Analyst® 1.6.

2 Software

Scripts User Guide

RUO-IDV-05-0270-A
Release Date: April 2013
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Contents

Foreword. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Analyst Software Scripts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Install or Uninstall Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Add Missing Zeros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
Add Normalized ADC Traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Analyst 1.2 Peak Finder Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Batch Script Driver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Change All Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Convert Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Create Quantitation Methods and Text Files . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
DBS Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Define Custom Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Delete Others . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26
DFT Tracker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Export IDA Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28
Export Sample Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30
Export to JCamp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
IDA Trace Extractor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Label Selections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40
Label XIC Traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Make Exclusion List from Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Make Subset File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
Manually Integrate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Mascot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Mass Defect Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52
Merge MRM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
MRM3 Optimization Script . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
MS3 Quant Optimization Script . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65
Multiple Batch Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .66
Open in Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Peak List from Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68
Regression Calculator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Remove Graph Selections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70
Repeat IDA Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71
Savitzky-Golay Smooth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .72
Selection Average and Standard Deviation . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Send to ACD SpecManager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .74
Signal-to-Noise Using Peak-to-Peak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76
Signal-to-Noise Using Standard Deviation . . . . . . . . . . . . . . . . . . . . . . . . . . . . .77
Split Graph Script . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .78
Subtract Control Data from Sample Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79

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Unit Conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .80

Wiff to MatLab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
XIC from BPC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
XIC from Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86

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Foreword

This guide provides information on how to use the Analyst® software scripts and is intended for
customers and FSEs.

Related Documentation
The guides and tutorials for the mass spectrometer and the Analyst® software are installed
automatically with the software and are available from the Start menu: All Programs > AB SCIEX
> Analyst. A complete list of the available documentation can be found in the online Help. To view
the Analyst software Help, press F1.

Technical Support
AB SCIEX and its representatives maintain a staff of fully-trained service and technical
specialists located throughout the world. They can answer questions about the system or any
technical issues that might arise. For more information, visit the Web site at www.absciex.com.

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Foreword

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Analyst Software Scripts

The purpose of this document is to explain how to install and use Analyst® software scripts. It
also provides an overview of the uses of each script and how to uninstall a script, if required.

Related Documentation
You can also create your own scripts using the Visual Basic Version 6 program. For more
information, refer to the Analyst® Automation Cookbook: A guide to controlling Analyst® Software
from Visual Basic .NET.

Install or Uninstall Scripts

Some scripts are automatically installed when the Analyst software is installed. The remaining
scripts are available in the Scripts folder. When you have decided which scripts you want to use,
use the following procedure to install them.

Note: This guide contains the scripts for all instruments and different software
versions. To determine which scripts the software version installed on your instrument
supports, refer to the Analyst software release notes.

Install a Script
1. Navigate to the following folder on your workstation: <drive>:\Program
Files\Analyst\Scripts.
2. Open the required folder, open the script folder, and then double-click
ScriptRunner.exe.
3. Follow the on-screen instructions to install the scripts.
The script is available on the Script menu.

Note: For some scripts, if you hold down the Shift key while accessing a
script on the Script menu, a description of the script is displayed.

Uninstall a Script
• To uninstall a script, do one of the following:
• For processing scripts, navigate to the <drive>:\Analyst Data\Projects\API
Instrument\Processing Scripts folder and then delete the script .dll or, if
applicable, .exe and .bmp files, manually.
• For acquisition scripts, navigate to the <drive>:\Analyst Data\Projects\API
Instrument\Acquisition Scripts folder and then delete the script .dll or, if
applicable, .exe and .bmp files, manually.

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Analyst Software Scripts

Add Missing Zeros

Use this script to add a value of zero intensity for the missing mass values in the spectrum. To
minimize storage requirements and to speed data display and processing, the Analyst® software
does not store or display spectral points with an original intensity of zero. If required, for example,
when exporting a spectrum for subsequent processing by custom software, you can add these
data points back to the spectrum.

Use the Script

• Click the spectrum and then click Script > Add Missing Zeros.
The script will add the zero values to all missing masses in the current spectrum.

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Add Normalized ADC Traces

Use this script to overlay the active chromatogram or chromatograms with normalized ADC data
from a corresponding data file. Run the script when a pane containing one or more
chromatograms is active in Explore mode. There may be a time region selected in a trace. If no
selection is made, then the entire chromatogram is overlayed.
In case that several ADC traces are part of the .wiff file, all of them will be displayed.

Notes
• If the data in the active pane came from several samples, then the ADC data for the
sample corresponding to the first data set (not the active data set) is shown.

Use the script

• Do one of the following:
• Click Script > AddNormalizedADC.
• To view the script description and add ADC data to an active Explore pane,
hold the Shift key down while clicking the script.

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Analyst Software Scripts

Analyst 1.2 Peak Finder Parameters

The Analyst® software uses an improved version of Peak Finder for better peak detection and ion
abundance measurement. If you are using the Peak Finder algorithm to analyze .wiff files that
were acquired using the Analyst software, then you can use this script to set the peak finder
algorithm parameters.

