MassLynx 4.1 Interfacing Guide · Save command, and can be imported into MassLynx in this format....

MassLynx 4.1Interfacing Guide

71500123505/Revision A

Copyright © Waters Corporation 2005.All rights reserved.

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© 2005 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF AMERICA AND IRELAND. ALL RIGHTS RESERVED. THIS DOCUMENT OR PARTS THEREOF MAY NOT BE REPRODUCED IN ANY FORM WITHOUT THE WRITTEN PERMISSION OF THE PUBLISHER.The information in this document is subject to change without notice and should not be construed as a commitment by Waters Corporation. Waters Corporation assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Waters Corporation be liable for incidental or consequential damages in connection with, or arising from, its use.Waters Corporation34 Maple StreetMilford, MA 01757USA

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Table of Contents

1 Importing data ........................................................................................ 1-1

Copying and pasting data from text editors ............................................... 1-2

Using the Import Worksheet command ....................................................... 1-3 Creating Import Worksheet Files ................................................................... 1-4

Access ........................................................................................................... 1-4Excel ............................................................................................................. 1-6Notepad ........................................................................................................ 1-6OpenLynx Batch Files ................................................................................ 1-6

Using the Import Data command .................................................................. 1-7 Creating Import Files ...................................................................................... 1-8

Access ........................................................................................................... 1-8Excel ............................................................................................................. 1-8Notepad ........................................................................................................ 1-9

2 Exporting Data ....................................................................................... 2-1

Exporting to a LIMS File ................................................................................. 2-2 The Header Section.......................................................................................... 2-2 The Samples Section........................................................................................ 2-2

Header Fields .............................................................................................. 2-2Samples Section .......................................................................................... 2-3

The Calibration Section................................................................................... 2-4

Exporting to an XML File ................................................................................ 2-6 XML Format..................................................................................................... 2-6 Running QuanLynx from the Command Line.............................................. 2-13

Quantify Command Line Options ............................................................ 2-13

Copying to and from the Windows Clipboard .......................................... 2-15 To Copy a Chromatogram as a Text List to the Clipboard.......................... 2-15 To Copy Integrated Chromatogram Peaks as a Text List to the Clipboard 2-15 To Copy a Spectrum as a Text List to the Clipboard................................... 2-16

Table of Contents iii

Exporting to a SEQUEST File ...................................................................... 2-17

3 File Formats ............................................................................................ 3-1

Sample lists ......................................................................................................... 3-2

OpenLynx Batch Files ...................................................................................... 3-9 Paragraphs ....................................................................................................... 3-9 Batch Block .................................................................................................... 3-10 Plate Block ..................................................................................................... 3-10 Sample Block.................................................................................................. 3-10 Fields .............................................................................................................. 3-10 Comments....................................................................................................... 3-11 File Format..................................................................................................... 3-11 An Example OpenLynx Batch File ............................................................... 3-17

OpenLynx report files .................................................................................... 3-19 Sections........................................................................................................... 3-19 Fields .............................................................................................................. 3-19 Comments....................................................................................................... 3-20 Tabulated Sections......................................................................................... 3-20 Free Format Text Sections ............................................................................ 3-20 File Section Descriptions............................................................................... 3-21

SAMPLE .................................................................................................... 3-21PLATE FIELD ........................................................................................... 3-23ANALOG .................................................................................................... 3-25TRACE ....................................................................................................... 3-25PEAK ......................................................................................................... 3-25COMPOUND ............................................................................................. 3-27FRACTION ................................................................................................ 3-27FUNCTION ............................................................................................... 3-28SPECTRUM .............................................................................................. 3-28MASSES .................................................................................................... 3-29RESULTS .................................................................................................. 3-30ELEMENTAL ............................................................................................ 3-30SEARCH .................................................................................................... 3-31HIT ............................................................................................................. 3-32

iv Table of Contents

MS .............................................................................................................. 3-32CHROMATOGRAM .................................................................................. 3-33QC .............................................................................................................. 3-33INLET PARAMETERS ............................................................................. 3-33

MetaboLynx report files ................................................................................ 3-34 Sections........................................................................................................... 3-34 Fields .............................................................................................................. 3-34 Comments....................................................................................................... 3-35 Tabulated Sections......................................................................................... 3-35 Free Format Text Sections ............................................................................ 3-35 File Section Descriptions............................................................................... 3-36

SAMPLE .................................................................................................... 3-36PLATE FIELD ........................................................................................... 3-38COMPOUND ............................................................................................. 3-40FUNCTION / FUNCTION_APPEND ...................................................... 3-40 SPECTRUM ............................................................................................. 3-42MASSES .................................................................................................... 3-43RESULTS .................................................................................................. 3-43MS .............................................................................................................. 3-44CHROMATOGRAM / CHROMATOGRAM_APPEND ............................ 3-44TRACE ....................................................................................................... 3-45PEAK ......................................................................................................... 3-45EXPECTED METABOLITES ................................................................... 3-47UNEXPECTED METABOLITES ............................................................. 3-49ELEMENTAL ............................................................................................ 3-49MSMS CORRELATION ............................................................................ 3-49METABOLITES ........................................................................................ 3-50CORRELATION TABLE .......................................................................... 3-51MOLFILE LIST ......................................................................................... 3-52MOLFILE .................................................................................................. 3-52INLET PARAMETERS ............................................................................. 3-52

ProteinLynx report files ................................................................................ 3-53 Sections........................................................................................................... 3-53

Table of Contents v

Fields .............................................................................................................. 3-53 Tabulated Sections......................................................................................... 3-54 File Section Descriptions............................................................................... 3-54

SAMPLE .................................................................................................... 3-54FUNCTION ............................................................................................... 3-56PROCESS_PARAMETERS ...................................................................... 3-56SEARCH_PARAMETERS ........................................................................ 3-58MODIFIERS .............................................................................................. 3-61SEARCH_RESULTS ................................................................................. 3-61SPECTRUM .............................................................................................. 3-61MONOISOMASSES .................................................................................. 3-61CORRECTION_FACTOR ......................................................................... 3-62PEAK_LIST ............................................................................................... 3-62Bio-Rad File Descriptions ......................................................................... 3-62VIEW_ONE ............................................................................................... 3-63VIEW_TWO ............................................................................................... 3-64VIEW_THREE ........................................................................................... 3-65

4 DataBridge ............................................................................................... 4-1

DataBridge file conversions ........................................................................... 4-2

Converting a file with DataBridge ............................................................... 4-3 Starting the DataBridge Program from the Windows Start Menu............... 4-3 Running the DataBridge Program from the MassLynx Sample List ........... 4-4 To Convert an ASCII File to MassLynx Format ............................................ 4-4

5 AutoLynx .................................................................................................. 5-1

Introduction to AutoLynx ............................................................................... 5-2

Starting AutoLynx ............................................................................................ 5-3

AutoLynx settings ............................................................................................. 5-4

Interfacing with external programs ............................................................. 5-7 Monitoring the Queue Status.......................................................................... 5-7 Aborting the Queue.......................................................................................... 5-7 Accessing Results............................................................................................. 5-8

vi Table of Contents

File Usage......................................................................................................... 5-8

6 Database Logging and MassLynx Status .......................................... 6-1

Introduction ....................................................................................................... 6-2

Database Logging .............................................................................................. 6-3

MassLynx Status ............................................................................................... 6-4 File Format....................................................................................................... 6-4 MS Status......................................................................................................... 6-5

Operate ........................................................................................................ 6-5Status ........................................................................................................... 6-5

LC Status ......................................................................................................... 6-6Status ........................................................................................................... 6-6Ready ........................................................................................................... 6-6%A, %B, %C and %D ................................................................................... 6-6Flow Rate ..................................................................................................... 6-6Queue Status ............................................................................................... 6-6Queue Paused .............................................................................................. 6-7Process Running .......................................................................................... 6-71, 2, …. N ..................................................................................................... 6-7“Batch No.” “MassLynx Batch ID” “Samples range”

“Sample status” “Batch status” ................................................... 6-7Total Samples .............................................................................................. 6-7Disk Space ................................................................................................... 6-8Time Stamp ................................................................................................. 6-8

7 Datafile Access Component ................................................................. 7-1

DAC Functions ................................................................................................... 7-2

DAC Class Descriptions ................................................................................... 7-4DACHeader ................................................................................................. 7-4DACCalibrationInfo .................................................................................... 7-5DACExperimentInfo ................................................................................... 7-7DACFunctionInfo ........................................................................................ 7-7DACSpectrum .............................................................................................. 7-9

Table of Contents vii

DACScanStats ........................................................................................... 7-10DACExScanStats ...................................................................................... 7-11DACProcessInfo ......................................................................................... 7-13

DACChromatogram ....................................................................................... 7-14DACAnalog ................................................................................................ 7-15Creating Visual Basic Programs using the DAC ..................................... 7-15Creating Visual C++ Programs using the DAC ....................................... 7-16

Index ..................................................................................................... Index-1

viii Table of Contents

1 Importing data

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

Topic PageCopying and pasting data from text editors 1-2Using the Import Worksheet command 1-3Using the Import Data command 1-7

1-1

Copying and pasting data from text editors

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

1. Select the Tool Bar button or select the Menu Bar File, New command. A Sample List, with one default row, will be created.

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 the Menu Bar File, Paste command.

Note: • If copying from a text editor, for example, Notepad, fields must be tab

delimited. Also, each line, including the last, must end in a carriage return. If the last line does not end in a carriage return, it will not be pasted into the Sample List.

• When copying from an Access database the last record is not pasted and will have to be entered manually. In addition to the last record not being pasted, the column headings are pasted (for example, if three rows are copied from the database, the column headings and the first two selected rows are pasted).

1-2 Importing data

Using the Import Worksheet command

Sample Lists can be created in a number of other packages and imported into MassLynx.

• Access 97 & 2000.• Tab and Comma delimited text files.• Excel 97 & 2000 and Excel 5.0, 6.0 and 7.0 files.• OpenLynx Batch Files.• MassLynx 2.3 Sample Lists.

To Import a Worksheet

1. Select the Menu Bar File, Import Worksheet command; the Import Worksheet dialogue is invoked.

The Import Worksheet dialog box:

2. Select the required file, or type a file name in the File name: box.

3. Select the type of file to be imported in the Files of type: list box, if required.Note: The first time that Import Worksheet is invoked, the default file type is Generic Batch Files (*.OLB), created in OpenLynx; if a new file

Using the Import Worksheet command 1-3

type is selected, this type will be the default the next time Import Worksheet is selected.

4. Select the Open button.Note: When a worksheet is imported, the sample list columns displayed will not change, and columns may need to be added/removed from the display to see all the imported data.

Creating Import Worksheet FilesThe following sections contain information on how to create Worksheet files suitable for importing into MassLynx.For all types of file fields must have the same name as in the Sample List (see File Formats on page 3-1) 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 dialogue, which is displayed by right-clicking anywhere on the sample list and selecting the Customize Display command.

Access

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 the field data type to be defined.The first column must be called Index and be the primary key. The Index column defines the order in which the rows will be displayed in MassLynx. The AutoNumber data type could be used to set up this column in Access.Column headings must match those shown in File Formats on page 3-1. Other columns may be present but they will not be imported into the Sample List.

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.

1-4 Importing data

To Save in Access Format:

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

Saving in Tab or Comma Delimited Format

For Access 97:

1. Select the Menu Bar File Save As/Export command, select the To an External File or Database option and select the OK button.

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 select the Export button.

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

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

5. Enter the required file name.

6. Select the Finish button.

For Access 2000:

1. With the ANALYSIS table open, select the Menu Bar File, Export command.

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 select the Save button.

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

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

5. Enter the required file name.

6. Select the Finish button.If files are saved as comma or tab delimited, they must be imported into MassLynx as comma or tab delimited files.

Using the Import Worksheet command 1-5

Excel

The first column must be called Index, the other column headings must match those shown in File Formats on page 3-1.Select the area containing the data to be imported, including the column headings, and name the area ANALYSIS. To do this, select the Menu Bar Insert, Name, Define command, type ANALYSIS and select OK.Leave all cells in General format.If the file is to be saved as tab or comma delimited, Excel will only allow one sheet to be saved. If the current workbook contains more than one worksheet, each worksheet must be saved as a separate text file.

Notepad

The first column must be called Index, the other column headings must match those shown in File Formats on page 3-1.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.The following example shows a comma delimited file which uses the first five datasets of the Diverse.pro example project:Index,FILE_NAME,SAMPLE_LOCATION,PROCESS,PROCESS_PARAMS,MASS_A1,DIV01,1,OPENLYNX,LC.olp,5042,DIV02,2,OPENLYNX,LC.olp,5683,DIV03,3,OPENLYNX,LC.olp,2404,DIV04,4,OPENLYNX,LC.olp,2515,DIV05,5,OPENLYNX,LC.olp,327

OpenLynx Batch Files

The .OLB files must be created following the format described in OpenLynx Batch Files on page 3-9.

