Copyright: © Steve Wood


Help Contents
Contents

Importing Data

Importing Data into a Sample List

Copying Data

Import Worksheet

Importing Data

Exporting Data

Exporting Data

Export to LIMS File

Export to XML File

Copying to and from the Windows NT Clipboard

Exporting a SEQUEST File

OpenLynx Batch Files

OpenLynx Browser

MetaboLynx Browser

ProteinLynx Browser

File Formats

File Formats: Sample List

AutoLynx

AutoLynx

The Status.ini File

The Status.ini File

File Format

Datafile Access Component

Datafile Access Component

DAC Functions


Importing Data into a Sample List

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

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

•	Import Worksheet, see  Import Worksheet.

•	Import Data, see  Importing Data.


Copying Data

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

1.	Select the Tool Bar [image] 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:

1.	If copying from a text editor, e.g. 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.

2.	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 (e.g. if three rows are copied from the database, the column headings and the first two selected rows are pasted).


Import Worksheet

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

•	Access 97 & 2000.

•	Tab and comma delimited text files.

•	Excel 97 & 2000, and Excel 5.0, 6.0 and 7.0 files.

•	OpenLynx Batch Files.

More:

To Import a Worksheet

Creating Import Worksheet Files

Access

Excel

Notepad

OpenLynx Batch Files


To Import a Worksheet

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

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

3.	The default file type is Generic Batch Files (*.OLB), created in OpenLynx; select a different file type in the Files of type: list box, if required.

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 Files

The 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: Sample List) 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 in the Customize Field Display dialog, which is invoked by right-clicking anywhere on the Sample List and selecting the Customize Display command.


Importing Data - Import Worksheet - Access
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 as 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: Sample List.  Other columns may be present but they will not be imported into the Sample List.

More:

To Define the Data Type as a Double

To Save in Access Format

To Save in Tab or Comma Delimited Format


To Define the Data Type as a Double

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

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


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; see  To Save in Tab or Comma Delimited Format.


To Save 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 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 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.


Importing Data - Import Worksheet - Excel
Excel

The first column must be called Index, the other column headings must match those shown in  File Formats: Sample List.

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.

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

If the file is to be saved as tab or comma delimited, 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.


Importing Data - Import Worksheet - Notepad
Notepad

The first column must be called Index, the other column headings must match those shown in  File Formats: Sample List.

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.


Importing Data - Import Worksheet - OpenLynx Batch Files
OpenLynx Batch Files

The .olb files must be created following the format described in  OpenLynx Batch Files.


Importing Data - Importing Data
Importing Data

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.

More:

To Import Data

Creating Import Data Files

Access

Excel

Notepad


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 dialog is invoked.

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

4.	The default file type is Excel 5.0 (*.XLS); select a different file type in the Files of type: list box, if required.

5.	Select the Open button.


Creating Import Data Files

For all types of file, the fields must be in the same order as they are to appear in the MassLynx Sample List.


Importing Data - Importing Data - Access
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.

To save in tab or comma delimited format, follow the instructions in  To Save in Tab or Comma Delimited Format, 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.


Importing Data - Importing Data - Excel
Excel

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 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.

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

If the file is to be saved as tab or comma delimited, 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 blank rows should NOT be included in the ANALYSIS area when saving to a text file.


Importing Data - Importing Data - Notepad
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, but the fields must be in the same order as in MassLynx.

Text fields should be enclosed in quotes.


Exporting Data - Exporting Data
Exporting Data

There are several ways of exporting data from MassLynx:

•	Export to LIMS.

•	Export to XML.

•	Copying Chromatogram and Spectrum peak lists.

•	Export SEQUEST file.

•	OpenLynx Batch files.

•	OpenLynx Browser files.

•	MetaboLynx Browser files.

•	ProteinLynx Browser files.


Export to 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 Quantify 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.

More:

The Header Section

The Samples Section

The Calibration Section


The Header Section

The 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 from which the LIMS file was 	generated.

•	SAMPLELIST	The Sample List file.

•	QUANMETHOD	The Quantification Method file.

•	QUANCALIBRATION	The Quantify curve file.

e.g. LIMS EXPORT FILE:

C:\Masslynx\lims1

Tue Aug 28 12:21:44 2001


The Samples Section

Header Fields

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 to SPARE_5 fields, there are fields indicating the date and time the sample was created.

e.g. 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.

Field Description	Data Type
The compound number shown in the Quantify Method Editor Compound: box.	Int
The text name of this compound.	Char
The scan at which the matching peak was found in the current sample data file.	Int
The retention time of the matching peak.	Float
The relative retention time at which the matching peak was found.	Float
The area of the matching peak.	Float
The height of the matching peak.	Float
The response of the sample for this compound.	Float
The flags associated with the peak.	Text
The concentration of compound recorded for this sample.	Float
The blank subtracted concentration of the compound for this sample.	Float
The chromatogram trace used to locate peaks for this compound.	Char
The error between the expected concentration and the calculated concentration.	Float
The ordinal number of the compound in the quantification method that is used as the reference peak for this compound.	Int
The area of the reference peak used for this compound for this sample.	Float
The height of the reference peak.	Float
The retention time of the reference peak.	Float
The modification date of the peak used to quantify this compound for this sample.  This refers manual modification of the peak.	Text
The modification time of the peak.	Text
The modification text (modification comment) of the peak.	Text
The MassLynx User who altered the peak.	Text
The mass of the peak.	Float
The retention time the peak was expected at for this compound.	Float
The relative retention time the peak was expected at for this compound.	Float
The User Peak Factor associated with this compound.	Float
The User RF Value associated with this compound.	Float
The Start Retention Time of the detected peak.	Float
The end retention time of the detected peak.	Float
Absolute peak response.	Float
Compound number of the Retention Time Reference.	Int
Secondary Ion chromatogram trace description.	Text
Number of secondary ions used.	Int
Ratio of Primary and Secondary ion absolute peak responses.	Float
Primary/Secondary peak ratio within tolerance flag.	Boolean
Area of Secondary ion Peak.	Float
Height of Secondary ion Peak.	Float


The Calibration Section

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

e.g.