Install the Script

• Make sure that the Analyst Data\Projects\API Instrument\Processing Scripts folder
contains the Analyst12PeakFinderParams.dll.

Note: This script is installed automatically when the Analyst 1.6.2

software is installed. There is no separate installation program for it.

Use the Script

1. Click Script > Analyst12PeakFinderParams.
The Analyst 1.2 Peak Finder Algorithm Parameter dialog opens.
2. To activate the Analyst 1.2 version of Peak Finder, select the Use Analyst 1.2 peak
finder algorithm for Analyst 1.2 files check box.
3. Do the following:
• In the Intensity Threshold (%) field, type the value, as a percentage, of the
minimum intensity required to distinguish between noise and peak.
• In the Centroid Height (%) field, type the value, as a percentage, to be used
by the centroiding algorithm to find the peak and to determine the centroid m/z
value at this percentage height.
• In the Centroid Peak Width (min) field, type the minimum value, in ppm, to
be used by the centroiding algorithm to find the peak width and to determine
the centroid m/z value at this width.
• In the Centroid Peak Width (max) field, type the maximum value, in ppm, to
be used by the centroiding algorithm to find the peak width and to determine
the centroid m/z value at this width.
• In the Centroid Merge Distance (amu) field, type a value, in amu, to be used
to determine whether two centroid peaks should be merged into one. If two
peaks are within this tolerance, then they will be merged together.
• In the Centroid Merge Distance (ppm) field, type a value, in ppm, to be used
to determine whether two centroid peaks should be merged into one. If two
peaks are within this tolerance, then they will be merged together.
4. Click OK.
5. To return to the Analyst 1.4.1 Peak Finder algorithm, clear the Use Analyst 1.2 peak
finder algorithm for Analyst 1.2 files check box.

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Batch Script Driver

With the Batch Acquisition Script Driver, you can run an acquisition script on multiple data files
(.wiff) by attaching the acquisition script to a batch that is submitted to the queue. These scripts
are used to immediately process the data either after a sample completes or after the batch
finishes. The script will process the data files as if they were separate batches submitted to the
queue. Occasionally, you might need to apply these acquisition scripts on previously acquired
data because either the script did not exist at the time of acquisition or a rerun of the script is
required.

Use the Script

1. Navigate to C:\Program Files\Analyst\bin and then double-click
BatchScriptDriver.exe.
Figure 1-1 Batch Acquisition Script Driver Dialog

2. To select an acquisition script, click Select.

3. To add a data file, click Add File. Click Add Folder to add an entire folder of data
files.
4. To remove a data file, select it from the list and then click Remove Selected. Click
Remove All to remove all the data files.
5. To process some of the samples contained in a .wiff data file, select the Process
Limited Sample Number Range check box. This field is available only if you have
selected only one data file to process.
6. In the from sample and to fields, type the sample number range to be processed.

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Analyst Software Scripts

7. To run the script on each data file in the list, click Run.
8. To stop the script, click Close.

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Change All Methods

It is often necessary to change the ion source conditions of a method, particularly with the
NanoSpray® ion source after changing the emitter tip. This script modifies every method in a
selected project with new values for IonSpray Voltage (IS), Ion Source Gas 1 (GS1), and
Interface Heater Temperature (IHT).

Note: This script is used with any QTRAP® system. It is not used by QSTAR®
instruments.

Use the Script

1. Click Script > change all methods.

Figure 1-2 Change All Methods Dialog

2. Select a project containing the methods that you want to modify.

3. Select the parameters that you want to change. If the parameter is not in the method
file, it will be ignored.
4. Type a value for positive experiments.
5. Type a value for negative experiments.
6. Select the update method with current instrument settings check box if you want
to change the AF3, EXB, and C2B parameters for all the methods in the selected
project.
7. Click Change All.

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Analyst Software Scripts

Convert Methods
Use this script to convert methods from one type of instrument to another. The script converts the
method to the currently active hardware profile, using appropriate values for each parameter.
Only the ion source and compound dependent parameters for mass ranges and experiments are
shown.
The Convert Methods script automatically optimizes mass ranges and, in addition to single
period, single experiment methods, converts multiple periods, multiple experiments, and IDA
criteria.

Prerequisites
• .Net framework 3.5 SP2 (will be automatically installed if required)

Install the Script

• To install the script, navigate to the <drive>:\Program Files\Analyst\Scripts\Convert
Methods folder and then double-click Convert Methods Setup.exe.

Use the Script

Make sure a hardware profile is active.
1. Click Script > Convert Methods.
Figure 1-3 Convert Methods Dialog

2. Click Open, navigate to the method that you want to convert, and then click Open.
The Method Converter dialog displays the instrument name of the original method.
3. Click Save, type a name for the converted method, and then click Save.