1-6 Importing data

Using the Import Data command

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

• Access 97 & 2000.• Tab and Comma delimited text files.• Excel 97 & 2000 and Excel 5.0, 6.0 and 7.0 files.

To Import Data

1. In MassLynx, ensure that the correct numbers of rows and columns required to accept the data are displayed. Data will be lost if this is not done.

2. Select the MassLynx Menu Bar File, Import Data command; the Import Data dialogue is invoked.

The Import Data dialog box:

3. Select the required file, or type a file name in the File name: box

4. Select the type of file to be imported in the Files of type: list box, if required.

Using the Import Data command 1-7

Note: The first time that Import Worksheet is invoked, the default file type is Excel 5.0 (*.XLS); if a new file type is selected, this type will be the default the next time Import Data is selected.

5. Select the Open button.

Creating Import FilesThe following sections contain information on how to create files suitable for importing into MassLynx.For all types of file, the fields must be in the same order as they are to appear in the MassLynx Sample List.

Access

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 the field data type to be defined. The field names do not have to correspond to the field names in MassLynx (but the order must be the same).To define the data type as a double see “To Define the Data Type as a Double” above.To save in tab or comma delimited format, follow the instructions under “To Save in Tab or Comma Delimited Format” above, except for step 4, where the Include Field Names on First Row option must not be selected.If files are saved as comma or tab delimited, 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 or a blank row at the start, and name the area ANALYSIS. To do this, select the Menu Bar Insert, Name, Define command, type ANALYSIS and select the OK button. The column headings do not have to correspond to the field names in MassLynx, but the order must be the same.Leave all cells in General format.If the file is to be saved as tab or comma delimited, Excel will only allow one sheet to be saved. If the current workbook contains more than one worksheet, each worksheet must be saved as a separate text file. Column headings or

1-8 Importing data

blank rows should NOT be included in the ANALYSIS area when saving to a text file.

Notepad

Type in the field name/value, then a comma (or press the tab key for tab delimited files) and enter the next value. End each line with a carriage return. Column headings should not be included and the fields must be in the same order as in MassLynx.Text fields should be enclosed in quotes.The following example shows a comma delimited file which uses the first five datasets of the Diverse.pro example project.DIV01,1,OPENLYNX,LC.olp,504DIV02,2,OPENLYNX,LC.olp,568DIV03,3,OPENLYNX,LC.olp,240DIV04,4,OPENLYNX,LC.olp,251DIV05,5,OPENLYNX,LC.olp,327

To import this file correctly using Import Data, the following fields must be displayed in MassLynx (in this order): FILE_NAME, SAMPLE_LOCATION, PROCESS, PROCESS_PARAMS, MASS_A.

Using the Import Data command 1-9

1-10 Importing data

2 Exporting Data

Contents:

Topic PageExporting to a LIMS File 2-2Exporting to an XML File 2-6Copying to and from the Windows Clipboard 2-15Exporting to a SEQUEST File 2-17

2-1

Exporting to a LIMS File

Quantification results can be written to a text file for use with LIMS. This can be performed automatically by selecting the Export Results to LIMS option on the Create QuanLynx Dataset dialogue (accessed through the QuanLynx Shortcut Bar Process Samples icon).The results can also be exported from the QuanLynx Browser Window. Select the Menu Bar File, Export, LIMS command, select a file from the displayed Export browser, or enter the name of a new file and select the Save button. 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 SectionThe header section contains the following five 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.• DATASET – The QuanLynx dataset the LIMS file was generated from.• SAMPLELIST – The Sample List file.• QUANMETHOD – The quantification method file.• QUANCALIBRATION – The quantify curve file.

For example, LIMS EXPORT FILE:C:\Masslynx\lims1Tue Aug 28 12:21:44 2001

The Samples Section

Header Fields

The Samples Section includes an entry for each sample in the current Sample List. The header contains the File Name, Sample ID and any text entered in the SPARE_1 to SPARE_5 fields in the Sample List. After the SPARE_1 –

2-2 Exporting Data

SPARE_5 fields, there are fields indicating the date and time the sample was created.For example, ASSAY01,ID,,,,,,12-Dec-94,17:37:45

Samples Section

For each sample, there is one entry for each compound named in the Quantify Method Editor Compound: box. Each entry has the following fields, separated by a comma. The Data Type column shows what type of field the data was exported from.

Samples section field descriptions:

Field Description Data TypeThe compound number shown in the Quantify Method Editor Compound: box.

Int

The text name of this compound. CharThe scan at which the matching peak was found in the current sample data file.

Int

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

Float

The area of the matching peak. FloatThe height of the matching peak. FloatThe response of the sample for this compound. FloatThe flags associated with the peak. TextThe concentration of compound recorded for this sample. FloatThe 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 reference peak for this compound.

Int

Exporting to a LIMS File 2-3

The Calibration SectionThe Calibration Section has a subsection for each calibration curve calculated for the current quantification calibration. Each subsection contains

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

Float

The height of the reference peak. FloatThe retention time of the reference peak. FloatThe modification date of the peak used to quantify this compound for this sample. This refers manual modification of the peak.

Text

The modification time of the peak. TextThe modification text (modification comment) of the peak. TextThe MassLynx User who altered the peak. TextThe mass of the peak. FloatThe retention time the peak was expected at for this compound.

Float

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

Float

The User Peak Factor associated with this compound. FloatThe User RF Value associated with this compound. FloatThe Start Retention Time of the detected peak. FloatThe end retention time of the detected peak. FloatAbsolute peak response. FloatCompound number of the Retention Time Reference. IntSecondary Ion chromatogram trace description. TextNumber of secondary ions used. IntRatio of Primary and Secondary ion absolute peak responses.

Float

Primary/Secondary peak ratio within tolerance flag. BooleanArea of Secondary ion Peak. FloatHeight of Secondary ion Peak. Float

Samples section field descriptions:

2-4 Exporting Data

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:, Weighting and Axis trans.:

For example,Compound 1 name: I. StdResponse Factor: 846.154Response type: External Std, AreaCurve type: RFCompound 2 name: ParentCoefficient of Determination: 1Calibration curve: 0.568051 * x + 0.0010347Response type: Internal Std ( Ref 1 ), Area * ( IS Conc. / IS Area )Curve type: Linear, Origin: Exclude, Weighting: 1/x, Axis trans: NoneCompound 3 name: MetaboliteCoefficient of Determination: 1Calibration curve: 0.336996 * x + -0.00516146Response type: Internal Std ( Ref 1 ), Area * ( IS Conc. / IS Area )Curve type: Linear, Origin: Exclude, Weighting: 1/x, Axis trans: NoneAll 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.

Exporting to a LIMS File 2-5

Exporting to an XML File

Quantification results can also be written to an .XML file. This can be performed by selecting the QuanLynx browser Menu Bar File, Export, XML command. Select a file from the displayed Export browser, or enter the name of a new one and select the Save button. If the selected file already exists, the User will be prompted to overwrite the existing file.

XML FormatThe export .XML file will begin a Processing instruction that will take the form<?xml version=“1.0” ?>

The export .XML file consists of several nodes and attributes. The start of a node is denoted by the angular bracket ‘<’. The text immediately following this is the name of the node. A node may be ended in two ways: the symbol ‘/>’ at the end of a line will terminate a node, or the statement </nodename> will also terminate a node. Following the node name are the node attributes. These are denoted attributename=“attribute value”. XML is case sensitive, so care must be taken to be consistent.The initial or root node in the export .xml file is called QUANDATASET. This node has two attributes and several sub-nodes exist within this node. A description of the nodes (UPPERCASE) and their respective attributes (lower case) follows, all of the attributes can be exported as text.QUANDATASET

description – a text description of the dataset.version – QuanLynx dataset version number.XMLFILE

filename – the text name of the .XML file.modifieddate – the date the file was last modified.modifiedtime – the time the file was last modified.

DATASETfilename – the name of the QuanLynx dataset file (*.QLD).modifieddate – the date the file was last modified.modifiedtime – the time the file was last modified.

2-6 Exporting Data

GROUPDATAcount – the number of groups in the dataset.GROUP

id – the identifier of the group.name – the name of the group.METHODDATA

id – the identifier of the method.filename – the name of the method data file (*.MDB).modifieddate – the date at which the file was last modified.modifiedtime – the time at which the file was last modified.

SAMPLELISTDATAfilename – the name of the sample list file (*.SPL).modifieddate – the date at which the file was last modified.modifiedtime – the time at which the file was last modified.count – the number of samples in the sample list.SAMPLE

id – the identifier of the sample.groupid – the identifier of the group of which the sample is a member.name – the name of the sample.createdate – the date the sample was created.createtime – the time the sample was created.type – the type of the sample.text – text description of sample type. desc – sample text description. dilutionfac – multiplier used during concentration calculation.extractvolume – multiplier used during concentration calculation.initamount – divisor used during concentration calculation.injectvolume – the volume of sample injected.

Exporting to an XML File 2-7

job – job description for samplemassA – the first mass in the sample list. massB – the second mass in the sample list. massC – the third mass in the sample list. massD – the fourth mass in the sample list. massE – the fifth mass in the sample list. massF – the sixth mass in the sample list. massG – the seventh mass in the sample list. massH – the eight mass in the sample list. massI – the ninth mass in the sample list. massJ – the tenth mass in the sample list. sampleid – the sample IDsamplenumber – the number of the sample in the sample list.stdconc – concentration of an analyte when used as an internal standard.stockdilutionfac – factor for stock concentrations.subjecttext – description of the subject used in the experiment.subjecttime – time at which the experiment was performed on the subject. userdilutionfac – multiplier used during concentration calculation.vial – the location of the sample. inletmethodname – name of the inlet method. msmethodname – name of the MS method.prerunmethodname – name of the pre run method.postrunmethodname – name of the post run method.switchmethodname – name of the switch method.hplcmethodname – name of the HPLC method.tunemethodname – name of the tune method.

2-8 Exporting Data

fractionlynxname – name of the FractionLynx method.COMPOUND

id – the identifier of the compound.sampleid – the identifier of the sample associated with the compound.groupid – the identifier of the group to which the compound is associated.name – the name of the compound.PEAK

foundscan – the scan at which the matching peak was found.foundrt – the retention time of the matching peak.foundrrt - the relative retention time of the matching peak.area – the area of the matching peak.height – the height of the matching peak.response – the response of the sample for this compound.pkflags – the flags associated with the peak.analconc – the concentration of the compound for this sample.bsanalconc – the background subtracted the concentration of the compound for this sample (not calculated at present).conccalc – the percentage deviation of calculated concentration from known concentration.modifieddate – the date at which the peak was last modified.modifiedtime – the time at which the peak was last modified.modifiedtext – text associated with the peak modification.modifieduser – the user who last modified the peak.


peakmass – mass at which peak was found.startrt – the start retention time of the detected peak.endrt – the end retention time of the detected peak.absresponse – the absolute response of the peak.rrtref – the id of the peak used as the response reference peak for this compound.ionratio – primary/secondary response ratio.chromnoise – the noise on the chromatogram.detectionthreshold – the limit of detection for the peak.quanthreshold – the limit of quantification for the peak.rrf – relative response factor (rf/conc).chromtrace – name of the chromatogram trace.peaks – the number of secondary peaks.pkwidth – the width of the peak at 50% height.pksigma – the standard deviation of the peak.pkskew – the degree of asymmetry of the peak.pkkurt – the relative “peakness” or “flatness” of the peak.heightdivarea – peak height to area ratio.baselinewidth – the difference, in seconds, between the end of the peak baseline and the start of it.peakquality – true/false depending on whether the peak quality criteria have been met.peakqualitydesc – description of why the peak quality test has failed.peakqualityref – flag for whether this peak is a reference peak.replimflag – true for analyte samples if the concentration is below the minimum threshold.maxreplimflag – true for analyte samples if the concentration is above the minimum threshold.

2-10 Exporting Data

recovlimflag – true for standard samples if the recovery level is outside the permitted tolerance.signoiseflag – true if the signal to noise ratio is below the minimum threshold.cdflag – true if coefficient of determination is below minimum threshold.blankflag – true for blank samples if the response is above the maximum threshold.stddevflag – true for QC samples if the sample falls outside the permitted number of standard deviations from the mean.rtflag – true if retention times have fallen outside the tolerance settings.

SECONDARYPEAKSsecondarychromnoise – the noise on the secondary chromatogram.actualionratio – the calculated primary/secondary peak response ratio.irwinflag – ion ratio flag.area – the area of the secondary peak.height – the height of the secondary peak.

ISPEAKarea – the area of the peak used as an internal standard peak.height – the height of the peak used as an internal standard.foundrt the retention time of the internal standard peak.

METHODrref – response reference.predrt – the expected retention time of the peak.predrrt – the expected relative retention time of the peak.userfactor – user factor.


userrf – user response factor.quantrace – the trace supplied in the method.secondarytrace – the trace of the secondary peak supplied in the method.