Compound 1 name: I. Std

Response Factor: 846.154

Response type: External Std, Area

Curve type: RF

Compound 2 name: Parent

Coefficient of Determination: 1

Calibration curve: 0.568051 * x + 0.0010347

Response type: Internal Std ( Ref 1 ), Area * ( IS Conc. / IS Area )

Curve type: Linear, Origin: Exclude, Weighting: 1/x, Axis trans: None

Compound 3 name: Metabolite

Coefficient of Determination: 1

Calibration curve: 0.336996 * x + -0.00516146

Response type: Internal Std ( Ref 1 ), Area * ( IS Conc. / IS Area )

Curve type: Linear, Origin: Exclude, Weighting: 1/x, Axis trans: None

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


Export to XML File

Quantification results can also be written to a .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.

More:

XML Format


XML Format

The 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 and their respective attributes follows:

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.

DATASET

•	filename: the name of the QuanLynx dataset file (*.qld).

•	modifieddate: the date the file was last modified.

•	modifiedtime: the time the file was last modified.

GROUPDATA

•	count: 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 t he file was last modified.

SAMPLELISTDATA

•	filename: 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.

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: not used.

•	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).

SECONDARYPEAKS

•	peaks: the number of secondary peaks.

•	secondarychromnoise: 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.

ISPEAK

•	area: 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.

METHOD

•	rref: 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.

CALIBRATIONDATA

•	filename: 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.

CURVE

•	type: 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).

CORRELATION

•	r: the correlation coefficient of the curve.

DETERMINATION

•	rsquared: the coefficient of determination for the curve.

     else:

CALIBRATIONCURVE

•	curve: calibration polynomial.

DETERMINATION

•	rsquared: the coefficient of determination for the curve.


Copying to and from the Windows NT Clipboard

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

More:

To Copy a Chromatogram as a Text List to the Clipboard

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

To Copy a Spectrum as a Text List to the Clipboard


To Copy a Chromatogram as a Text List to the Clipboard

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

2.	Select the Tool Bar [image] 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

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 [image] 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.

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	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
The fields are separated by tabs.


To Copy a Spectrum as a Text List to the Clipboard

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

2.	Select the Tool Bar [image] 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.

3.	To read the information into another application, select the other application’s Menu Bar Edit, Paste command.

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.


Exporting a SEQUEST File

MassLynx has a facility to convert files into a format that 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.

More:

To Export a SEQUEST File


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 dialog is invoked.

3.	Make the required changes, see below.

4.	Select the OK button.

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.
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 dialog.
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.


Exporting Data - OpenLynx Batch Files
OpenLynx Batch Files

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

OpenLynx Batch files can be used as input files for  AutoLynx, and they can be imported into MassLynx as Sample Lists, see  Import Worksheet.

More:

Paragraphs

Batch Block

Plate Block

Sample Block

Fields

Comments

File Format

An Example OpenLynx Batch File


Paragraphs

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

e.g.	[SectionName1]

....Data Item 1…

....Data Item 2…

[SectionName2]

….Data Item 1…

….Data Item 2…

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

[Batch]

….Data Item 1…

….Data Item 2…

[Plate:1]

....Data Item 1…

....Data Item 2…

[Sample:1:1]

....Data Item 1…

....Data Item 2…

[Sample:1:n]

....Data Item 1…

....Data Item 2…

[Plate:2]

....Data Item 1…

....Data Item 2…

[Sample:2:1]

....Data Item 1…

....Data Item 2…

[Sample:2:n]

....Data Item 1...

....Data Item 2…

[Plate:m]

....Data Item 1...

....Data Item 2…

[Sample:m:1]

....Data Item 1...

....Data Item 2…

[Sample:m:n]

....Data Item 1...

....Data Item 2…


Batch Block

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


Plate Block

A file contains a plate block for each plate that contains 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 Block

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


Exporting Data - OpenLynx Batch Files - Fields
Fields

Sections 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.

i.e.	[SectionName]

FieldName1=Data1

FieldName2=Data2

e.g.	[Plate:3]

JobCode=JB123456

NumberOfWells=96


Exporting Data - OpenLynx Batch Files - Comments
Comments

A 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.


Exporting Data - OpenLynx Batch Files - File Format
File Format

[Batch]

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

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 parameters will be used.
LCMethod	Text	The name of the acquisition Inlet method to be used.
Economy Scheduling	Integer	Non-zero if the batch is to be run as a Night-Time task.  Otherwise, it will be scheduled normally.
Priority Scheduling	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.
Process Parameters	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 necessary 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.
SampleReport Enable	Boolean	Indicates if per sample printing is required; 0 = False, 1 = True.
NumberOfPlates (M)	Integer	Number of plates in analysis.
InletPreRun Method	Text	The name of the acquisition Inlet pre-run method to be used.  If not specified, no pre-run is performed.
InletPostRun Method	Text	The name of the acquisition Inlet post-run method to be used.  If not specified, no post-run is performed.
InletSwitch Method	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.
FractionMethod	Text	The walk-up fraction method to use for acquisition.
AcquProcess	Text	The acquisition process to be used.
AcquProcess Parameters	Text	The acquisition process parameter file to be used.
AcquProcess Options	Text	The acquisition process options to be used.
SampleReport Scheme	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.
QuanLynxMethod	Text	Name of the QuanLynx method used.
OAQuanMethDB	Text	Quantitation method template file name, used for processing the Quantitation results.
OverrideOptimise	Boolean	Flag to enable/disable compound optimizations.
AcquireQuantify	Boolean	Flag to enable/disable acquisition of the analytical samples.
[Plate:N]

