction has been performed,

otherwise 0.

PolynomialOrder Int Number indicating the polynomial order used in

background subtraction.

BelowCurve Int Number indicating the below curve % used in

background subtraction.

DoSmooth Boolean 1 if smoothing has been performed, otherwise 0.

SmoothChannels Float Number of channels smoothed.

NumberOfSmooths Int Number of smooths performed.

Smooth_Mode Text The smoothing method used. E.g. Savitzky-Golay

Min_Peak_Width Int Minimum spectral peak width.

Centroid_Percent Float Intensity of peak as a percentage of the base peak.

Centroid_Mode Text Spectrum centroid mode used.

PreCharge Int Pre charge state.

Min_Mass_To_Start Float Minimum start search mass.

Isotope_Factor Float Minimum isotopic factor value.

Relative_Deiso_Intensity Int The relative deiso intensity.

LockMassPeak_1 Int First lock mass value.

LockMassPeak_2 Int Second lock mass value..

LockMassPeak_3 Int Third lock mass value.

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SEARCH_PARAMETERS

Field Name Data Type Description

Do_Search Boolean 1 if search performed, otherwise 0.

Database_Type Text Type of database searched.

Index_Path Text Path of database index.

Sequence_File Text Database sequence file name.

Trembl_Path Text Path of Trembl database

SearchServer Text Name of search server

Output_Type Text Type of output file.

PEAKLIST_location Text Location of Sequest output file.

MASS Text Location of mascot output file.

PepSea_location Text Location of PepSea output file.

MOWSE_location Text Location of mass intensity output file.

Organism Text Search organism.

Freetext Text Search free text.

Keyword Text Search key word.

Author Text Search author.

Accession Text The database accession code.

Subsequence Text Search sub sequence.

BileEqual Boolean 1 if treat I/L and Q/K as equivalent box checked,

otherwise 0

Do_Monoiso Boolean 1 if search monoisotopic peaks box checked, otherwise

0.

MAX_HITS Integer Maximum number of hits to return from the search. 0 if

All selected.

SORT_TYPE Text BIO_SORT_PROB, BIO_SORT_LIKELIHOOD,

BIO_SORT_ENTRY, BIO_SORT_COVERAGE or
BIO_SORT_MATCH depending on the sort method.

Exclude_Lockmass Boolean 1 if lockmass excluded, otherwise 0.

Tolerance Float Peptide tolerance value.

Tolerance_Units Text Peptide tolerance units.

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Field Name Data Type Description

Charge Float Peptide charge state.

MinToMatch Int Number of required matches.

Do_Digest Boolean 1 if digest simulation was performed, otherwise 0.

Fast_Digest_Reagent Text Name of digest reagent when using and index.

Digest_Index Text Digest index’s file path and name.

Simulated_Digest_Reagent Text Name of primary digest reagent.

Secondary_Digest_Reagent Text Name of secondary digest reagent.

pFactor Float The pFactor value entered.

Missed_cleavages Integer Number of missed cleavage sites.

Do_Incomplete Boolean 1 if incomplete cleavage processing performed,

otherwise 0.

Do_MW Boolean 1 if molecular weight restriction was specified, otherwise

0.

MW_from Float Molecular weight range minimum.

MW_to Float Molecular weight range maximum.

Do_PI Boolean 1 if isoelectric point restriction was specified, otherwise

0.

PI_from Float Isoelectric point range minimum.

PI_to Float Isoelectric point range maximum.

Do_Modifiers Boolean 1 if modification was specified, otherwise 0.

Reduced_cysteine Boolean 1 if reduced cysteine was specified, otherwise 0.

MODIFIERS Section Description of the modifiers used during processing.

MODIFIERS

Field Name Data Type Description

Name of modifier Boolean 1 if always use this modifier box checked, 0 if use when
needed to match peptide box checked.

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SEARCH_RESULTS

Field Name Data Type Description

File_Name Text Search result file name with its full path

PRP_File_Name Text The hit section does not appear in this file but in the file
named above. One HIT section defines one database
Hit. There can be more than one HIT sections.