CALIBRATIONDATAfilename – the name of the file containing calibration data.modifieddate – the date at which the calibration was last modified.modifiedtime – the time at which the data was last modified.count – the number of compounds used in the calibration.COMPOUND

id – the identifier of the compound.name – the name of the compound used in the calibration.RESPONSE

type – the type of the compound (Internal Standard, etc.).ref – response reference.rah – response calculation method.

CURVEtype – the type of the curve (RF, etc.).origin – the origin of the response curve.weighting – the weighting applied to the response curve.axistrans – the type of axis transformation used.If curve type is RF then:RESPONSEFACTOR

cc – calibration coefficient (gradient).stddev – standard deviation.percrelsd – relative standard deviation (percentage).

CORRELATIONr – the correlation coefficient of the curve.

2-12 Exporting Data

DETERMINATIONrsquared – the coefficient of determination for the curve.

If curve type is not RF then: CALIBRATIONCURVE

curve – calibration polynomial.DETERMINATION

rsquared – the coefficient of determination for the curve.

Running QuanLynx from the Command LineQuantification results can be printed or written to a LIMS text file or an XML export file. A full description of the QuanLynx command line options is included below.

Quantify Command Line Options

This information can be displayed from the command prompt by typing Quantify /h or Quantify /?. In the notation below [ ] contain optional parameters and | indicates that the options on either side may be selected.

To open a file:

Quantify <filename>

To print the results:

Quantify /p [/g[roup]:<range>][/s[ample]:<range>]

[/c[ompound]:<range>]

[/s: | /layout:<formatfile>]

<filename>

To produce a LIMS export file:

Quantify /r: | /lims:[<outputname>] <filename>


To produce an XML export file:

Quantify /xml:[<outputname>] <filename>

In all options / can be replaced by – .The range parameter can be specified as:

If an output name is not specified it will default to the name of the dataset.If a layout name is not specified it will default to the last used layout.

44-81-3,5,7,10-20

a single numbera rangea combination of ranges and numbers

2-14 Exporting Data

Copying to and from the Windows Clipboard

The Windows Clipboard provides temporary storage for information that is being transferred between application programs (word processors, spreadsheets, MassLynx, etc.). The Clipboard can be used 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.

To Copy a Chromatogram as a Text List to the Clipboard1. Display the required time range in the Chromatogram window.

2. Select the Tool Bar button, or select the Menu Bar Edit, Copy Chromatogram List command. The section of the chromatogram on display will be copied 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, select the other application’s Menu Bar Edit, Paste command.

Copying the Chromatogram list to the clipboard gives the following format:Retention Time or Scan Number Intensity

Retention Time or Scan Number Intensity



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

To Copy Integrated Chromatogram Peaks as a Text List to the Clipboard

1. Display the required time range in the Chromatogram window.

2. Select the Tool Bar button, or select the Menu Bar Edit, Copy Detected Peaks command. The section of the chromatogram on display will be copied to the Clipboard as (time, intensity) pairs, or (scan, intensity) pairs, depending on the horizontal axis setting.


Copying to and from the Windows Clipboard 2-15

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

The fields are separated by tabs.

To Copy a Spectrum as a Text List to the Clipboard1. Display the required mass range in the Spectrum window.

2. Select the Tool Bar button, or select the Menu Bar Edit, Copy Spectrum List command. The section of the spectrum on display will be copied to the Clipboard as (mass, intensity) pairs.


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 tabs.

Retention Time

Peak Height

Peak Area

Peak Start RT

Peak End RT

Peak Start Intensity

Peak End Intensity

Retention Time

Peak Height

Peak Area

Peak Start RT

Peak End RT

Peak Start Intensity

Peak End Intensity

2-16 Exporting Data

Exporting to a 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 was written by Jimmy Eng and John Yates (University of Washington). Further details can be obtained via the Internet at http://fields.scripps.edu/sequest.Note: This option is only enabled if BioLynx is installed.

To Export a SEQUEST File

1. Display the relevant centered MS/MS data file in the Spectrum window.

2. Select the Menu Bar File, Export SEQUEST file command. The Export SEQUEST compatible file dialogue is invoked.

3. Make the required changes, see below.

4. Select the OK button.

Export SEQUEST compatible file dialog box:

Export SEQUEST compatible file options

Precursor ion mass:

The precursor ion mass is picked up from the data file, if it was entered in the Function Editor, otherwise, a value may be entered in this text box.

Precursor charge state:

This value defaults to 2, it may be changed as required.

Exporting to a SEQUEST File 2-17

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

Mass Intensity

Mass Intensity

Mass Intensity

Mass Intensity

Each mass/intensity pair is separated by a space.

Partial sequence information:

Any known sequence information may be entered in this box.

File Path and Destination:

The location and file name 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, type a new destination in this box, or select the Browse button and select a new destination from the displayed dialogue.

Export SEQUEST compatible file options

2-18 Exporting Data

3 File Formats

Several MassLynx output files can be read independently of MassLynx.Contents:

Topic PageSample lists 3-2OpenLynx Batch Files 3-9OpenLynx report files 3-19MetaboLynx report files 3-34ProteinLynx report files 3-53

3-1

Sample lists

MassLynx Sample Lists are accessible by Microsoft Access 2000, which means their contents are readily available to numerous other Windows programs. Sample Lists created by the MassLynx system have the .SPL extension.

MassLynx Sample List:

Label Format DescriptionVERSION Double Database version number.FILE_NAME Text Raw data file name for this sample. This can

be the name, or a full path.FILE_TEXT Text Sample text description to be used for

sample; this will be recorded in data file header.

MS_FILE Text MS method parameter file to use when acquiring this sample. This can be the name, or a full path.

MS_TUNE_FILE Text MS tuning parameter file to use when acquiring this sample. This can be the name, or a full path. If this label is empty, the current tune settings are used.

INLET_FILE Text Inlet method parameter file to use when acquiring this sample. This can be the name, or a full path. This is only required if a programmable inlet acquisition system is being used to acquire sample.

INLET_PRERUN Text Inlet pre-run method parameter file to use prior to acquiring this sample. This can be the name, or a full path. If this label is empty, no pre-run is performed. This is only required if a programmable inlet acquisition system is being used to acquire sample.

3-2 File Formats

INLET_POSTRUN Text Inlet post-run method parameter file to use subsequent to acquiring this sample. This can be the name, or a full path. If this label is empty, no post-run is performed. This is only required if a programmable inlet acqui-sition system is being used to acquire sample.

INLET_SWITCH Text 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. This can be the name, or a full path. If this label is empty, no column switch pre-run is performed. This is only required if a programmable inlet acquisition system is being used to acquire sample.

AUTO_FILE Text Autosampler method parameter file to use when acquiring this sample. This can be the name, or a full path. This is only required if a programmable autosampler system is being used to acquire sample.

PROCESS Text External process to run to perform processing of sample. Can be name or full path. Only required if external processes are being run. If this label is empty, no process will be run for this sample.

PROCESS_PARAMS

Text Name of external process parameter file to use when processing samples. Available to external process via MLCURSMP.TXT file.

PROCESS_OPTIONS

Text Options to specify on command line of external process when it is executed.

ACQU_PROCESS Text External process to run when acquiring data. This can be the name, or a full path. This is only required if external processes are being run. If this label is empty, no process will be run for this sample.

MassLynx Sample List: (Continued)

Sample lists 3-3

ACQU_PROCESS_PARAMS

Text Name of external process parameter file to use when acquiring samples. Available to external process via MLCURSMP.TXT file.

ACQU_PROCESS_OPTIONS

Text Options to specify on command line of external process when it is executed.

PROCESS_ACTION

Text The Action that the process manager is to perform, should the external application return an error.

SAMPLE_LOCATION

Text Defines the location of the sample to be acquired on the autosampler bed. The format will depend on the type of autosam-pler being used.


3-4 File Formats

SAMPLE_GROUP Text Used to inform QuanOptimize that the opti-mization file for an Analysis sample should combine the optimizations for a number of compounds. 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, all the compounds will be optimized; one method file will be created and used for all the anal-ysis samples.If a sample group in the analysis sample list does not have a corresponding entry in the compound list, that group will not be run.In QuanLynx, used to define which group a sample belongs to. Each contiguous unique section will be regarded as a single experi-ment and reported as a group in the QuanLynx browser,For example, AAA | BA | BB B | AB | AA | B A forms three groups, A (4 samples) B (6 samples) A (4 samples).

JOB Text Job description for sample. Will be recorded in the data file header.

TASK Text Task description for sample. Will be recorded in the data file header.

USER Text User name for sample. Will be recorded in the data file header.


Sample lists 3-5

SUBMITTER Text Submitter for sample. Will be recorded in data file header.

CONDITIONS Text Condition information for sample. Will be recorded in the data file header.

TYPE Text Sample type to use during Quantify. Currently can be one of ANALYTE, BLANK, QC or STANDARD.

CONTROL Text Identifies whether the sample is a CONTROL or an ANALYTE.

ID Text The sample ID from OpenLynx.CONC_A … CONC_T

Text Twenty fields used to specify the concentra-tion levels of compounds within this sample. Used during the quantify process.

WAVELENGTH_A…WAVELENGTH_J

Double Ten fields used to specify wavelengths to analyze for this sample. Used during Open-Lynx processing.

MASS_A … MASS_DD

Text Thirty fields used to specify masses to analyze for this sample. Used during the OpenLynx process. Masses can be real numbers or chemical formulae.

COMPOUND_A…COMPOUND_DD

Text In ProfileLynx, allows the compound to be set on a per sample basis, rather than in the method.

FRACTION_FILE Text Raw data file name for this sample. Can be name or full path.

FRACTION_1 … FRACTION_10

Text References to the masses (MASS_A to MASS_T) to be monitored when performing fraction collection acquisition.

FRACTION_START

Text The first collection tube for the sample. Only applicable for sequential collection using FractionLynx.

INJ_VOL Double Volume of sample to inject when acquiring with programmable autosampler.

STOCK_DIL Double Not currently used, reserved for future use.


3-6 File Formats

USER_DIVISOR_1 Double Divisor used during concentration calcula-tion stage of Quantify. Defaults to 1 if not specified.

USER_FACTOR_1 … USER_FACTOR_3

Double Multipliers used during concentration calcu-lation stage of Quantify. Default to 1 if not specified.

SPARE_1 … SPARE_5

Text General purpose fields available to the User to store extra information about the sample.

HPLC_FILE Text The additional LC information for this sample (used by OpenLynx).

QUAN_REF Text 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 Text 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 (;), for example, A:1;A:2;A:3. The volume specified in the INJ_VOL field is drawn from each vial.

MOLFILE Text The file name of the ACD Labs .mol file.SUBJECT_TEXT Text Description of the subject used in the

experiment.SUBJECT_TIME Double Time at which the experiment was

performed on the particular subject.SUBJECT_GENDER

Text Male/Female

SUBJECT_SPECIES

Text Description of subject’s species.

METH_DB Text The full path to the quantify method file used for this sample group in QuanLynx.

CURVE_DB Text The full path to the calibration curve file used for this sample group in QuanLynx.


Sample lists 3-7

RETENTION_TIME_OFFSET

Double In staggered chromatography the time in this field is added to the MS retention time prior to being stored in the raw file.

PREP_INJ_VOL Double Volume used during AutoPurify in the prep stage if an analytical stage has been carried out.

QUALITY_REFERENCE

Text Set to X, Y, 1 or T if the peaks in this sample are to be used as reference peaks in Quan-Lynx and TargetLynx.

MIT_FILE Text MIT file to be written or read by the sample list.

FORMAT_FILE Text The full path of the format file associated with this sample list.

DUMP_FILE Text The full path to the text export file used for this sample group in QuanLynx.

Index Double Used internally to keep samples sequenced when editing.


3-8 File Formats

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\OALogin\BatchDB folder. When they have been acquired and processed they are moved to the Masslynx\OALogin\BatchDB\Processed folder.OpenLynx batch files can be used as input files for AutoLynx (see page 5-1) and they can be imported into MassLynx as Sample Lists (see page 1-3).

ParagraphsThe file holds section blocks of data called paragraphs. A file has a “Batch” paragraph and at least one “Plate” paragraph, followed by a paragraph for each sample to be analyzed. 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 always starts with the name of the section surrounded by square parentheses on a line by itself. i.e. [SectionName].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]

OpenLynx Batch Files 3-9

Data Item 1 Data Item 2[Plate:m] Data Item 1 Data Item 2[Sample:m:1] Data Item 1 Data Item 2[Sample:m:n] Data Item 1 Data Item 2

Batch BlockThe first paragraph in the file contains information that is pertinent to the whole batch.

Plate BlockFor each plate, the file contains a plate block that holds information that is pertinent to the whole plate rather than a specific well. Within this plate block is 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.

Sample BlockFor each sample to be analyzed there is a sample block that contains well position, and other information, specific to a certain sample.