Where N = Plate Number

Field/Section Name	Data Type	Description
PlateID	Text	Plate Identifier.  A text description of the plate can be defined in files created externally.  This is not generated in files created from the OpenLynx Login program.
PlatePosition	Text	The description of the plate position, as co-ordinates for plate position in the autosampler bed. 1. X,Y. 2. Not used for a linear autosampler e.g. HP GC type. where X and Y are integers.
Origin	Text	The description of the start well position, as a pair of co-ordinates for well position in plate, or an absolute position. WellAwellX(or wellXwellA ) e.g. A1 where X is an integer and A is an alphabetical character, or: TL=Top Left, TR=Top Right, BL=Bottom Left, BR=Bottom Right.
JobCode	Text	Job or Batch Identifier.
UserName	Text	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.
NumberOfWells (M)	Integer	The number of wells used in the plate, or vials in an autosampler tray.
[Sample:N:M]

Where N = Plate Number, M = Well Number.

Field/Section Name	Data Type	Description
Well (M)	Text	The description of the well position, as co-ordinates for well position in the plate, or an absolute position.  This field can be used to identify a vial position in a non-XY autosampler.  There are two formats for a Well: 1. wellAwellY (or wellYwellA ) e.g. B6, 6B or 2,6. 2. Absolute rack position.  e.g. 18 where X and Y are integers and A is an alphabetical character.
SampleType	Integer	Sample type. 0 = Unknown, 1 = Standard, 2 = QC and 3 = Blank.
NumberOfMasses	Integer	The number of masses defined.
Mass1	Float	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 FractionTriggers	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.
NumberOf Formulae	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.
NumberOf Wavelengths	Integer	The number of wavelengths defined.
Wavelength1	Text	The first wavelength, if used.
Wavelength2	Text	The second wavelength.
WavelengthN	Text	The nth wavelength.
NumberOfConcs	Integer	The number of concentrations defined.
Conc1	Text	The first concentration, if used.
Conc2	Text	The second concentration.
ConcN	Text	The nth concentration.
NumberOfFactors	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.
Sample Description	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.
MSInjection Volume	Float	The amount of sample to inject, for an MS analysis.
NumberOfUser Fields	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.


An Example OpenLynx Batch File

Below 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


OpenLynx Browser

Sections

Fields

Comments

Tabulated Sections

Free Format Text Sections

File Section Descriptions


Exporting Data - OpenLynx Browser - Sections
Sections

The file holds section blocks of data.  The start of a section block always starts with the name of the section surrounded by square parentheses on a line by itself, e.g. [SectionName].

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

i.e.	[SectionName]

{

....Data...

}

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

e.g.	[SectionName1]

{

....Data...

[SectionName2]

{

....Data...

{

{


Exporting Data - OpenLynx Browser - Fields
Fields

Sections 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.

i.e.	[SectionName]

{

FieldName1	Data1

FieldName2	Data2_1	Data2_2

...

}


Exporting Data - OpenLynx Browser - Comments
Comments

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


Exporting Data - OpenLynx Browser - Tabulated Sections
Tabulated Sections

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

e.g.	[TableSection]

{

;Field1	Field2

Data1_1	Data1_2

Data2_1	Data2_2

...

}


Exporting Data - OpenLynx Browser - Free Format Text Sections
Free Format Text Sections

The 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.


Exporting Data - OpenLynx Browser - File Section Descriptions
File Section Descriptions

SAMPLE

Field/Section Name	Data Type	Description
Sample	Integer	The number of the sample in the batch.
Well	Text	The description of the well position, as a pair of co-ordinates for 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 alphabetical 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.
Sample Description	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, i.e. OpenLynx.
MSTune	Text	The tune file used.
MSMethod	Text	The MS method used.
InletMethod	Text	The inlet method used.
PreRunMethod	Text	The Pre-Run method used.
PostRunMethod	Text	The Post-Run method used.
SwitchMethod	Text	The switch method used.
FractionMethod	Text	The fraction method used.
Acquisition Process	Text	The acquisition process used.
Acquisition Process Parameters	Text	The acquisition process parameters used.
Acquisition ProcessOptions	Text	The acquisition process options used.
InjectionVolume	Float	The injection volume used.
ReportScheme	Text	The batch report scheme used.
SampleReport Enable	Int	Whether per sample printing was enabled: 0 = disabled and 1 = enabled.
SampleReport Format	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.
FUNCTION	Section	MS function data and test results.  There will be one FUNCTION section per MassLynx MS and DAD data functions.
INLET PARAMETERS	Section	Inlet device experimental record description. Note: Only ACE inlet devices are currently supported.
PLATE FIELD

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

Version Number (two digits).

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

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

Reference scheme (  LN - letter number, NL - number letter, NN - number number, LL - letter letter,  SC - sequential continuous, SD sequential discontinuous  )

1.	Number Of Rows.

2.	Number Of Columns.

3.	Row Spacing.

4.	Column Spacing.

5.	Row Offset.

6.	Column Offset.

7.	Which Rows Offset (O or E).

8.	Which Columns Offset (O or E).

9.	Plate Width.

10.	Plate Height.

11.	Vial/Well Depth.

12.	Vial/Well Diameter.

13.	Vial One X.

14.	Vial One Y.

Note:

All spacings, etc., are given to 0.1 of a millimeter.

e.g.

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.

ANALOG

Field/Section Name	Data Type	Description
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.
TRACE

This is a tabulated section.