SPECTRUM

Field/Section Name Data Type Description

LockMassUsed Float The lock mass value used

MONOISOMASSES Section MS monoisomasses data. There will only be one

MONOISOMASSES in a SPECTRUM.

CORRECTION_FACTOR Section MS raw spectrum data. There will only be one

CORRECTION_FACTOR in a SPECTRUM.

MONOISOMASSES

Field Name Data Type Description

Float One monoisomass value per line. There can be more

than one line

CORRECTION_FACTOR

Field Name Data Type Description

Correction_Factor Float Correction factor applied to the whole spectrum.

Calculated from the lock mass.

Offset_Factor Float Correction factor applied to the whole spectrum.

Calculated from the lock mass.

ProcessHistory Text Process history information text string

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PEAK_LIST

Field Name Data Type Description

Output_Filename Text The name of the Mascot or Sequest compatible peak

information file.

e.g.

Mascot file

C:\TEMP\hilo07.004.2.1.pkl

where 004 = the scan number

2 = the function number
1 = the charge state

Sequest file

C:\MASSLYNX\hilo07.0100001.dta

where 0001 = the scan number

01 = the function number.

Bio-Rad File Descriptions

If the Bio-Rad box was checked then a SampleID.txt file is produced with the
following format.

Field Name Data Type Description

VIEW_ONE Section Database protein entry information. There will only be

one VIEW_ONE section per HIT.

VIEW_TWO Section Database match information There will only be one

VIEW_TWO section per HIT.

VIEW_THREE Section Database protein sequence There will only be one

VIEW_THREE section per HIT.

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VIEW_ONE

Some entries do not contain data on all the line types, and some line types occur
many times in a single entry.

Field Name Description

ID Identification line showing the entry name of the sequence.

AC The accession number, a unique number used to identify entries.

DT Date of entry or last modification.

DE Description line containing general descriptive information.

GN Gene name.

OS The organism species line specifies the organism which was the source of the
sequence. In most cases this is the Latin name followed by the English name (in
parentheses). For viruses only the common English name is given. If the sequence is
identical for more than one species the OS lines will list the names of all those species.

OG The Organelle lines indicate if the gene coding for a protein originates from the
mitochondria, the chloroplast, a cyanelle or a plasmid.

OC The organism classification lines contain the taxonomic classification of the source
organism.

RN Reference number

RP Reference position

RC Reference comment

RX Reference cross-reference

RA Reference authors

RL Reference location (Journal information)

CC Comments or notes used to convey useful information.

DR The database cross-reference lines are used as pointers to related information in other
data collections. E.g. Protein Data Bank (PDB).

KW Keyword lines provide information which can be used to generate cross-references to

other entries.

FT Feature table data lists regions of interest in the sequence - post-transitional

modifications, binding sites, enzyme active sites etc.

SQ Sequence header followed by sequence data .

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VIEW_TWO

Some entries do not contain data on all the line types, and some line types occur
many times in a single entry.

Field Name Description

ID Identification line showing the entry name of the sequence.

Accession number The accession number, a unique number used to identify entries.

Description Description line containing general descriptive information.

Species The organism species line specifies the organism which was the source of the
sequence.

Number of matched The number of matched peptides

peptides

Probability score MOWSE type score.

Percent coverage % sequence coverage.

Isoelectric point The isoelectric point of the entry.

Molecular weight The molecular weight of the entry.

Matching peptides A list of matching fragment masses with their molecular weight (MW), mass
error (Delta), the position of the peptide in the sequence (start and end) and
the sequence. If a * appears to the left of one of these entries then it is a
single partial fragment (i.e. one missed cleavage site), if ** appears it is a
double partial fragment (i.e. two missed cleavage sites).

Unmatched masses A list of unmatched masses showing the Searched mass, the Query mass and
the Charge State.

VIEW_THREE

This view displays the sequence specific to the entry as a text string.

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File Formats
Sample List
The Sample Lists are held in Microsoft Access which mean their contents are
readily available to numerous other windows programs. Sample Lists created by the
MassLynx system have the .SPL extension.

Label Format Description

VERSION Double Database version number.