FieldsSections have a group of fields, each field being on one line. The field name is the first item on the line, followed by “=” and then the data item for that field. The type of data depends on the field type.For example,

[Plate:3]JobCode=JB123456NumberOfWells=96

3-10 File Formats

CommentsA comment line is denoted by the first character being a semi-colon. A comment line can be anywhere in a section. Multiple line comments must have a semi-colon preceding each line.

File Format

[Batch]

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

Batch block:

Field/Section Name

Data Type Description

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 param-eters will be used.

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

EconomyScheduling

Integer Non-zero if the batch is to be run as a Night-Time task. Otherwise, it will be scheduled normally.

PriorityScheduling

Integer Non-zero if the 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.

ProcessParameters

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

Process Text Path of the External Program to be executed for sample processing. The directory is not neces-sary if the file exists in the current directory.

UserName Text Name of the User submitting the batch.BatchID Text Name of the batch.UserAddress Text The e-mail address to send batch results to.


SampleReportEnable

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

NumberOf-Plates (M)

Integer Number of plates in analysis.

InletPreRunMethod

Text The name of the acquisition Inlet pre-run method to be used. If not specified, no pre-run is performed.

InletPostRunMethod

Text The name of the acquisition Inlet post-run method to be used. If not specified, no post-run is performed.

InletSwitchMethod

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

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

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

Fraction-Method

Text The walk-up fraction method to use for acquisition.

AcquProcess Text The acquisition process to be used.AcquProcessParameters

Text The acquisition process parameter file to be used.

AcquProcessOptions

Text The acquisition process options to be used.

SampleReportScheme

Text The sample report scheme to be used for Per Sample Printing.

ActionOnError Text The action to be taken in the event of an error with a sample.

LabName Text Laboratory name.EmailResults Boolean True, if the results are to be emailed to the user.UserAddress Text Email address for mailing results. QuanL-ynxMethod

Text Name of the QuanLynx method used.

Batch block: (Continued)

3-12 File Formats

[Plate:N]

Where N = Plate Number

OAQuan-MethDB

Text Quantitation method template file name, used for processing the Quantitation results.

OverrideOpti-mise

Boolean Flag to enable/disable compound optimizations.

AcquireQuan-tify

Boolean Flag to enable/disable acquisition of the analyt-ical samples.

Plate block:

Field/Section 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 Open-Lynx Login program.

PlatePosition Text The description of the plate position, as co-ordi-nates for plate position in the autosampler bed.1 X,Y.2 Not used for a linear autosampler, for

example, HP GC type.where X and Y are integers.

Origin Text The description of the start well position, as a pair of coordinates for well position in plate, or an absolute position.WellAwellX(or wellXwellA), for example, A1Where 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.

Batch block: (Continued)


[Sample:N:M]

Where N = Plate Number, M = Well Number

UserName Text The name of the operator performing the analysis.

Rows Integer The number of rows on the plate.Columns Integer The number of columns on the plate.Track Text R=Rows, C=Columns, RS=Rows Snake,

CS=Columns Snake. NumberOf-Wells (M)

Integer The number of wells used in the plate, or vials in an autosampler tray.

Sample block:

Field/Section Name


Well (M) Text The description of the well position, as co-ordi-nates for well position in the 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 1. wellAwellY (or wellYwellA), for example,

B6, 6B or 2,6.2 2. Absolute rack position. For example, 18.where X and Y are integers and A is an alpha-betical character.

SampleType Integer Sample type.0 = Analyte, 1 = Standard, 2 = QC and 3 = Blank.

InletPreRunMethod

Text The name of the acquisition Inlet pre-run method to be used for this sample only. If speci-fied, this method supersedes the InletPreRunMethod entered in the [Batch] section. If not specified, the InletPreRunMethod from the [Batch] section is used (if there is one).

Plate block: (Continued)

3-14 File Formats

InletPostRunMethod

Text The name of the acquisition Inlet post-run method to be used for this sample only. If speci-fied, this method supersedes the InletPostRunMethod entered in the [Batch] section. If not specified, the InletPostRun-Method from the [Batch] section is used (if there is one).

NumberOf-Masses

Integer The number of masses defined.

Mass1 Float The first 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, this field is mandatory, unless a formula is supplied.

Mass2 Float The second Mass.MassN Float The nth Mass. NumberOf-MassFractionTrig-gers

Integer The number of fractions defined. MassLynx currently supports only one fraction mass.

Fraction1 Float The first mass to be monitored by the Fraction Collection system.

Fraction2 Float The second Fraction Mass. Not currently used.FractionN Float The nth Fraction Mass.NumberOfFormulae

Integer The number of formulae defined.

Formula1 Text The first chemical composition, if used.Formula2 Text The second chemical composition.FormulaN Text The nth chemical composition.NumberOfWavelengths

Integer The number of wavelengths defined.

Wavelength1 Text The first wavelength, if used.Wavelength2 Text The second wavelength.

Sample block: (Continued)


WavelengthN Text The nth wavelength. NumberOf-Concs

Integer The number of concentrations defined.

Conc1 Text The first concentration, if used.Conc2 Text The second concentration.ConcN Text The nth concentration. NumberOfFac-tors

Integer The number of user factors defined.

Factor1 Float The first User Factor, if required. MassLynx currently only supports one User Factor.

Factor2 Float The second User Factor. Not currently used.FactorN Float The nth User Factor. Not currently used.SampleID Text Sample Identifier.SampleDescription

Text Sample Description.

SampleGroup Text Sample Group.QuanRef Text Quantitation reference.Conditions Text 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.

NumberO-fUserFields

Integer The number of User fields defined.

User1 Text The first User Field, if required.User2 Text The second User Field.UserN Text The nth User Field.

Sample block: (Continued)

3-16 File Formats

An Example OpenLynx Batch FileBelow is an example of a small single sample generic sample list file for importing into MassLynx.[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

3-18 File Formats

OpenLynx report files

OpenLynx Report files (*.RPT) are created when samples are processed using the OpenLynx program. They are used as input files for the OpenLynx browser.

SectionsThe file holds section blocks of data. A section block always starts with the name of the section surrounded by square parentheses on a line by itself.The main body of the data is enclosed by a pair of braces, the opening and closing braces are the only characters on their respective lines.For example,[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.For example,[SectionName1]{Data[SectionName2]{Data}}

FieldsSections have a group of fields, with each field on one line. The field name is the first item on the line, followed by a list of tab-separated data items for that field. The type of data depends on the field type.

OpenLynx report files 3-19

For example,[SectionName]{FieldName1 Data1FieldName2 Data2_1 Data2_2...}

CommentsA 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.

Tabulated SectionsSome 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.For example,[TableSection]{;Field1 Field2Data1_1 Data1_2Data2_1 Data2_2...}

Free Format Text SectionsThe information in these sections contains free format text that may stretch over several lines. A line will be terminated with a <carriage return><linefeed> pair.

3-20 File Formats

File Section Descriptions

SAMPLE

Field/Section Name


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 the plate position in the rack and the well position in the 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 alpha-betical character.

FileName Text The MassLynx NT MS data file name.SampleType Integer Sample type unknown = 0, standard = 1 or QC =

2.SampleID Text MassLynx Sample List input field.SampleDescription

Text MassLynx Sample List input field.

Date Text The date that the MS data file was acquired.Time Text The time that the 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 a detailed description.Method Text The full path and name of the OLP method used.


Process Text The full path and name of the process, for example, OpenLynx.

MSTune Text The tune file used.MSMethod Text The MS method usedInletMethod Text The inlet method used.PreRun-Method

Text The Pre-Run method used.

PostRun-Method

Text The Post-Run method used.

SwitchMethod Text The switch method used.Fraction-Method

Text The fraction method used.

AcquisitionProcess

Text The acquisition process used

AcquisitionProcessParameters

Text The acquisition process parameters used

AcquisitionProcessOp-tions

Text The acquisition process options used

Injection-Volume

Float The injection volume used.

ReportScheme Text The batch report scheme used.SampleReportEnable

Int Whether per sample printing was enabled: 0 = disabled and 1 = enabled.

SampleReportFormat

Text The sample report scheme used.

AnalysisTime Float The time taken, in minutes, to analyze the sample.

ANALOG Section Analogue chromatographic data.COMPOUND Section Description of compound for testing.FRACTION Section Results of any FractionLynx fraction collection.PLATE Section Description of micro-titre plate.

3-22 File Formats

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.

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

INLET PARAME-TERS

Section Inlet device experimental record description.Note:Only ACE inlet devices are currently supported.


14:Vial One Y.Note: All spacings, etc., are given to 0.1 of a millimeter.For example,01TL,XY,LN,1:8,2:12,3:120.0,4:120.0,5:0.0,6:0.0,7:O,8:O,9:1250.0,10:870.0,11:400.0,12:90.0,13:80.0,14:130.0

This 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 = 12 mm.4:Column Spacing = 12 mm.5:Row Offset = 0.0 mm.6:Column Offset = 0.0 mm.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 = 125 mm.10:Plate Height = 87 mm.11:Vial/Well Depth = 40 mm.12:Vial/Well Diameter = 9 mm.13:Vial One X = 8.0 mm.14:Vial One Y = 13.0 mm.

3-24 File Formats

ANALOG

TRACE

This is a tabulated section.

PEAK

Field/Section 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.PEAK Section Section(s) that hold information about peak(s)

detected in the chromatogram.

Field Name Data Type Description

Time Float The time of the chromatographic point.Int. %Max Float The intensity of the chromatographic point as a

percentage of the maximum intensity.


Peak ID Integer Peak Identification number.Peak Ref Integer Peak Reference Number. Reserved for internal

use.Time Float Peak retention time, in decimal minutes.Peak Float +

FloatThe peak start and end retention times, in decimal minutes. Two floats separated by a TAB character.

Intensity Float + Float

The peak baseline start and end intensities. 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. The field is only

output if RT Index has been calculated.RT LogP Float Retention time LogP for peak. The field is

output if RT LogP has been calculated.Calc Conc Float Calculated concentration for peak. The field is

output if it has been calculated.Calc Amount Float Calculated amount for peak. The field is output

if it has been calculated.Response Test Integer The result of the chromatogram test. 0=test was

run, but not on this peak; 1=test was run on this peak and passed; 2=test was run on this peak and failed.

3-26 File Formats

COMPOUND


FRACTION



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.


Mass Float The mass collected.Org. Target Float The original mass minus any adducts.Ion Mode Text The ionization 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 collec-

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

in.


FUNCTION

SPECTRUM

Field/Section Name


Function Integer The MassLynx MS data function number.IonMode Text The type of ionization mode, for example,

AP+.Type Text The type of MS scan function, for example,

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.

CHROMATO-GRAM

Section Chromatographic data. There can be more than one CHROMATOGRAM section in a function.

Field/Section Name


ProcDesc Text Description of processing performed on spec-trum, for example, Combine (54:56-(38:39+74:75))

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

State Text The result of testing the quality of the mass spectral data. Only OK means it is a good spectrum.

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 inten-

sities in the spectrum.

3-28 File Formats

MASSES


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.

ELEMENTAL Section Section holding results of elemental calcula-tions. This section will not be created if no calculations are defined.

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

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


Mono. Mass Float The input mass.Exp. Mass Float The expected mass due to adduction.Obs. Mass Float The mass that was actually observed.Int. %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


ELEMENTAL

This is a tabulated section that contains results of elemental calculations if defined, otherwise this section does not appear.


Mass Float The input mass.Found Boolean True if any of the possible adduct ions has been

found for this compound.Rel. 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.QCIntensity Text This field is only present if this is a QC sample

and is only present in the RESULTS section of the spectrum in which the target spectral peak was found. If the intensity of the target spectral peak is above the value specified, the value is “QC OK”, otherwise it is “QC Fail – Intensity”.


Mass Float The actual observed mass for which elemental composition was searched.

Calc. Mass Float The calculated mass of reported formula.mDa Float The difference between the observed mass and

the calculated mass, in mulligatawnies.

3-30 File Formats

SEARCH

This section contains Spectrum library search results if the library search was defined, otherwise this section does not appear.

PPM Float The difference between the observed mass and the calculated mass, in parts per million.

DBE Float Double Bond Equivalence.Formula Text Representation of the calculated chemical

formula, for example, C19 H14 O2

Score Int The goodness of fit of the spectrum compared to a calculated isotope model for the specified formula. The formula with the best fit has a score of 1, the next best formula has a score of 2, etc.


Library Text The name of the 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

MS



Entry Integer The library entry number the 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.Flags Text Library entry general purpose flags.


Mass Float The observed mass of peak.% BPI Float The Intensity of peak as a percentage of the base

peak.

3-32 File Formats

CHROMATOGRAM

QC

INLET PARAMETERS

This is a free format text section.

Field/Section Name


TraceNumber Integer Number of chromatogram trace. Reserved for internal use.

Description Text The description of the chromatogram data source.

ProcDesc Text Description of processing performed on chro-matogram, for example, 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. The format is the same as for the TRACE component of the ANALOG paragraph above.