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

Field Name	Data Type	Description
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 + Float	The 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.
COMPOUND

This is a tabulated section.

Field Name	Data Type	Description
Mono Mass	Float	The mass used for targeting.  This could be the mono-isotopic mass or the mass with the greatest intensity, derived from the formula’s isotope cluster.
Formula	Text	The chemical composition, if entered.
Name	Text	The name of the compound.  Unused at present.
FRACTION

This is a tabulated section.

Field Name	Data Type	Description
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 collection started.
No. Of Tubes	Integer	The number of tubes the fraction was collected in.
FUNCTION

Field/Section Name	Data Type	Description
Function	Integer	The MassLynx MS data function number.
IonMode	Text	The type of ionization mode, e.g. AP+.
Type	Text	The type of MS scan function, e.g. MS for full scan.
Description	Text	A brief description of the MS scan function.
SPECTRUM	Section	MS data and results of testing.  There can be more than one SPECTRUM section in a function.
CHROMATOGRAM	Section	Chromatographic data. There can be more than one CHROMATOGRAM section in a function.
SPECTRUM

Field/Section Name	Data Type	Description
ProcDesc	Text	Description of processing performed on spectrum, e.g. Combine (54:56-(38:39+74:75)).
Process	Integer	The number of the MassLynx saved mass spectrum.  Only present if the processed spectrum was saved with data file.
State	Text	The result of testing the quality of the mass spectral data.  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 intensities in the spectrum.
BPI	Float	The intensity of the base peak in the mass spectrum.
BPM	Float	The mass of the base peak in the mass spectrum.
Continuum	Text	TRUE if the spectrum is stored in continuum format, otherwise FALSE.
Saved	Text	TRUE if the processed spectrum was saved with the data file, otherwise FALSE.
MASSES	Section	Section describing the results of testing, and finding significant masses.  This includes all adducts.
RESULTS	Section	Section describing the results of the targeting of the expected compound.  Masses from the same compound are combined into one item.
ELEMENTAL	Section	Section holding results of elemental calculations.  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.
MASSES

This is a tabulated section.

Field Name	Data Type	Description
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

This is a tabulated section.

Field Name	Data Type	Description
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".
ELEMENTAL

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

Field Name	Data Type	Description
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 milliDaltons.
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,  e.g. 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.
SEARCH

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

Field Name	Data Type	Description
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

Field Name	Data Type	Description
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.
MS

This is a tabulated section.

Field Name	Data Type	Description
Mass	Float	The observed mass of peak.
% BPI	Float	The Intensity of peak as a percentage of the base peak.
CHROMATOGRAM

Field/Section Name	Data Type	Description
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 chromatogram, e.g. Smooth (Mn, 2x2).
MaxIntensity	Float	The absolute intensity of the point with maximum intensity in the chromatographic data.
TRACE	Section	A section that holds the chromatographic data.  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 ANALOG paragraph above.
QC	Section	Section that holds information about the QC result.  This section is only present if this is a QC sample.
QC

Field/Section Name	Data Type	Description
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).
INLET PARAMETERS

This is a free format text section.


MetaboLynx Browser

Sections

Fields

Comments

Tabulated Sections

Free Format Text Sections

File Section Descriptions


Exporting Data - MetaboLynx Browser - Sections
Sections

The file holds section blocks of data.  The start of a section block always starts with the name of the section surrounded by square parentheses on a line by itself, e.g. [SectionName].

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

i.e.	[SectionName]

{

....Data...

}

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

e.g.	[SectionName1]

{

....Data...

[SectionName2]

{

....Data...

}

}


Exporting Data - MetaboLynx Browser - Fields
Fields

Sections 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.

i.e.	[SectionName]

{

FieldName1	Data1

FieldName2	Data2_1	Data2_2

...

}


Exporting Data - MetaboLynx Browser - Comments
Comments

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


Exporting Data - MetaboLynx Browser - Tabulated Sections
Tabulated Sections

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

e.g.	[TableSection]

{

;Field1	Field2

Data1_1	Data1_2

Data2_1	Data2_2

...

}


Exporting Data - MetaboLynx Browser - Free Format Text Sections
Free Format Text Sections

The 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.


Exporting Data - MetaboLynx Browser - File Section Descriptions
File Section Descriptions

SAMPLE

Field/Section Name	Data Type	Description
Sample	Integer	The number of the sample in the batch.
Process Parameters	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.
InjectionVolume	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.
MSMethodFile Name	Text	MassLynx Sample List input field.  Name of the Method File used to acquire the data.
MSTuneFile Name	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.
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 alphabetical 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,wellY 2. MSMSplateX,plateY:wellAwell1 (or well1wellA ) 3. MSMS:Absolute rack position.
SampleID	Text	MassLynx Sample List input field.
Sample Description	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 a  detailed description.
COMPOUND	Section	Description of parent drug(s); the masses taken from the MassLynx Sample List.
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 function <n> previously declared in report.  There is one FUNCTION_APPEND section per MassLynx data function.
EXPECTED METABOLITES	Section	Description of metabolites searched for.
UNEXPECTED METABOLITES	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 CORRELATION	Section	Table of correlation results of MS/MS spectra.
INLET PARAMETERS	Section	Inlet device experimental record description.  For future use.
PLATE FIELD

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

Version Number (two digits)

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

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

Reference scheme (LN - letter number, NL - number letter, NN - number number, LL - letter letter,  SC - sequential continuous, SD sequential discontinuous).