Index Double Used internally to keep samples sequenced when editing.

FILE_NAME Char (255) Raw data file name for this sample. Can be name or full path.

MS_FILE Char (255) MS method parameter file to use when acquiring this sample. Can
be name or full path.

MS_TUNE_FILE Char (255) MS tuning parameter file to use when acquiring this sample. Can
be name or full path. If empty the current tune settings will be
used.

INLET_FILE Char (255) Inlet method parameter file to use when acquiring this sample. Can
be name or full path. Only required if a programmable inlet
acquisition system is being used to acquire sample.

INLET_PRERUN Char (255) Inlet pre-run method parameter file to use prior to acquiring this
sample. Can be name or full path. If empty no pre-run is
performed. Only required if a programmable inlet acquisition
system is being used to acquire sample.

INLET_POSTRUN Char (255) Inlet postrun method parameter file to use subsequent to acquiring
this sample. Can be name or full path. If empty no post-run is
performed. Only required if a programmable inlet acquisition
system is being used to acquire sample.

INLET_SWITCH Char (255) Inlet pre-run method parameter file to use prior to acquiring this
sample if inlet system has had to make a column switch, this will be
used in preference to INLET_PRERUN. Can be name or full path.
If empty no column switch pre-run is performed. Only required if a
programmable inlet acquisition system is being used to acquire
sample.

AUTO_FILE Char (255) Autosampler method parameter file to use when acquiring this
sample. Can be name or full path. Only required if a
programmable autosampler system is being used to acquire sample.

SAMPLE_LOCATION Char (255) Defines location of sample to be acquired on autosampler bed.

Format will depend on type of autosampler being used.

INJ_VOL Double Volume of sample to inject when acquiring with programmable

autosampler

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Label Format Description

PROCESS Char (255) External process to run to perform processing of sample. Can be
name or full path. Only required if external processes are being
run, if empty no process will be run for this sample.

PROCESS_PARAMS Char (255) Name of external process parameter file to use when processing
samples. Available to external process via MLCURSMP.TXT file.

PROCESS_OPTIONS Char (255) Options to specify on command line of external process when it is
executed

FILE_TEXT Char (255) Sample text description to be used for sample. Will be recorded in
data file header.

JOB Char(255) Job description for sample. Will be recorded in data file header.

TASK Char(255) Task description for sample. Will be recorded in data file header.

USER Char(255) User name for sample. Will be recorded in data file header.

SUBMITTER Char(255) Submitter for sample. Will be recorded in data file header.

CONDITIONS Char(255) Condition information for sample. Will be recorded in data file
header.

TYPE Char (255) Sample type to use during Quantify. Currently can be one of
ANALYTE, BLANK, QC or STANDARD

ID Char(255) The sample ID from OpenLynx.

CONC_A … CONC_T Char (255) 20 fields used to specify the concentration levels of compounds
within this sample. Used during the quantify process.

WAVELENGTH_A… Double 10 fields used to specify wavelengths to analyse for this sample.
WAVELENGTH_J Used during OpenLynx processing.

MASS_A … MASS_T Char (255) 20 fields used to specify masses to analyse for this sample. Used
during the OpenLynx process. Masses can be real numbers or
chemical formulae

STOCK_DIL Double Not currently used reserved for future use

USER_DIVISOR_1 Double Divisor used during concentration calculation stage of Quantify.

Defaults to 1 if not specified.

USER_FACTOR_1 … Double Multipliers used during concentration calculation stage of Quantify.

USER_FACTOR_3 Defaults to 1 if not specified.

HPLC_FILE Char(255) The additional LC information for this sample (used by OpenLynx)

SPARE_1 … Char (255) General purpose fields available to the User to store extra
SPARE_5 information about the sample.

ACQU_PROCESS Char (255) External process to run when acquiring data. Can be name or full
path. Only required if external processes are being run, if empty no
process will be run for this sample.

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Label Format Description

ACQU_PROCESS_ Char (255) Name of external process parameter file to use when acquiring
PARAMS samples. Available to external process via MLCURSMP.TXT file.