PEAK Section Section(s) that hold information about peak(s) detected in the chromatogram. The format is the same as for the PEAK component of the ANALOG paragraph above.

QC Section Section that holds information about the QC result. This section is only present if this is a QC sample.

Field/Section Name


RT_AreaQC Text The result of the QC test on this chromatogram.The possible values are “OK”, “QC Fail - PeakX RT” and “QC Fail - PeakX Area” where X is the number of the peak specified in the setup (1, 2 or 3).


MetaboLynx report files



FieldsSections have a group of fields, with each field on one line. The field name is the first item on the line, followed by a list of tab-separated data items for that field. The type of data depends on the field type.For example,[SectionName]{FieldName1 Data1FieldName2 Data2_1 Data2_2

3-34 File Formats

...}

CommentsA 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.

Tabulated SectionsSome 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.For example,[TableSection]{;Field1 Field2Data1_1 Data1_2Data2_1 Data2_2...}

Free Format Text SectionsThe information in these sections contains free format text that may stretch over several lines. A line will be terminated with a <carriage return><linefeed> pair.

MetaboLynx report files 3-35


SAMPLE

Field/Section Name


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.

SampleType Text MassLynx Sample List input field. “QC” for control sample, “Analyte” for metabolized sample.

Injection-Volume

Float MassLynx Sample List input field. Volume of sample injected, in microliters.

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.

FileName Text The MassLynx NT MS data file name.

3-36 File Formats

Well Text The description of the well position, as a pair of co-ordinates for the plate position in the rack and the well position in the plate, or an absolute position. There are three formats for Well:1 plateX,plateY:wellX,wellY2 plateX,plateY:wellAwell1 (or well1wellA)3 Absolute rack position.where X and Y are integers and A is an alpha-betical character.The file section can be flagged as containing MSMS data by adding the string “MSMS” to the start of the plate part of the well descriptor, i.e.1 MSMSplateX,plateY:wellX,wellY2 MSMSplateX,plateY:wellAwell1 (or

well1wellA)3 MSMS:Absolute rack position.

SampleID Text MassLynx Sample List input field.SampleDescription

Text MassLynx Sample List input field.

Date Text Date that the MS data file was acquired.Time Text Time that the MS data file was acquired.JobCode Text MassLynx Sample List input field.TaskCode Text MassLynx Sample List input field.UserName Text The 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.COMPOUND Section Description of parent drug(s); the masses taken

from the MassLynx Sample List.


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).

FUNCTION Section Function header and chromatogram trace data. There is one FUNCTION section per MassLynx data function. Old format files will contain all function information here.

FUNCTION_APPEND <n>

Section Optional section.Chromatogram peaks and test results for func-tion <n> previously declared in report. There is one FUNCTION_APPEND section per Mass-Lynx data function.

EXPECTED METABO-LITES

Section Description of metabolites searched for.

UNEX-PECTED METABO-LITES

Section Description of potential metabolites found as a result of comparing the sample with a control.

ELEMENTAL Section Table of elemental composition results for the unexpected metabolites. These sections will only be present if the Elemental Composition option was selected in the MetaboLynx Setup program. If present, there will be one ELEMENTAL section for each reported unexpected metabolite mass.

MSMS CORRELA-TION

Section Table of correlation results of MS/MS spectra.

INLET PARAME-TERS

Section Inlet device experimental record description. For future use.

3-38 File Formats

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 Rows2: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: All spacings, etc are given to 0.1 of a millimeter.An example of the plate field is as follows:01TL,XY,LN,1:8,2:12,3:120.0,4:120.0,5:0.0,6:0.0,7:O,8:O,9:1250.0,10:870.0,11:400.0,12:90.0,13:80.0,14:130.0

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 = 12 mm.


4:Column Spacing = 12 mm.5:Row Offset = 0.0 mm.6:Column Offset = 0.0 mm.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 = 125 mm.10:Plate Height = 87 mm.11:Vial/Well Depth = 40 mm.12:Vial/Well Diameter = 9 mm.13:Vial One X = 8.0 mm.14:Vial One Y = 13.0 mm.

COMPOUND


FUNCTION / FUNCTION_APPEND

Note: Old format files contain all information in a [FUNCTION] section with no [FUNCTION_APPEND] section.


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.

Field/Section Name


Function Integer The MassLynx MS data function number.IonMode Text The type of ionization mode, for example,

ES+. Not present in analog function.

3-40 File Formats

Type Text MS function: The type of scan function, for example, TOF MS for full scan Time of Flight.PDA function: “Diode Array”.Analog function: Field not present.

Description Text MS/PDA function: A brief description of the scan function.Analog function: “ANALOG”.

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.Cone Voltage Integer The cone voltage, in volts.SPECTRUM Section MS data and results of testing. There can be

more than one SPECTRUM in a function. CHROMATO-GRAM

Section Chromatographic data (header and trace). Old format files will contain all information in this section.

CHROMATOGRAM_APPEND <n>

Section Optional section.Chromatographic data (peak information) for chromatogram <n> previously declared in report.


SPECTRUM

Field/Section Name


ProcDesc Text Description of processing performed on spectrum.

State Text The result of testing the quality of the mass spectral data. Only OK means it is a good spectrum.

Peak ID Integer Spectrum Peak Identification number. This is the unique number of the peak over all chro-matograms, in time order.

Peak Ref Integer Peak Reference Number. Reserved for internal use.

Peak Cluster ID

Integer If this peak is considered to be the same as another, according to Setup parameter Min Peak Separation, 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 this is an analyte sample and this spectrum was matched with a similar one in the control, this value is the Peak ID of the control spec-trum. 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 inten-

sities 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.Process Integer The number of the MassLynx saved mass spec-

trum. Only present if processed spectrum was saved with data file.

3-42 File Formats

MASSES


RESULTS


MASSES Section Section describing the masses searched for in the spectrum. This includes all adducts.

RESULTS Section Section describing the search results of the expected mass(es).

MS Section Section that will hold all the mass-intensity pairs, for this mass spectrum.


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.


Mass Float The input mass.Found Boolean

integer1 (true) if any of the possible adduct ions has been found for this mass; otherwise 0 (false).

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

% Purity Float A measure of the contribution of this mass to the spectrum as a percentage of the TIC. This includes all MS peaks associated with this mass.


MS

This is a tabulated section, containing mass-intensity pairs.

CHROMATOGRAM / CHROMATOGRAM_APPEND

Note: Old format files will contain all information in a [CHROMATOGRAM] section with no [CHROMATOGRAM_APPEND] section.

Confirmed Boolean integer

1 (true) if optional confirmation tests have passed; 0 (false) if optional confirmation tests have failed. If the field is not specified then its value is 1 (regarded as true).

Status Text Description of confirmation failure.


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

peak.

Field/Section Name


TraceNumber Integer Number of chromatogram trace. Reserved for internal use.

TraceNum-berInFunction

Integer Number of chromatogram trace relative to the start of the function. Reserved for internal use.

Description Text The description of the chromatogram data source.

ProcDesc Text Description of integration processing performed on chromatogram, for example, Smooth (Mn, 2x2).

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

3-44 File Formats

TRACE

This is a tabulated section containing pairs of time and intensity. The section has no header.

PEAK

IntensityShift Float Optional field used when the original chromato-gram contained negative intensities, and all the intensities were shifted by this amount to bring the minimum intensity up to zero.

TRACE Section A section that holds the chromatographic data.PEAK Section Section(s) that hold information about peak(s)

detected in the chromatogram.


Time Float The time of the chromatographic point.Int. %Max Float Intensity of the chromatographic point as a

percentage of the maximum intensity.


Peak ID Integer Peak Identification number. This is the unique number of the peak over all chromatograms, in time order.

Peak Ref Integer Peak Reference Number. Reserved for internal use.

Peak Cluster ID

Integer If this peak is considered to be the same as another, according to Setup parameter Min Peak Separation, 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 Peak height.AreaAbs Float Peak area.Area %BP Float If a metabolite was found in this peak, this is 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 If a metabolite was found in this peak, this is 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.

3-46 File Formats

EXPECTED METABOLITES



Compound Float Index into the list of Compounds. The Compound list starts with entry zero. For example, if this metabolite is related to the first entry in the Compound list, this field will be 0; if this metabolite is related to the second entry in the Compound list, this field will be 1.

Precursor Float Mono-isotopic mass to be searched for, it is the sum of the parent drug mass and the metabolite.

Metabolite Float Mass of the metabolite. If the metabolite was found, this is the exact mass difference between the mass found and the theoretical parent drug mass. Otherwise it is the mass of the metabolite, as specified on the MetaboLynx Setup Metabo-lites tab page.

Found Boolean integer

1 indicates mass was found, 0 not found, or not wanted.

Formula Text Formula of the metabolite, where known. This is an absolute formula if the parent mass was specified as a formula (for example, C18H24O2), or a relative formula if the parent mass was specified as a mass (for example, +CO2). If the metabolite is not recognized, the formula is 0 (zero). The value of this field can be modified using the MetaboLynx Browser.

ChroTrace Integer list

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 peaks in which the mass was found. Each peak is identi-fied by a string of text containing four stroke-separated numbers in the following format:peak-number/func-tion-number/trace-number/mass-foundwhere 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. The value of this field can be modified using the MetaboLynx Browser.

mDa Float list

Difference between observed mass (or masses if more than one entry in the Peak field) and calcu-lated mass of the suggested formula, in milliDaltons. If the Formula field is empty, mDa cannot be calculated and is also empty.

PPM Float list

Parts Per Million difference between observed mass (or masses if more than one entry in the Peak field) and calculated mass of the suggested formula. If the Formula field is empty, PPM cannot be calculated and is also empty.

MSMS Boolean Flag to indicate whether or not this metabolite is suitable as a Set Mass for the AutoStart MS/MS Processing. By default it has the same value as the Found field. The value of this field can be modified using the MetaboLynx Browser.

Confirmed Boolean Flag to indicate whether or not this entry has been confirmed as a metabolite. By default all found metabolites in the expected list have this flag set to true; all not found expected metabo-lites and unexpected metabolites have this flag set to false. The value of this field can be modi-fied using the MetaboLynx Browser.

Molfile Text Name of the molecule file for this metabolite.

3-48 File Formats

UNEXPECTED METABOLITES

This is a tabulated section with the same format as the Expected Metabolites section.

ELEMENTAL

This section contains the results of elemental calculations. These sections will only be present if the Elemental Composition option was checked in the MetaboLynx Setup program. If present, there will be one ELEMENTAL section for each reported unexpected metabolite mass.

MSMS CORRELATION

This section contains the results of an MS/MS Correlation analysis. It is only present if the Compare MS/MS Spectra option was selected on the MS/MS Settings tab page in the MetaboLynx Setup program and the data file contains MS/MS data.


Mass Float Actual observed mass used as input for elemental composition.

Calc. Mass Float Calculated mass of reported formula.mDa Float Difference between observed mass and calcu-

lated mass in milliDaltons.PPM Float Difference between observed mass and calcu-

lated mass in parts per million.DBE Float Double Bond Equivalence.Formula Text Representation of calculated chemical formula.

Field/Section Name


MassWindow Float The mass window is the full window used around a peak for mass matching between MS/MS spectra, i.e. Mass ± 0.5*Mass Window.


METABOLITES

This is a tabulated section. There is one entry for every MS/MS chromatogram peak in the data file.

ParentEntry Integer The entry in the METABOLITES section that has been selected as the most likely parent. It is the most intense parent drug spectrum, that is, the one with the largest BPI.The value of this field can be modified using the MetaboLynx Browser.

METABO-LITES

Section One entry for each MS/MS spectrum. The section provides details of the precursor metabo-lite and its spectrum, along with status.

CORRELA-TION TABLE

Section Entry1 spectrum is correlated with Entry2 spec-trum (entry numbers as used in the METABOLITES table) and the masses from spectrum Entry1 are listed in column Entry1MassesMatched.


Entry Integer Index into this table. The list starts with entry zero. It is referenced by ParentEntry and Entry1,Entry2 of Correlation Table.

SetMass Float Set Mass for the spectrum. MS/MS switching takes place on this mass and the spectrum contains its daughters.

ParentMass Float Adducted parent mass for the function in which this spectrum was acquired.

TraceNum Integer The number of the trace in which this MS/MS peak was found.

Metabolite Float Mass of the metabolite. It is the mass difference between the mass of the parent drug and the Set Mass.

3-50 File Formats

CORRELATION TABLE

This is a tabulated section. Each MS/MS spectrum is correlated with every other MS/MS spectrum.

Status Boolean integer

Value 1 indicates that there is at least one mass for this spectrum in the Correlation Table, or at least one mass in NeutralLosses. If both the Correlation Table and NeutralLosses are empty for this spectrum, the status is 0.

PeakID Integer The unique Peak ID that identifies the chro-matogram peak. For internal use only.

Cluster Integer The cluster number in which this peak exists. It is the peak label, common to all chromatogram peaks that occur at the same time.