1.	Number Of Rows

2.	Number Of Columns.

3.	Row Spacing.

4.	Column Spacing.

5.	Row Offset.

6.	Column Offset.

7.	Which Rows Offset (O or E).

8.	Which Columns Offset (O or E).

9.	Plate Width.

10.	Plate Height.

11.	Vial/Well Depth.

12.	Vial/Well Diameter.

13.	Vial One X.

14.	Vial One Y.

Note:

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

This is a tabulated section.

Field Name	Data Type	Description
Mono Mass	Float	The parent drug used for targeting.  This could be the monoisotopic mass or the mass with the greatest intensity, derived from the formula’s isotope cluster.
Formula	Text	The chemical composition, if entered.
FUNCTION/FUNCTION_APPEND

Note:

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

Field/Section Name	Data Type	Description
Function	Integer	The MassLynx MS data function number.
IonMode	Text	The type of ionization mode, e.g. ES+.  Not present in analog function.
Type	Text	MS function: The type of scan function, e.g. 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.
CHROMATOGRAM	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	Data Type	Description
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 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.
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 spectrum.  Only present if this spectrum has a matching control spectrum.
Time	Float	The retention time of the mass spectrum.
TIC	Float	Total Ion Current, the sum of all the peak intensities in the spectrum.
BPI	Float	The intensity of the base peak in the mass spectrum.
BPM	Float	The mass of the base peak in the mass spectrum.
Continuum	Text	TRUE if the spectrum is stored in continuum format, otherwise FALSE.
Process	Integer	The number of the MassLynx saved mass spectrum.  Only present if processed spectrum was saved with data file.
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.
MASSES

This is a tabulated section.

Field Name	Data Type	Description
Mass	Float	The input mass.
Exp. Mass	Float	The expected mass due to adduction.
Obs. Mass	Float	The mass that was actually observed.
% BPI	Float	The intensity of the mass peak as a percentage of the base peak intensity.
Int. Abs	Float	The absolute intensity of the MS peak.
RESULTS

This is a tabulated section.

Field Name	Data Type	Description
Mass	Float	The input mass.
Found	Boolean integer	1 (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.
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.
MS

This is a tabulated section, containing pairs of mass and intensity.

Field Name	Data Type	Description
Mass	Float	Observed mass of peak.
%BPI	Float	Intensity of peak as a percentage of the base peak.
CHROMATOGRAM/CHROMATOGRAM_APPEND

Note:

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

Field/Section Name	Data Type	Description
TraceNumber	Integer	Number of chromatogram trace.  Reserved for internal use.
TraceNumberIn Function	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, e.g. Smooth (Mn, 2x2).
MaxIntensity	Float	The absolute intensity of the point with maximum intensity in the chromatographic data.
IntensityShift	Float	Optional field used when the original chromatogram 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.
TRACE

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

Field Name	Data Type	Description
Time	Float	The time of the chromatographic point.
Int. %Max	Float	Intensity of the chromatographic point as a percentage of the maximum intensity.
PEAK

Field Name	Data Type	Description
Peak ID	Integer	Peak Identification number.  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.
EXPECTED METABOLITES

This is a tabulated section.

Field Name	Data Type	Description
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 Metabolites 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 (e.g. C18H24O2), or a relative formula if the parent mass was specified as a mass (e.g. +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 identified by a string of text containing four stroke-separated numbers in the following format: peak-number/function-number/trace-number/mass-found where the first three 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 calculated 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 metabolites and unexpected metabolites have this flag set to false.  The value of this field can be modified using the MetaboLynx Browser.
Molfile	Text	Name of the molecule file for this metabolite.
UNEXPECTED METABOLITES

This is a tabulated section.  See File Section Descriptions for the format.

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.

Field Name	Data Type	Description
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 calculated mass in milliDaltons.
PPM	Float	Difference between observed mass and calculated mass in parts per million.
DBE	Float	Double Bond Equivalence.
Formula	Text	Representation of calculated chemical formula.
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.

Field/Section Name	Data Type	Description
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.
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.
METABOLITES	Section	One entry for each MS/MS spectrum.  The section provides details of the precursor metabolite and its spectrum, along with status.
CORRELATION TABLE	Section	Entry1 spectrum is correlated with Entry2 spectrum (entry numbers as used in the METABOLITES table) and the masses from spectrum Entry1 are listed in column Entry1MassesMatched.
METABOLITES

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

Field Name	Data Type	Description
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.
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 chromatogram 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.
CORRELATION TABLE

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

Field Name	Data Type	Description
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.
Entry1Neutral Losses 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).
Entry1Common NeutralLosses	Text list	List of Neutral Losses.  It is the comma-separated 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)
MOLFILE LIST

Field/Section Name	Data Type	Description
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.
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.


ProteinLynx Browser

Sections

Fields

Tabulated Sections

File Section Descriptions

Bio-Rad File Descriptions


Exporting Data - ProteinLynx Browser - Sections
Sections

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

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

e.g.	[SectionName]

{

....Data...

}

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

e.g.	[SectionName1]

{

....Data...

[SectionName2]

{

....Data...

}

}


Exporting Data - ProteinLynx Browser - Fields
Fields

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

i.e.	[SectionName]

{

FieldName1	Data1

FieldName2	Data2_1	Data2_2

...

}


Exporting Data - ProteinLynx Browser - Tabulated Sections
Tabulated Sections

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

e.g.	[TableSection]

{

;Field1	Field2

Data1_1	Data1_2

Data2_1	Data2_2

...