ACQU_PROCESS_ Char (255) Options to specify on command line of external process when it is
OPTIONS executed

SAMPLE_GROUP Char (255) Used too inform QuanLynx that the optimisation file for an
Analysis sample should combine the optimisations for a number of
compounds sample groups are used. Each sample group item is a
unique one or two letter code in upper case. Thus ‘A:B:C’, ‘AA
BB CC’, ‘A….ZZ….QP’ are all valid three item groups.

If the sample group field is empty then all the compounds will be
optimised; one method file will be created and used for all the
analysis samples.

If a sample group in the analysis sample list does not have a

corresponding entry in the compound list, then that group will not
be run.

FRACTION_FILE Char (255) Raw data file name for this sample. Can be name or full path.

FRACTION_1 to Char (255) References to the masses (MASS_A to MASS_T) to be monitored

FRACTION_4 when performing fraction collection acquisition.

QUAN_REF Char (255) This field specifies which sample (if any) is to be used to adjust the
retention time window of the quantification method created for the
analysis. The first sample in the current group that has this field set
to anything other than blank will be used.

AUTO_ADDITION Char (255) The Waters 2790 autosampler can take samples from up to 15 vials
and inject them sequentially. This field contains a list of the sample
locations separated by a semi-colon (;) e.g. A:1;A:2;A:3. The
volume specified in the INJ_VOL field is drawn from each vial.

METH_DB Char (255) The full path to the quantify method file used for this sample group
in QuanLynx.

CURVE_DB Char (255) The full path to the calibration curve file used for this sample group
in QuanLynx.

DUMP_FILE Char (255) The full path to the text export file used for this sample group in
QuanLynx.

PROCESS_ACTION Char (255) The Action that the process manager is to perform should the
external application return an error

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An Example Generic Sample List File

Below is an example of a small single sample generic sample list file.

[Batch]

MSMethod=DEFAULT.MDB
MSTune=DEFAULT.DBF
LCMethod=DEFAULT
ProcessParameters=C:\MASSLYNX\LC1.olp
Process=C:\MASSLYNX\OPENLYNX.EXE
UserName=john doe
BatchID=13
NumberOfPlates=1

[Plate:1]

JobCode=13
UserName=john doe
Rows=0
Columns=0
Track=R
NumberOfWells=1

[Sample:1:1]

Well=25
SampleDescription=testsample
SampleID=tst11
MSDataName=test1
SampleType=0
MSInjectionVolume=15.0000
NumberOfMasses=1
Mass1=504.00
NumberOfWaveLengths=1
Wavelength1=254.0
NumberOfConcs=2
Conc1=50.000
Conc2=100.000
NumberOfFormulae=1
Formula1=CH3CH2Cl

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AutoLynx
AutoLynx is an application that enables batches to be submitted to the MassLynx
queue for automatic acquisition, processing and report generation.

Applications can be written (e.g. in Visual Basic) to:

• Take information from other software packages (e.g. LIMS systems) and
automatically create batch files.

• Add these batch files to the AutoLynx queue. (AutoLynx will then add them to
the MassLynx queue and perform the processing defined on the AutoLynx
settings dialog).

• Monitor the progress of the batch file.

• Automatically read the acquired data, or processed results, for further

processing and/or exporting into other software packages.

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To produce the required Browser file the Process column in the Sample List must be
defined as:

• OpenLynx to produce an OpenLynx Browser file.

• PeptideAuto to produce an ProteinLynx Browser file.

• MetaboLynx to produce an MetaboLynx Browser file.

For more information on AutoLynx see the MassLynx NT Users Guide.

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Status.ini
The Status.ini file contains details of the current status of the Mass Spectrometer,
LC system and the MassLynx Queue.

To create a Status.ini file select Options from the MassLynx Tools menu to display
the options dialog.

Figure 3 The Options dialog

On the Status page check the Update Status box to write details to a status file.

By default the details in this file are updated every 60 seconds, to change this enter a
new time in the Refresh rate box.

The default filename and location is C:\MASSLYNX\status.ini. To change this

press the File Name button, select a directory using the browser displayed, enter a
new file name and press Open. Note: do not use the name of an existing *.ini file
in the current directory as this will cause problems with other software.