Time Float Retention time of the mass spectrum, in decimal minutes.

NeutralLoss Text The common neutral loss between metabolite and parent drug. It is the mass difference between the actual m/z found in the spectrum and the parent mass. Recorded as m/z found – delta mass. The field is allowed to contain either “0” or a non-numeric string if the mass was not found in the spectrum.

Spare Left blank

This field is presently unused.

Name Text Descriptive name of the metabolite.


Entry1 Integer Index into the metabolite table.Entry2 Integer Index into the metabolite table.Entry1Masses Matched

Float list

List of Common Product Ions.It is the comma-separated list of actual masses found in the metabolite spectrum Entry1, that match with masses in spectrum Entry2 inside MassWindow.


MOLFILE LIST

MOLFILE

This is a free format text section, which contains a direct copy of the molfile.

INLET PARAMETERS

This is a free format text section.

Entry1NeutralLosses Matched

Text list

List of Neutral Losses from All Parent Spectrum Masses. It is the comma-separated list of actual masses found in the metabolite spectrum Entry1, that match with neutral losses of masses in spectrum Entry2 inside MassWindow. The neutral losses are calculated as the mass differences between the MS/MS Set Masses and the parent drug mass. Each match is recorded as m/z found(parent spectrum mass – neutral loss).

Entry1CommonNeutralLosses

Text list

List of Neutral Losses. It is the comma-sepa-rated list of neutral losses found in the metabolite spectrum Entry1 that resulted in metabolic pathways generated from masses in spectrum Entry2 inside MassWindow. Each match is recorded as m/z found(spectrum2 mass – neutral loss)

Field/Section Name


Reference Text The reference for this list of molfiles. It is made up of the report file name, and underscore, then the metabolite name.

MOLFILE Section One section for each molfile.

3-52 File Formats

ProteinLynx report files



FieldsSections have a group of fields, with each field on one line. The field name is the first item on the line, followed by a list of tab-separated data items for that field. The type of data depends on the field type.For example,[SectionName]{FieldName1 Data1FieldName2 Data2_1 Data2_2

ProteinLynx report files 3-53

...}

Tabulated SectionsSome 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.For example,[TableSection]{;Field1 Field2Data1_1 Data1_2Data2_1 Data2_2...}


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


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,wellY2 wellAwell1 (or well1wellA)3 Absolute rack position.Where X and Y are integers and A is an alpha-betical character.

Data_File_Name

Text The MassLynx NT MS data file name.

3-54 File Formats

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.

FUNCTION Section MS function data and results. There is one FUNCTION section per MassLynx MS data function.


FUNCTION

PROCESS_PARAMETERS

Field/Section Name


Function Integer The MassLynx MS data function number.IonMode Text The type of ionization mode, for example, AP+.Type Text The type of MS scan function, for example, MS

for full scan.Description Text A brief description of the MS scan function.PROCESS_PARAME-TERS

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

SEARCH_PARAME-TERS

Section MS search parameter data. There is only one SEARCH_PARAMETERS section in a FUNCTION.

SEARCH_RESULTS

Section MS search results. There is only one SEARCH_RESULTS section in a FUNCTION.

SPECTRUM Section MS raw spectrum data. There is only one SPECTRUM in a function.Note: Only present for MALDI data.

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


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.

Polynomia-lOrder

Int Number indicating the polynomial order used in background subtraction.

3-56 File Formats

BelowCurve Int Number indicating the below curve percentage used in background subtraction.

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

Float Number of channels smoothed.

NumberOfSmooths

Int Number of smooths performed.

Smooth_Mode Text The smoothing method used, for example, 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.


SEARCH_PARAMETERS


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 databaseSearchServer Text Name of search serverOutput_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 the Treat I/L and Q/K as equivalent option is

selected, otherwise 0Do_Monoiso Boolean 1 if the Search monoisotopic peaks option is

selected, otherwise 0.MAX_HITS Integer Maximum number of hits to return from the

search. 0 if All selected.

3-58 File Formats

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.

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.

3-60 File Formats

MODIFIERS

SEARCH_RESULTS

SPECTRUM

MONOISOMASSES


Name of modifier

Boolean 1 if the Always use this modifier option is selected, 0 if Use when needed to match peptide option selected.


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 section.

Field/Section Name


LockMassUsed Float The lock mass value usedMONOISOMASSES

Section MS monoisomasses data. There is only one MONOISOMASSES in a SPECTRUM.

CORRECTION_FACTOR

Section MS raw spectrum data. There is only one CORRECTION_FACTOR in a SPECTRUM.


<Blank> Float One monoisomass value per line (without a field name). There can be more than one line.


CORRECTION_FACTOR

PEAK_LIST

Bio-Rad File Descriptions

If the Bio-Rad option was selected, a SampleID.txt file is produced with the following format.


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


Output_Filename

Text The name of the Mascot or SEQUEST compat-ible peak information file.For example, Mascot fileC:\TEMP\hilo07.004.2.1.pklwhere 004 = the scan number2 = the function number1 = the charge stateSEQUEST fileC:\MASSLYNX\hilo07.0100001.dtawhere 0001 = the scan number01 = the function number.


VIEW_ONE Section Database protein entry information. There is only one VIEW_ONE section per HIT.

3-62 File Formats

VIEW_ONE

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

VIEW_TWO Section Database match information. There is only one VIEW_TWO section per HIT.

VIEW_THREE Section Database protein sequence. There is only one VIEW_THREE section per HIT.

Field Name DescriptionID 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 that 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).


VIEW_TWO

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

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, for example, Protein Data Bank (PDB).

KW Keyword lines provide information that 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.

Field Name DescriptionID 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 that was the source of the sequence.

Number of matched peptides

The number of matched 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.

3-64 File Formats

VIEW_THREE

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

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, 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.


3-66 File Formats

4 DataBridge

Contents:

Topic PageDataBridge file conversions 4-2Converting a file with DataBridge 4-3

4-1

DataBridge file conversions

DataBridge is the file conversion program for use with MassLynx; it can perform the following file conversions:

DataBridge allows data to be imported into MassLynx from other sources. This can be LAB-BASE data, ASCII data, PDP11 data, OPUS Data or data which is in the NetCDF format. NetCDF is the common data format for mass spectral data specified by the American Instrumentation Association (AIA). NetCDF allows interchange of mass spectral data from different manufacturer's instruments. DataBridge will convert any non-library data in NetCDF format to MassLynx format for analysis with the MassLynx software. When converting from PDP11 data, the data must be mass-measured on the PDP11 prior to conversion, unless the data has been acquired on a TRIO-2 or a 12-250 instrument.

DataBridge file conversions:

From: To:MassLynx NetCDF MassLynx ASCII LAB-BASE MassLynx NetCDF MassLynx ASCII MassLynx PDP11 MassLynx OPUS MassLynx Stables OS/2 MassLynx LAB-BASE Library

MassLynx Library

JCAMP Library MassLynx LibraryMassLynx Library

JCAMP Library

4-2 DataBridge

Converting a file with DataBridge

The DataBridge program may be run from the Windows Start Menu, MassLynx Folder. Alternatively, DataBridge may be selected in the MassLynx Sample List Process column.

Starting the DataBridge Program from the Windows Start Menu1. Run DataBridge by selecting the Windows Start button, then selecting

Programs > MassLynx > Databridge; the DataBridge dialog is invoked.

2. To define the type of conversion required, select the Options button; the DataBridge - Options dialog is invoked.

3. Select the appropriate file type to convert from, in the Source frame.

4. Select the appropriate file type to convert to, in the Target frame.

5. Select the OK button; the DataBridge - Options dialog is closed.

6. To select the source file select the Select button; the Source file select dialog is invoked.

7. Select the file, or files, to be converted. Tip: Information about a file can be obtained by selecting the File info button. This invokes the File Information dialog that displays information such as time and date of acquisition, instrument, number of scans, etc. Select the OK button to close the dialog.

8. Select the Source file, select dialog OK button; the dialog is closed.

9. To select the directory for the target file, select the Directory button; the Target directory select dialog is invoked.

10. Select the drive and directory where the converted files are to be saved. DataBridge will remember the last directory used for each target file type.

11. Select the OK button; the Target directory select dialog is closed.

12. By default the converted file(s) will have the same filename(s) as the original file(s) (but with the appropriate file extension). If a single source file has been selected, a new name for the converted file can be entered in the Target frame Filename: text box.

Converting a file with DataBridge 4-3

13. Select the Convert button to convert the selected file(s). A scrolling display details the progress of the conversion. Tip: If an ASCII file is being converted to MassLynx spectrum format, the Header Information dialog is invoked, see below.

14. Select the Close button to exit DataBridge.

Running the DataBridge Program from the MassLynx Sample ListTip: Before first running the DataBridge Program from the MassLynx Sample List, the options must be selected as described above.

1. Double-click on the Process column cell for the sample for which DataBridge is to run; a drop-down list is invoked.

2. Select the Dbridge option.

3. Start the data acquisition; the DataBridge Program will run as part of the acquisition process, using the current options.

To Convert an ASCII File to MassLynx FormatIt is possible to create a single MassLynx format spectrum from an ASCII file. This can be used, for example, to create a spectrum for a user library. The ASCII file can be created using any plain text editor, for example, Windows Notepad. The ASCII file must contain pairs of mass and intensity values in ascending order from low to high mass. The values can be separated by any separator, for example, a TAB character or a comma. The final value in the file must also be followed by a separator. When the DataBridge dialog Convert button is selected, the Header Information dialog is invoked. The information entered here will be displayed when the converted file is selected using the MassLynx Data Browser dialog, see Opening Data Files: The MassLynx Window Data Browser Dialog. To display the spectrum as a continuum spectrum select the Continuum option; leave it deselected to display the spectrum as a centroid spectrum.

4-4 DataBridge

5 AutoLynx

Contents:

Topic PageIntroduction to AutoLynx 5-2Starting AutoLynx 5-3AutoLynx settings 5-4Interfacing with external programs 5-7

5-1

Introduction to 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 (for example, in Visual Basic) to:

• Take information from other software packages (for example, LIMS systems) and automatically create OpenLynx Batch Files (see page 3-9).

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

• Monitor the progress of a batch file.• Automatically read the acquired data, or processed results, for further

processing and/or exporting into other software packages.• Create an abort file when necessary to terminate the MassLynx queue.

In addition to batch files, AutoLynx will also accept tab or comma delimited text files as input. These files must be in the format defined in the Import Worksheet section (see page 1-3).

5-2 AutoLynx

Starting AutoLynx

In Windows Explorer, double click on the AutoLynx file in the main MassLynx directory; the AutoLynx dialog is invoked.Tip: Normal Windows procedures may be used to create a Shortcut to the file.This dialog displays the batches in the AutoLynx queue, and the date and time they were submitted. If MassLynx is not running, a message informing the User that MassLynx must be running to submit batches is also displayed.

Starting AutoLynx 5-3

AutoLynx settings

Select the AutoLynx dialog box Settings button to invoke the AutoLynx Settings dialog; this has four pages:

Directories Page:

Directory DescriptionQueue Contains all the Batch files in the current AutoLynx queue.

This directory must exist. Processed Contains all successfully completed Batch files and any asso-

ciated results files. This directory will be created if it does not exist.

Failed Contains all unsuccessful, or aborted, Batch files and any associated results files. This directory will be created if it does not exist.

Control Page:

Parameter DescriptionStatus file The name of the file indicating the current AutoLynx queue

status. If AutoLynx has batches in its queue, this file will exist; it will be deleted once the queue is empty. By moni-toring this file, an external application can determine when all the batches submitted to the AutoLynx system have been processed.

Abort file The name of the file that AutoLynx will monitor to determine if the current batches in the queue should be aborted. If the abort file exists the current batch will be stopped and all batches in the queue will be moved to the Failed directory. Any batch file written to the Queue directory when abort is set will be immediately moved to the Failed directory. Once all the batches in the queue have been removed the Status file will be deleted. The external application must create this file to cause an abort, the file must then be deleted to clear the abort.

5-4 AutoLynx

Queue Filter The batch file extension type. All files with this extension in the Queue directory will be added to the AutoLynx queue. Files of the following formats are supported:OpenLynx batch file (*.olb)MassLynx sample list (*.spl)Comma delimited value text files (*.csv, *.txt)Tab delimited text files (*.tab, *.tdl, *.txt)Tab and comma delimited text files allow AutoLynx to auto-matically run the spreadsheet that would be otherwise submitted to MassLynx by the Menu Bar File > Import Worksheet command, see page 7).

Queue Delay The minimum time, in seconds, between a batch being written to the Queue directory and it being submitted to MassLynx for processing. This is intended to ensure that creation of the batch file by the external program has been completed before the batch is processed.

Operations Page:

Parameter DescriptionAcquire Performs a data acquisition.Process Runs the process specified in the sample list.Quantify Performs a quantification on the entire sample listProfile Performs candidate profiling on the entire sample list.