}


Exporting Data - ProteinLynx Browser - File Section Descriptions
File Section Descriptions

SAMPLE

Note:

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

Field/Section Name	Data Type	Description
Sample	Integer	The number of the sample in the batch.
Well	Text	The description of the well position, as a pair of co-ordinates for plate position in rack and well position in plate, or an absolute position.  There are three formats for Well: 1. wellX,wellY 2. wellAwell1 (or well1wellA ) 3. Absolute rack position where X and Y are integers and A is an alphabetical character.
Data_File_Name	Text	The MassLynx NT MS data file name.
Sample_ID	Text	MassLynx Sample ID.
Sample_ Description	Text	MassLynx Sample description.
Spare1	Text	User definable spare.
Spare2	Text	User definable spare.
Spare3	Text	User definable spare.
Spare4	Text	User definable spare.
Spare5	Text	User definable spare.
Date	Text	Date that MS data file was acquired.
Time	Text	Time that MS data file was acquired.
Job_Code	Text	MassLynx Sample List Jobcode field.
Task_Code	Text	MassLynx Sample List Taskcode field.
User_Name	Text	Current MassLynx User name.
Instrument	Text	Instrument name.
Plate	Text	Description of micro-titre plate, if applicable.
MS_File	Text	The MassLynx MS data file name.
Process_ Parameters	Text	The MassLynx process parameter file name.
FUNCTION	Section	MS function data and results.  There is one FUNCTION section per MassLynx MS data function.
FUNCTION

Field/Section Name	Data Type	Description
Function	Integer	The MassLynx MS data function number.
IonMode	Text	The type of ionization mode e.g. AP+.
Type	Text	The type of MS scan function, e.g. MS for full scan.
Description	Text	A brief description of the MS scan function.
PROCESS_ PARAMETERS	Section	MS process parameter data and results.  There is only one PROCESS_PARAMETERS section in a FUNCTION.
SEARCH_ PARAMETERS	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.
PROCESS_PARAMETERS

Field Name	Data Type	Description
Do_Process	Boolean	1 if processing has been performed, otherwise 0.
Combine_Mode	Text	Spectrum combine mode.
DoBackground Subtract	Boolean	1 if background subtraction has been performed, otherwise 0.
PolynomialOrder	Int	Number indicating the polynomial order used in background subtraction.
BelowCurve	Int	Number indicating the below curve percentage used in background subtraction.
DoSmooth	Boolean	1 if smoothing has been performed, otherwise 0.
SmoothChannels	Float	Number of channels smoothed.
NumberOf Smooths	Int	Number of smooths performed.
Smooth_Mode	Text	The smoothing method used, e.g. Savitzky-Golay.
Min_Peak_Width	Int	Minimum spectral peak width.
Centroid_Percent	Float	Intensity of peak as a percentage of the base peak.
Centroid_Mode	Text	Spectrum centroid mode used.
PreCharge	Int	Pre-charge state.
Min_Mass_To_ Start	Float	Minimum start search mass.
Isotope_Factor	Float	Minimum isotopic factor value.
Relative_Deiso_ Intensity	Int	The relative deiso intensity.
LockMassPeak_1	Int	First lock mass value.
LockMassPeak_2	Int	Second lock mass value.
LockMassPeak_3	Int	Third lock mass value.
SEARCH_PARAMETERS

Field Name	Data Type	Description
Do_Search	Boolean	1 if search performed, otherwise 0.
Database_Type	Text	Type of database searched.
Index_Path	Text	Path of database index.
Sequence_File	Text	Database sequence file name.
Trembl_Path	Text	Path of Trembl database.
SearchServer	Text	Name of search server.
Output_Type	Text	Type of output file.
PEAKLIST_ location	Text	Location of SEQUEST output file.
MASS	Text	Location of mascot output file.
PepSea_location	Text	Location of PepSea output file.
MOWSE_ location	Text	Location of mass intensity output file.
Organism	Text	Search organism.
Freetext	Text	Search free text.
Keyword	Text	Search key word.
Author	Text	Search author.
Accession	Text	The database accession code.
Subsequence	Text	Search sub sequence.
BileEqual	Boolean	1 if the Treat I/L and Q/K as equivalent option is selected, otherwise 0.
Do_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.
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.
MODIFIERS

Field Name	Data Type	Description
Name of modifier	Boolean	1 if the Always use this modifier option is selected, 0 if Use when needed to match peptide option selected.
SEARCH_RESULTS

Field Name	Data Type	Description
File_Name	Text	Search result file name with its full path.
PRP_File_Name	Text	The HIT section does not appear in this file but in the file named above.  One HIT section defines one database Hit.  There can be more than one HIT section.
SPECTRUM

Field/Section Name	Data Type	Description
LockMassUsed	Float	The lock mass value used.
MONOISO MASSES	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.
MONOISOMASSES

Field Name	Data Type	Description
<Blank>	Float	One monoisomass value per line (without a field name).  There can be more than one line.
CORRECTION_FACTOR

Field Name	Data Type	Description
Correction_Factor	Float	Correction factor applied to the whole spectrum.  Calculated from the lock mass.
Offset_Factor	Float	Correction factor applied to the whole spectrum.  Calculated from the lock mass.
ProcessHistory	Text	Process history information text string.
PEAK_LIST

Field Name	Data Type	Description
Output_Filename	Text	The name of the Mascot or SEQUEST compatible peak information file. e.g.  Mascot file C:\TEMP\hilo07.004.2.1.pkl where 004 = the scan number 2 = the function number 1 = the charge state SEQUEST file C:\MASSLYNX\hilo07.0100001.dta where 0001 = the scan number 01 = the function number.


Bio-Rad File Descriptions

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

Field Name	Data Type	Description
VIEW_ONE	Section	Database protein entry information.  There is only one  VIEW_ONE section per HIT.
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.
VIEW_ONE

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

Field Name	Description
ID	Identification line, showing the entry name of the sequence.
AC	The accession number, a unique number used to identify entries.
DT	Date of entry or last modification.
DE	Description line containing general descriptive information.
GN	Gene name.
OS	The organism species line specifies the organism 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).
CC	Comments or notes used to convey useful information.
DR	The database cross-reference lines are used as pointers to related information in other data collections, e.g. Protein Data Bank (PDB).
KW	Keyword lines provide information 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.
VIEW_TWO

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

Field Name	Description
ID	Identification line showing the entry name of the sequence.
Accession number	The accession number, a unique number used to identify entries.
Description	Description line containing general descriptive information.
Species	The organism species line specifies the organism 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.
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.
VIEW_THREE

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


File Formats: Sample List

The 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.