If any of these fields are changed MassLynx must be closed down and restarted for
the changes to take effect.

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These files can be viewed in Notepad or by third party software across a network.
This allows users to detect software or hardware errors, to decide which instrument
should be used to acquire samples or when data has been acquired and is ready for
further processing.

File Format
The format of the Status.ini file is as follows:

[MS Status]

Operate=2
Status=Scanning

[LC Status]

Status=0
Ready=0
%A=100.0
%B=0.0
%C=0.0
%D=0.0
Flow Rate=0.000

[Queue Status]

Queue Paused=0
Process Running=1
1=test Samples 1 to 5: Sample 1 Acquiring Running
2=test1 Samples 1 to 5: Waiting
3=test2 Samples 1 to 2: Waiting
Total samples=12

[Time Stamp]

Time=06-002-1999,10:37:59

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MS Status

The MS Status section shows mass spectrometer information.

Operate Shows the state of the mass spectrometers high voltage electronics. It has
two values:

1 The mass spectrometer is in standby

2 The mass spectrometer is in operate

Status Shows the status of the mass spectrometer. It can have one of the following
values:

No Instrument There is no mass spectrometer attached to the PC.

Not Scanning The mass spectrometer is idle.

Solvent Delay The mass spectrometer has started acquiring data and is
in solvent delay.

Scanning The mass spectrometer is acquiring sample data.

Waiting for Injection The mass spectrometer is waiting for the autosampler to
inject the sample.

This information is useful during automation of a list of samples. For example the
inlet system will continually poll this parameter while the mass spectrometer is
acquiring in order to determine when it has reached a suitable status (Waiting for
injection) for the next sample to be injected and a new data file to be acquired.

LC Status

This section shows inlet system information.

Status Shows whether there is an error with the inlet system. If an error occurs
then the appropriate action can be taken by the software to stop the automation. It
has two values:

0 There is no error in the inlet system

1 Inlet system has an error

Ready Shows whether the inlet system is ready to inject a new sample. It has two
values:

0 Inlet system is not ready to inject the next sample

1 The inlet system is ready to inject the next sample

%A, %B, %C and %D These parameters detail what percentage of the four
possible reservoirs will be used for the mobile phase.

Flow Rate This gives the flow rate of the HPLC (ml/min).

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Queue Status

This section shows sample list queue information.

Queue Paused This shows whether the process queue is paused. It has two states:

0 The process queue is not paused

1 The process queue is paused

Process Running This shows whether the sample list is running a process. It has
two states:

0 MassLynx is not running a process

1 MassLynx is running a process

1, 2, …. N These lines refer to the queue of batches waiting to be processed. The

format of the lines is as follows, from left to right:

“Batch No.” “MassLynx Batch ID” “Samples range” “Sample status” “Batch status”

Batch No. is an index of the batches in the queue.

MassLynx Batch ID is the identifier of the batch (e.g. sample list name).

Samples range indicates the range of samples in the batch.

Sample status has the form “Sample n Acquiring” to indicate which sample is
running.

Batch status is “Running” if a sample from that batch is being processed, or

“Waiting” if the batch is in the queue.

Total Samples

This parameter gives the total number of samples in all the batches in the queue

Time Stamp

This shows the time the data system last updated a data file. If this value does not
increase as often as its refresh rate assume the data system is no longer responding.

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Notes
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Notes
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Index
A
AutoLynx, 60

C
Copying a Chromatogram as a Text List, 13
Copying a Spectrum as a Text List, 14
Copying Data, 5
Copying Integrated Chromatogram Peaks as a Text List, 13

E
Export to LIMS, 10
Exporting Data, 10

F
File Formats, 56
Sample List, 56

I
Import Data, 8
Import Worksheet, 6

M
MetaboLynx Browser Files, 34

O
OpenLynx Batch Files, 16
OpenLynx Browser Files, 23

P
ProteinLynx Browser Files, 46

S
SEQUEST Files
Exporting, 15
Status.ini, 62

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