Results Page:

Parameter DescriptionPrint Report Prints the batch results report file. If *.olb files are to be

created and OpenLynx has been specified as the processing type, OpenLynx Browser *.rpt files are created. The format of this file is defined in the OpenLynx Browser Report Scheme Settings, refer to the "OpenLynx User's Guide" for details.

Control Page: (Continued)

AutoLynx settings 5-5

Create Summary File

Select this option to create a tab-delimited text file containing a summary of the Batch processing results. If OpenLynx is specified as the processing type, the fields output in the Results Summary file are defined in the Open-Lynx Browser Report Scheme Settings, refer to the "OpenLynx User's Guide" for details.

Default Report Scheme

Enter the name of the OpenLynx Browser report scheme to be used if no scheme is defined in the Batch file. If this field is empty, and no scheme is defined in the batch file, the last scheme selected in the OpenLynx Browser will be used, refer to the "OpenLynx User's Guide" for details.

OpenLynx Browser Location

Enter the location of the OpenLynx Browser program; this will normally be in the MassLynx installation directory. Selecting the browse button will invoke a browser to help locate the required executable file.

Results Page: (Continued)

5-6 AutoLynx

Interfacing with external programs

To add batches to the AutoLynx queue, place the relevant batch file in the Queue directory. AutoLynx displays a list of the batches currently in the queue. Batches will be submitted to MassLynx for acquisition/processing in the order that they were placed in the Queue directory. If MassLynx is not running, batches can still be queued, but they will not be processed until MassLynx is active. When a batch has been completed, the batch file, and all other files with the same base name as the batch (for example, OpenLynx report files), will be moved from the Queue directory. If the batch was completed successfully they will be moved to the Processed directory; if the batch failed, or an abort was set, they will be moved to the Failed directory.

Monitoring the Queue StatusThe state of the queue can be determined by monitoring the AutoLynx Status file. This file will only exist if the AutoLynx queue is not empty, or if MassLynx is currently processing a batch; this file will be deleted once the queue becomes empty and MassLynx is idle. By monitoring this file, an external process can determine when all the batches submitted to the queue have been run.

Aborting the QueueAn external program can abort all batches in the queue, and stop the acquisition of the current batch, by creating the Abort file. AutoLynx looks for the Abort file and, if found, all batches will be removed from the queue. While the Abort file exists, any batch placed in the Queue directory will be immediately aborted. The Status file will be deleted once all batches have been removed from the queue and MassLynx is idle. The external program must monitor the Status file and when this has been deleted, delete the Abort file. Tip: AutoLynx does not try to open and read the contents of the Abort file.

Interfacing with external programs 5-7

Accessing ResultsIf the batch was successfully processed and the AutoLynx Settings dialog, Results page, Print Report option was selected, a report will be printed on successful completion of a batch. Tip: OpenLynx processing must have been performed on the samples in the batch to produce the necessary OpenLynx Report.If the batch was successfully processed and the AutoLynx Settings dialog, Results page, Create Summary File option was selected, a file batch_name.txt will have been created in the Processed directory. This is a tab-delimited text file, the contents of which are dictated by the OpenLynx Report Scheme Settings used. Tip: The Results Summary file is produced by the OpenLynx Browser program which requires an OpenLynx Report file as input (batch_name.rpt). Consequently, OpenLynx processing must have been performed on the samples in the batch to produce the necessary OpenLynx Report.

File Usage

File Name Description Status File User definable in

the Settings dialog. Default: c:\sampling.sem

Exists if AutoLynx is busy, deleted when all batches have been processed.

Abort File User definable in the Settings dialog. Default: c:\abort.sem

Created by external applications to abort the AutoLynx queue.

OpenLynx Batch File

Batch_name.OLB Placed in Queue directory to submit batch.

Describes the samples and processing information for a batch. Moved to the Processed, or Failed, directories after being processed. Refer to OpenLynx Batch Files on page 3-9 for more information.

5-8 AutoLynx

OpenLynx Report File

Batch_name.RPT Generated by OpenLynx processing of the sample. Placed in the Processed directory upon successful completion. Refer to OpenLynx report files on page 3-19 for more information.

Results Summary File

Batch_name.TXT Tab-delimited results file gener-ated by OpenLynx Browser. The format of the file is User-definable through the Browser Report Schemes Settings. Placed in the Processed directory upon successful completion.

Interfacing with external programs 5-9

5-10 AutoLynx

6 Database Logging and MassLynx Status

Contents:

Topic PageIntroduction 6-2Database Logging 6-3MassLynx Status 6-4

6-1

Introduction

The MassLynx status and database logging files are controlled from the Options dialogue, which is displayed by selecting Options from the MassLynx Tools shortcut bar.

Options dialog box:

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

6-2 Database Logging and MassLynx Status

Database Logging

Details of every acquired sample can be written to a Access database file. The format of the file will be the same as that used for importing Access databases (see page 1-3).Check the Log Samples box to write sample information to a database.The default database and location is C:\MassLynx\samples.mdb. To change this, select the Database button, select a directory using the invoked Select File Name dialogue, enter a new file name, and select the Open button.Note: If using an existing database, it must have the correct format already set up, as described on page 1-3).

Database Logging 6-3

MassLynx Status

The status.ini file contains details of the current status of the Mass Spectrometer, LC system, and the MassLynx Queue.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, select the File Name button, select a directory using the invoked Select File Name dialogue, enter a new file name, and select the Open button.Note: Do not use the name of an existing *.ini file in the current directory, as this will cause problems with other software.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 determine when data has been acquired and is ready for further processing.

File FormatThe format of the status.ini file is as follows:[MS Status]Operate=2Status=Scanning

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

[Queue Status]Queue Paused=0Process Running=11=testSamples 1 to 5: Sample 1 AcquiringRunning2=test1Samples 1 to 5: Waiting


3=test2Samples 1 to 2: WaitingTotal samples=12

[Disk Space]CurrentDrive=C:FreeDiskSpace=365925888

[Time Stamp]Time=10-012-2001,17:22:52

MS StatusThe MS Status section shows mass spectrometer information.

Operate

This shows the state of the mass spectrometers high voltage electronics. It has two values:

Status

This shows the status of the mass spectrometer. It can have one of the following values:

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.

1 The mass spectrometer is in operate2 The mass spectrometer is in standby

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.

MassLynx Status 6-5

LC StatusThe LC Status section shows inlet system information.

Status

This shows whether there is an error with the inlet system. If an error occurs, the appropriate action can be taken by the software to stop the automation. It has three values:

Ready

This shows whether the inlet system is ready to inject a new sample. It has three values:

%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).

Queue Status

The Queue Status section shows sample list queue information.

0 There is no information available on the inlet system.1 There is no error in the inlet system.2 The inlet system has an error.

0 There is no information available on the inlet system.1 The inlet system is ready to inject the next sample.2 The inlet system is not ready to inject the next sample.


Queue Paused

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

Process Running

This shows whether MassLynx is running a process. It has two states:

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 (for example, 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

0 The process queue is not paused1 The process queue is paused

0 MassLynx is not running a process1 MassLynx is running a process

MassLynx Status 6-7

Disk Space

The Disk Space section shows the disk drive currently in use and the amount of space remaining on it.

Time Stamp

The Time Stamp section 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.


7 Datafile Access Component

The MassLynx Datafile Access Component (DAC) is a suite of Visual C++ Active Template Library (ATL) classes which allows relatively simple access to the MassLynx raw data files. Access to these objects can be via Visual C++ or Visual Basic. Notes: • The DAC is for accessing data only, it cannot perform any data

processing; information on the MassLynx VB functions for data processing can be found in the “MassLynx Macro User Guide”.

• Following updates to the DAC for MassLynx V4.1, some older programs which use the DAC may not work, in most cases simply recompiling the affected program should fix the problem.

Contents:

Topic PageDAC Functions 7-2DAC Class Descriptions 7-4

7-1

DAC Functions

The DAC comprises of the suite of ATL classes described in DAC Class Descriptions on page 7-4. To use a class, an instance must be created and then initialized using that class’s initialize function. For example, to create an instance of the DACSpectrum class in Visual Basic:Dim sSpectrum As New DACSpectrum

the sSpectrum object can then be initialized:nRtn = sSpectrum.GetSpectrum("C:\Masslynx\Default.pro\Data\Pest03.raw", 1, 0, 1)

Each class has its own initialize function that has slightly different parameters. In the DACSpectrum example above, the GetSpectrum parameters are: File name, function number, process number and scan number. So, the sSpectrum object will be populated by data from the first scan of the first function in the Pest03 dataset.Each initialization function returns a value indicating whether the initialization was successful. A successful initialization will return 0, a failure will return a non-zero value, the commonest are shown below:

Once an object has been initialized it holds information that can be accessed from its members. The members of the DACSpectrum class are: Intensities,

Return values:

Error Possible Reason2001 Cannot find the data file specified.4010 Part of the RAW file is missing, or the process specified does not

exist (could be a process "greyed out" in the history list).4003 A handle cannot be found for the data specified (check that the

scan/process number combination is valid).2004 The requested scan number cannot be found.4006 Could not close the data file correctly after reading it.8001 One of the function parameters is out of its permitted range.8002 Memory could not be allocated to read the required data.8003 An unrecognized chromatogram type was specified.8004 The specified process does not exist.

7-2 Datafile Access Component

Masses and NumPeaks. Intensities and Masses are arrays describing mass-intensity pairs from the spectrum defined in the GetSpectrum initialize function. The size of these arrays is held in the NumPeaks member which represents the number of peaks in the spectrum. To access the number of peaks:Dim nNumberOfPeaks as integer

nNumberOfPeaks = sSpectrum.NumPeaks

As the Intensities and Masses members are arrays, an index must be provided:Dim fMass as single

fMass = sSpectrum.Masses(0)

this will access the first mass in the spectrum. Note: Unless specified otherwise, all arrays returned by the DAC are zero-indexed (i.e. the first element will be number 0). All parameters used by the DAC (for example, function number, scan number) start at 1.The DAC member variables are for reading only, they cannot be written to, for example,sSpectrum.NumPeaks = 5

will produce an error.

DAC Functions 7-3

DAC Class Descriptions

The descriptions of each of the DAC classes are given below. For each class the initialize function is described along with its parameters, then the class members are listed in a table.

DACHeader

This class allows access to the header information from a data file. The initialize function is GetHeader, which takes the data file name as its parameter. The following member variables are then available:

Member Format DescriptionAcquDate String Date of acquisition of data.AcquName String Name of data file.AcquTime String Time of acquisition of data.AnalogOffset Single Array

– size 4Offsets for each analog channel.

Autosampler-Type

Long Type of autosampler.

BottleNumber String Well number of sample.Conditions String Acquisition conditions.Encypted Long Encrypted flag.GasName String Ionization gas.Instrument String Name of instrument.Instrument-Type

String Type of instrument.

JobCode String Job code string.LabName String Name of lab.MuxStream Long MUX flag.PepFileName String PEP file name.PlateDesc String Plate description string.Process String Process description string.Resolved Long Resolved flag.SampleDesc String Sample description.


DACCalibrationInfo

This class allows access to the calibration information from a data file. The initialize function is GetCalibration, which takes the data file name as its parameter. The following member variables are then available:

SampleID String Sample ID.SolventDelay Double Solvent delay.Submitter String Name of submitter.TaskCode String Task code string.UserName String Name of user.VersionMajor Integer Major version number.VersionMinor Integer Minor version number.

Member Format Description MS1DynamicParams

String MS1 dynamic parameters, for format description, see below.

MS1FastParams String MS1 fast parameters, for format description, see below.

MS1StaticFunction

String MS1 function coefficients, for format description, see below.

MS1StaticParams String MS1 static parameters, for format description, see below.

MS2DynamicParams

String MS2 dynamic parameters, for format description, see below.

MS2FastParams String MS2 fast parameters, for format description, see below.

MS2StaticFunction

String MS2 function coefficients, for format description, see below.

MS2StaticParams String MS2 static parameters, for format description, see below.

CalTime String Calibration time.CalDate String Calibration date.NumCalFunctions Long Number of calibration functions.

DAC Class Descriptions 7-5

The format of each of the longer strings is as follows:

MS1StaticFunction & MS2StaticFunction

<Coefficient1>,<Coefficient2>,…,<Coefficientn>,T<Function Type>

MS1StaticParams & MS2StaticParams

<Low Mass>,<High Mass>,<Dwell Time>,<Span>,<Low Mass Resolution>,<High Mass Resolution>,<Ion Energy>,<Reference File>,<Acquisition File>

MS1DynamicParams & MS2DynamicParams

<Low Mass>,<High Mass>,<Scan Time>,<Inter-scan Delay>,<Low Mass Resolution>,<High Mass Resolution>,<Ion Energy>,<Reference File>,<Acquisition File>

MS1FastParams & MS2FastParams

<Low Mass>,<High Mass>,<Scan Time>,<Inter-scan Delay>,<Low Mass Resolution>,<High Mass Resolution>,<Ion Energy>,<Reference File>,<Acquisition File>

CalFunctions

<Coefficient1>,<Coefficient2>,…,<Coefficientn>,T<Function Type>

Example: An MS1StaticParams string of:85,1625,0.00,9.00,15.0,15.0,1.0,Peg1600,STAT

would mean the following values:Low Mass = 85High Mass = 1625Dwell Time = 0

CalFunctions String Array – size NumCalFunc-tions

Calibration function coefficients, for format description, see below.