Label	Format	Description
VERSION	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.
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 acquisition 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.
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 autosampler being used.
SAMPLE_GROUP	Text	Used to inform QuanLynx that the optimization 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 analysis 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.
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.
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 concentration 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 OpenLynx 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.
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_ BOOLEAN_LOGIC	Text	Defines the criteria for a mixed trigger fraction collection. e.g. Mass A AND NOT Wavelength B.
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.
USER_DIVISOR_1	Double	Divisor used during concentration calculation stage of Quantify.  Defaults to 1 if not specified.
USER_FACTOR_1 … USER_FACTOR_3	Double	Multipliers used during concentration calculation 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 (;) e.g. 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.
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.
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.


AutoLynx - AutoLynx
AutoLynx

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

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

•	Take information from other software packages (e.g. LIMS systems) and automatically create batch files (see the OpenLynx Batch Files for the batch file format).

•	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 dialog).

•	Monitor the progress of the batch file.

•	Automatically read the acquired data, or processed results, for further processing and/or exporting into other software packages.

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  Notepad.

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

•	OpenLynx to produce an OpenLynx Browser file.

•	PeptideAuto to produce a ProteinLynx Browser file.

•	MetaboLynx to produce a MetaboLynx Browser file.

For more information on AutoLynx, see the "MassLynx NT User’s Guide".


The Status.ini File - The Status.ini File
The Status.ini File

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

To create a status.ini file, select the MassLynx Tools Shortcut Bar Options icon; the Options dialog is invoked.

Select the Update Status option 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 dialog, 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.

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

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


The Status.ini File - File Format
File Format

The format of the status.ini file is as follows:

[MS Status]

Operate=2

Status=Scanning

[LC Status]

Status=0

Ready=0

%A=100.0

%B=0.0

%C=0.0

%D=0.0

Flow Rate=0.000

[Queue Status]

Queue Paused=0

Process Running=1

1=test	Samples 1 to 5: Sample 1 Acquiring	Running

2=test1	Samples 1 to 5: 	Waiting

3=test2	Samples 1 to 2: 	Waiting

Total samples=12

[Disk Space]

CurrentDrive=C:

FreeDiskSpace=365925888

[Time Stamp]

Time=10-012-2001,17:22:52

More:

MS Status

LC Status

Queue Status

Disk Space

Time Stamp


MS Status

The [MS Status] section shows mass spectrometer information.

Operate

Shows the state of the mass spectrometer’s high voltage electronics.  It has two values:

1	The mass spectrometer is in operate.
2	The mass spectrometer is in standby.
Status

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

No Instrument	There is no mass spectrometer attached to the PC.
Not Scanning	The mass spectrometer is idle.
Solvent Delay	The mass spectrometer has started acquiring data and is in solvent delay.
Scanning	The mass spectrometer is acquiring sample data.
Waiting for Injection	The mass spectrometer is waiting for the autosampler to inject the sample.
This information is useful during automation of a list of samples.  For example, the inlet system will continually poll this parameter while the mass spectrometer is acquiring, in order to determine when it has reached a suitable status (waiting for injection) for the next sample to be injected and a new data file to be acquired.


LC Status

The [LC Status] section shows inlet system information.

Status

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:

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.
Ready

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

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.
%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.

Queue Paused

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

0	The process queue is not paused.
1	The process queue is paused.
Process Running

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

0	MassLynx is not running a process.
1	MassLynx is running a process.
1, 2, …. N

These lines refer to the queue of batches waiting to be processed.  The format of the lines is as follows (from left to right):

"Batch No." "MassLynx Batch ID" "Samples range" "Sample status" "Batch status".

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

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

"Samples range" indicates the range of samples in the batch.

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

"Batch status" is "Running" if a sample from that batch is being processed, or "Waiting" if the batch is in the queue.

Total Samples

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


Disk Space

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


Time Stamp

This 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 that the data system is no longer responding.


Datafile Access Component - Datafile Access Component
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.

Note:

The DAC is for accessing data only, no processing can be performed; information on the MassLynx VB functions for data processing can be found in the "Macro User Guide", which is available in the Start Menu MassLynx folder.


DAC Functions

The DAC comprises of the suite of ATL classes described below.  To use a class, an instance must be created and then initialized using the initialize function for that class.  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:

Call sSpectrum.GetSpectrum("C:\Masslynx\Default.pro\Data\Pest03.raw", 1, 0, 1)

Each class has its own initialize function that will have 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.

Once an object has been initialized, it will be holding information that can be accessed from its members.  The members of the DACSpectrum class are: Intensities, 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 used in the DAC are zero-indexed (i.e. the first element will be number 0).

The DAC member variables are for reading only, they cannot be written to, e.g.

sSpectrum.NumPeaks = 5

will produce an error.

More:

DAC Class Descriptions

Creating Visual Basic Programs using the DAC

Creating Visual C++ Programs using the DAC


DAC Class Descriptions

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	Description
AcquDate	String	Date of acquisition of data.
AcquName	String	Name of data file.
AcquTime	String	Time of acquisition of data.
AnalogOffset	Single Array - size 4	Offsets for each analog channel.
AutosamplerType	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.
InstrumentType	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.
SampleID	String	Sample IDENTIFICATION.
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.
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:

Member	Format	Description
MS1StaticFunction	String	MS1 function coefficients, for format description, see below.
MS2StaticFunction	String	MS2 function coefficients, for format description, see below.
MS1StaticParams	String	MS1 static parameters, for format description, see below.
MS1DynamicParams	String	MS1 dynamic parameters, for format description, see below.
MS1FastParams	String	MS1 fast parameters, for format description, see below.
MS2StaticParams	String	MS2 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.
CalTime	String	Calibration time.
CalDate	String	Calibration date.
NumCalFunctions	Long	Number of calibration functions.
CalFunctions	String Array - size NumCalFunctions	Calibration function coefficients, for format description, see below.
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>

E.g. 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 = 85
High Mass = 1625
Dwell Time = 0
Span = 9.00
Low Mass Resolution = 15.0
High Mass Resolution = 15.0
Ion Energy = 1.0
Reference 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 dialog).  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:

Member	Format	Description
ExperimentText	String (up to 32000 characters)	Full experimental record text.
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	Description
FunctionType	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".
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".
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.

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
Scan number

Once initialized, the following member variables are available:

Member	Format	Description
NumPeaks	Long	Number of peaks.
Masses	Single Array - size NumPeaks	Array of masses.
Intensities	Single Array - size NumPeaks	Array of intensities.
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	Description
AccurateMass	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.
RetnTime	Single	Retention time.
Segment	Int	Scan segment ID number.
TIC	Single	TIC value.
DACExScanStats

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

File name
Function number
Process number
Scan number

Once initialized, the following member variables are available:

Member	Format
AccVoltage	Integer
CoarseLaserControl	Integer
CollisionEnergy	Single
CollisionRF	Integer
CounterElectrodeVoltage	Integer
Entrance	Integer
FineLaserControl	Integer
Focus	Integer
Guard	Integer
HMResolution	Integer
IonEnergy	Integer
LaserAimXPos	Single
LaserAimYPos	Single
LaserRepetitionRate	Integer
LinearDetectorVoltage	Integer
LinearSensitivity	Integer
LMResolution	Integer
LockMassCorrection	Single
Multiplier1	Integer
Multiplier2	Integer
Needle	Integer
NumShotsPerformed	Integer
NumShotsSummed	Integer
ProbeTemperature	Integer
ReferenceScan	Byte
Reflectron	Integer
ReflectronDetectorVoltage	Integer
ReflectronLensVoltage	Integer
ReflectronSensitivity	Integer
RFVoltage	Integer
SamplingConeVoltage	Integer
SegmentNumber	Integer
SetMass	Single
Skimmer	Integer
SkimmerLens	Integer
SourceAperture	Integer
SourceCode	Integer
SourceTemperature	Integer
Steering	Integer
TempCoefficient	Single
TempCorrection	Single
TOF	Integer
TOFAperture	Integer
TransportDC	Integer
TransportRF	Integer
UseLockMassCorrection	Byte
UseTempCorrection	Byte
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:

Member	Format	Description
NumProcesses	Long	Number of processes.
ProcessDescs	String Array - size NumProcesses	Array of process descriptions, using the following format: <Process Number>: <Description> <Saved Flag> e.g.  1: Center  1 (Top,4, Ht)  13-Dec-01 16:52 (Saved).
DACChromatogram

This 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).  The function RawReadAnalogChrom is used to generate analog chromatograms.

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).

Once initialized, the following member variables are available:

Member	Format	Description
NumScans	Long	Number of scans in chromatogram
Intensities	Single Array - size NumScans	Array of intensities.
Scans	Integer Array - size NumScans	Array of scan numbers.
Times	Single Array - size NumScans	Array of scan times.
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:

Member	Format	Description
NumAnalogs	Long	Number of analog channels.
AnalogTypes	String Array - size NumAnalogs	Analog types.


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.

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 DACFunctionInfo
Dim strFileName As String
Dim nNumFunctions As Long
strFileName = "C:\Masslynx\Default.pro\Data\Pest03.raw"

nNumFunctions = sFuncInfo.GetNumFunctions(strFileName)

'Note that the function array is 1 - indexed
Dim nFunction As Long
For nFunction = 1 To nNumFunctions
    Call sFuncInfo.GetFunctionInfo(strFileName, nFunction)
    If sFuncInfo.FunctionType = "Scan" Then
        nFunction = nNumFunctions
    End 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.

Two important points should be noted from this code; DAC functions which take more than one parameter should always be called using the "Call" keyword, and the DAC objects should be set to "Nothing" after they have been used.


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 retention time - intensity pairs for a mass subtraction chromatogram:

IDACChromatogramPtr pChromatogram;

pChromatogram = IDACChromatogramPtr(CLSID_DACChromatogram);

pChromatogram->GetChromatogram("C:\\Masslynx\\Default.pro\\Data\\
Pest03.raw", 1, 0, 235, 400, false, "200-300");

long nNumScans = pChromatogram->NumScans;

VARIANT pfIntensities;
float HUGEP *afIntensities;

pChromatogram->get_Intensities(&pfIntensities);

HRESULT hr = SafeArrayAccessData(pfIntensities.parray, (void HUGEP**)&afIntensities);

SafeArrayUnaccessData(pfIntensities.parray);

float fInten = afIntensities[4];

Here the DACChromatogram class is declared as a smart pointer, pChromatogram.  The GetChromatogram initialise function is called, as before, and the number of scans can be accessed.  However, the Intensities array is accessed through a SafeArray and called using the function get_Intensities.  All DAC array access in VC++ are via functions with the name get_function member name.  Note that, once the SafeArrayAccessData function has been called, a SafeArrayUnaccessData function should follow.  The intensities array can then be accessed as normal.