Span = 9.00Low Mass Resolution = 15.0High Mass Resolution = 15.0Ion Energy = 1.0Reference File =Peg1600 Acquisition File = STAT

DACExperimentInfo

This class allows access to the information supplied when the MassLynx Data Browser dialogue Experiment button is selected (this invokes the Experimental Record dialogue). The initialize function is GetExperimentInfo, which takes the data file name as its parameter. All the experiment information is stored in a single buffer, which is the only member variable available:

DACFunctionInfo

This class allows access to the function information in a data file. The initialize function is GetFunctionInfo, which takes the data file name and the function number as its parameters. This populates the following member variables with information from the function number specified:

Member Format DescriptionExperimentText String (up to

32000 characters)

Full experimental record text.

Member Format DescriptionFunctionType String The function type.StartRT Single Start retention time.EndRT Single End retention time.NumScans Long Number of scans in function.FunctionSetMass Double Set mass for function. Only used if

the function type is “Parents”, “Daughters”, “Neutral Loss”, or “Neutral Gain”.


In addition to the initialize function, DACFunctionInfo also has a member function called GetNumFunctions which takes the data file name as a parameter and returns the number of functions in the data file. In this way, the number of functions can be determined and then each function can be examined with GetFunctionInfo. If an error occurs, GetNumFunctions uses the same error codes as the initialization functions (see above), but the values are negative.A full list of possible function types is included below:

NumSegments Long Number of SIR/MRM segments. Only used if the function type is “SIR”, or “MRM”.

SIRChannels Single Array – size NumSegments

SIR channel masses. Only used if the function type is “SIR”.

MRMParents Single Array – size NumSegments

MRM parent masses. Only used if the function type is “MRM”.

MRMDaughters Single Array – size NumSegments

MRM daughter masses. Only used if the function type is “MRM”.

Function Type DescriptionScan Standard MS scanning functionSIR Selected ion recordingDelay No longer supportedConcatenated No longer supportedOff No longer supportedParents MSMS Parent scanDaughters MSMS Daughter scanNeutral Loss MSMS Neutral LossNeutral Gain MSMS Neutral GainMRM Multiple Reaction MonitoringQ1F Special function used on Quattro II's for scanning

MS1 (Q1) but uses the final detector


DACSpectrum

This class allows access to the Mass-Intensity pairs of a single spectrum. The initialize function is GetSpectrum, which takes four parameters:

• File name• Function number• Process number

MS2 Special function used on triple quads for scanning MS2. Used for calibration experiments

Diode Array Diode array type functionTOF TOFTOF PSD TOF Post Source Decay type functionTOF Survey QTOF MS Survey scanTOF Daughter QTOF MSMS scanMaldi TOF Maldi-Tof functionTOF MS QTOF MS scanTOF Parent QTOF Parent scanVoltage Scan AutoSpec Voltage ScanMagnetic Scan AutoSpec Magnet ScanVoltage SIR AutoSpec Voltage SIRMagnetic SIR AutoSpec Magnet SIRAuto Daughters Quad Automated daughter scanningAutoSpec B/E Scan AutoSpec B/E ScanAutoSpec B^2/E Scan AutoSpec B^2/E ScanAutoSpec CNL Scan AutoSpec CNL ScanAutoSpec MIKES Scan

AutoSpec MIKES Scan

AutoSpec MRM AutoSpec MRMAutoSpec NRMS Scan

AutoSpec NRMS Scan

AutoSpec-Q MRM Quad

AutoSpec-Q MRM Quad


• Scan numberOnce initialized, the following member variables are available:

DACScanStats

This class allows access to the scan statistics of a single spectrum. The initialize function is GetScanStats, which takes four parameters:

• File name• Function number• Process number• Scan number

Once initialized, the following member variables are available:

Member Format DescriptionNumPeaks Long Number of peaks.Masses Single Array –

size NumPeaksArray of masses.

Intensities Single Array – size NumPeaks

Array of intensities.

Member Format DescriptionAccurateMass Long Accurate mass measure flag.BPI Single Base Peak Intensity.BPM Single Base Peak Mass.Calibrated Long Calibrated data flag.Continuum Boolean Continuum data flag.HiMass Single Highest mass in scan.LoMass Single Lowest mass in scan.MolecularMass Long Molecular mass value.Overload Long Overload flag.PeaksInScan Long Number of peaks scan.


DACExScanStats

This class allows access to the instrument control statistics of a single spectrum’s acquisition. The initialize function is GetExScanStats, which takes four parameters:

• File name• Function number• Process number• Scan number


RetnTime Single Retention time.Segment Integer Scan segment ID number.TIC Single TIC value.

Member FormatAccurateMass BooleanAccurateMassFlags IntegerAccVoltage IntegerCoarseLaserControl IntegerCollisionEnergy SingleCollisionRF Integer CounterElec-trodeVoltage

Integer

Entrance IntegerFaimsCV SingleFineLaserControl IntegerFocus IntegerGuard IntegerHMResolution IntegerIonEnergy IntegerLaserAimXPos SingleLaserAimYPos Single


LaserRepetitionRate IntegerLinearDetector-Voltage

Integer

LinearSensitivity IntegerLMResolution IntegerLockMassCorrection SingleMultiplier1 IntegerMultiplier2 IntegerNeedle IntegerNumShotsPerformed IntegerNumShotsSummed IntegerProbeTemperature IntegerPSDFactor1 SinglePSDMajorStep SinglePSDMinorStep SinglePSDSegmentType IntegerReferenceScan ByteReflectron Integer ReflectronDetector-Voltage

Integer

ReflectronField-Length

Single

ReflectronField-LengthAlt

Single

ReflectronLength SingleReflectronLengthAlt SingleReflectronLens-Voltage

Integer

ReflectronSensitivity IntegerReflectronVoltage SingleRFVoltage IntegerSamplePlateVoltage Single


DACProcessInfo

This class allows access to the process information held in a single function. The initialize function is GetProcessInfo, which takes the data file name and function number as its parameters. The following member variables are then available:

SamplingConeVoltage IntegerSegmentNumber IntegerSetMass SingleSkimmer IntegerSkimmerLens IntegerSourceAperture IntegerSourceCode IntegerSourceRegion1 SingleSourceRegion2 SingleSourceTemperature IntegerSteering IntegerTempCoefficient SingleTempCorrection SingleTFMWell IntegerTIC_A SingleTIC_B SingleTOF IntegerTOFAperture IntegerTransportDC IntegerTransportRF Integer UseLockMassCorrec-tion

Byte

UseTempCorrection Byte

Member Format DescriptionNumProcesses Long Number of processes.


DACChromatogramThis class allows access to chromatogram data held in a data file. The initialize function is GetChromatogram which takes the following parameters:

• File name• Function number• Process number• Chromatogram start time (or scan)• Chromatogram end time (or scan)• Times flag• Chromatogram type

The Times flag is a boolean value which should be set to True if the boundaries entered for the chromatogram are times rather than scan numbers. The type of chromatogram is identified by the chromatogram type parameter:Analog chromatograms are generated by specifying the channel number prefixed with ‘An’ (not case sensitive). Mass chromatograms are identified by number, mass range chromatograms are identified by start range_end range, mass sum chromatograms are identified by number+number and mass subtraction chromatograms are identified by number-number.Mass channel numbers can be used in place of masses if they are prefixed with ‘Ch’ (not case sensitive).

ProcessDescs String Array – size NumProcesses

Array of process descriptions, using the following format:<Process Number>: <Description> <Saved Flag>For example, 1: Center 1 (Top,4, Ht) 13-Dec-01 16:52 (Saved)



DACAnalog

This class allows access to the analog information held in a data file. The initialize function is GetAnalogChannels, which takes the data file name as its parameter. The following member variables are then available:

Creating Visual Basic Programs using the DAC

In order to use the DAC in VB, a reference to the DAC library must be included. To set this up, go to the Project menu in VB and select References. Search the list of available references for “DACServer X.Y Type Library” and ensure that its check-box has been selected. If the reference is not on the list, select Browse and add the DACServer.dll file from the MassLynx installation directory (usually C:\MassLynx).Once the reference has been set, the DAC classes will be available for use as described above and can be viewed in the VB Object Browser by selecting the F2 key.

Member Format DescriptionNumScans Long Number of scans in chromatogramIntensities Single Array –

size NumScansArray of intensities.

Scans Integer Array – size NumScans

Array of scan numbers.

Times Single Array – size NumScans

Array of scan times.

Member Format DescriptionNumAnalogs Long Number of analog channels.AnalogTypes String Array –

size NumAnalogs

Analog types.

NumDataPoints Long Number of data points in each channel.


The following extract of code searches the list of functions in the Pest03 dataset and looks for the first “Scan” function type.Dim sFuncInfo As New DACFunctionInfoDim strFileName As StringDim nNumFunctions As Long

Dim nRtn as Long

strFileName = "C:\Masslynx\Default.pro\Data\Pest03.raw"

‘Determine number of functions in this filenNumFunctions = sFuncInfo.GetNumFunctions(strFileName)

'Search for the first “Scan” function. Note that the function array is 1 – indexed

Dim nFunction As Long

For nFunction = 1 To nNumFunctionsnRtn = sFuncInfo.GetFunctionInfo(strFileName, nFunction)If sFuncInfo.FunctionType = "Scan" Then Exit ForEnd If

Next nFunction

<specific processing for first “Scan” function here>

Set sFuncInfo = Nothing

This code uses the member function GetNumFunctions to determine the number of functions. It then repeatedly calls the initialize function GetFunctionInfo until a function of type “Scan” is found.

Creating Visual C++ Programs using the DAC

Using the DAC from VC++ is quite different to using it with VB, instead of a project reference the DACServer.dll file needs to be imported into a header file as follows:#import "C:\MassLynx\DACServer.dll" no_namespace named_guids


The major difference between using the DAC with VC++ and VB is that to access the member variables of a DAC class, smart pointers need to be used. The following code accesses the mass – intensity pairs for a spectrum and writes them to a text file.// Create the DACSpectrum object

IDACSpectrumPtr pSpectrum;

pSpectrum = IDACSpectrumPtr(CLSID_DACSpectrum);

// Set the input parameters

CComBSTR bstrFileName("C:\\Masslynx\\Default.pro\\Data\\Pest03.raw");

int nFunctionNumber = 1;

int nProcessNumber = 0;

int nScanNumber = 1;

// Populate the DACSpectrum object

int nRtn = pSpectrum->GetSpectrum(bstrFileName.Detach(), nFunctionNumber, nProcessNumber, nScanNumber);

// Write the mass-intensity pairs

CString strOutput;

CString strLine;

for (int nPeakCount = 0; nPeakCount < pSpectrum->NumPeaks; nPeakCount++)

{

strLine.Format("%f,%f", ((float*)pSpectrum->Masses.parray->pvData)[nPeakCount],

((float*)pSpectrum->Intensities.parray->pvData)[nPeakCount]);strOutput += strLine + "\r\n";

}

// Open the output file and write the data

CFile sOutputFile;


sOutputFile.Open("C:\\MassLynx\\Default.pro\\Data\\Pest03.txt",CFile::modeCreate|CFile::modeWrite);

sOutputFile.Write(strOutput, strOutput.GetLength());

Here the DACSpectrum class is declared as a smart pointer, pSpectrum. The GetSpectrum initialize function is then called for the first scan of the first function. Access to the NumPeaks member variable is by a similar method as for VB, but DAC array access in VC++ is via the .parray->pvData members as shown above.


Index

AAccess

Creating Import Data 1-8Creating Import Worksheet Data

1-4AutoLynx 5-1

CCopying a Chromatogram as a Text

List 2-15Copying a Spectrum as a Text List 2-16Copying Data 1-2Copying Integrated Chromatogram

Peaks as a Text List 2-15

DDatabase Logging and MassLynx

Status 6-1DataBridge 4-1Datafile Access Component 7-1Dialog boxes

Export SEQUEST compatible file 2-17

Import Data 1-7Import Worksheet 1-3Options 6-2

EExcel


1-6Export SEQUEST compatible file

dialog box 2-17Export to LIMS 2-2, 2-6Exporting Data 2-1

FFile Formats 3-1

Sample lists 3-2

IImport data 1-7Import Data dialog box 1-7Import worksheet 1-3Importing 1-1

MMetaboLynx report files 3-34

OOpenLynx Batch Files 3-9OpenLynx report files 3-19Options dialog box 6-2

PProteinLynx report files 3-53

SSEQUEST Files

Exporting 2-17

TText Files


1-6

Index-1

Index-2

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