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 Analyst Software Scripts

Create Quantitation Methods and Text Files

The Create Text File From Quan Method script exports a quantitation method to a tab-delimited
text file. The Create Quan Method From Text Files script imports the information contained in a
tab-delimited text file to a Quantitation Method File (.qmf). Currently, the Quantitation Method
component in the Analyst® software does not support this functionality.
The Create Text File from Quan Method script creates a text file representation of a quantitation
method file. A column in the text file is created only for all of the required fields. The optional
fields will be created if the field value is not the same for all peaks in the quantitation method.
The Create Quan Method From Text Files script specifies the default values for any of the non-
required fields in the text file such as integration algorithm or regression parameters. For more
information, refer to Text File Format on page 17.

Use the Create Quan Methods From Text Files Script

1. Click Script > Create Quan Methods From Text Files.
Figure 1-4 Create Quantitation Methods from Text Files Dialog

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Analyst Software Scripts

2. Use the parameters in the Default Generic Parameters group to create a

quantitation method. The Algorithm, Extraction Type, Period, and Experiment
fields are not available in the Analyst software. Set the following parameters as
required:
• In the Algorithm drop-down list, select a peak-finding algorithm. The Window
Summation algorithm sums all the intensities in the retention threshold and will
not find any peaks.
• In the Extraction Type drop-down list, select the type of data that will be
integrated.
• In the Period and Experiment drop-down lists, select the period number and
experiment number.
The Default Analyst Classic Parameters, Default General IntelliQuan Parameters,
Default IntelliQuan MQ III Parameters, and the Default Window Summation
Parameters groups contain the parameters that are used by the algorithm selected
in the Algorithm field.

Note: The Smoothing Width field in the Default General IntelliQuan

Parameters group is half the smoothing width.

3. Select the Use Baseline Subtraction check box to have the Window Summation
algorithm sum the intensities to the horizontal line at the minimum intensity of the
data points within the summation window, as opposed to summing down to the
intensity zero.
4. In the Regression Parameters group, select the regression information. The
information specified here is applied to every analyte peak. Unlike the previous
parameters, it is not possible to indicate this information in the text files; therefore,
the same regression parameters are applied to all analytes. For a full description of
the parameters, refer to the Help.
5. To create one quantitation method, click Create One Method and then navigate to
the text file that will be used to create the quantitation method.
6. To create multiple methods from multiple text files, click Create Multiple Methods
and then navigate to the folder. A quantitation method is created for each text file in
this folder.

Use the Create Text File from Quan Method Script

1. Create and save a quantitation method in the Analyst software.
2. Click Script > Create Text File from Quan Method.

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Figure 1-5 Options Dialog

s.

3. Select the Export all columns check box and then click OK.
4. Navigate to and select the quantitation method file (.qmf).
5. Navigate to and select the location of the text file.
The script will generate the text file.

Text File Format

The text files used to create the quantitation methods (Create Quan Methods from Text Files) and
generated from the methods (Create Text File from Quan Method) are in the following format:
• Separate the various fields with tab characters and end each line with a carriage
return / line feed characters.
• The very first row of the file should contain column headings. All of the columns
shown in the following table marked as Required must be present; the remaining
columns are optional. The actual order of the columns is not important.
• Each subsequent line should contain the information as shown in the table for either
one analyte or an internal standard peak.
Table 1-1 Text File Formats
Column Name Required Description
Peak Name Yes The name of the analyte or internal standard peak.
First Mass Yes For MRM data, the Q1 mass for the peak; for full-scan data,
the starting mass for the XIC to integrate; for Q1 MI or Q3
MI data, the mass.
Second Mass Maybe This field is required when integrating full-scan or MRM
data, but not for Q1 MI or Q3 MI data. For MRM data, this is
the Q3 mass for the peak; for full-scan data, it is the ending
mass for the XIC to integrate.
Extraction Type No The type of data to integrate. If present, this should be one
of:
0 – MRM data
1 – Q1 MI or Q3 MI data
2 – full-scan data

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Table 1-1 Text File Formats (Continued)

Column Name Required Description
Is IS No Specifies whether the current peak is an internal standard or
an analyte. Select Yes if the peak is an internal standard;
otherwise select No. If this column is not present, then all
peaks defined are assumed to be analytes.
Note: Internal standard peaks should be defined first in the
text file before any analyte peaks that use that IS.
IS Name No For analyte peaks, specifies the name of the corresponding
internal standard (if any). If a given analyte will not use an
internal standard, leave the contents of this field empty. For
internal standard peaks themselves, the contents of this
field are ignored.
Period No The period number for the peak (from 1 to the number of
periods in the data).
Experiment No The experiment number for the peak (from 1 to the
maximum number of experiments in the period).
Use Relative RT No For analyte peaks that are using an internal standard,
specifies whether or not the expected retention time is
relative to that of the IS. Select Yes if so; otherwise, select
No. The contents of this field are ignored for other peaks,
but must still contain either Yes or No.
Conc Units No The concentration units.
Calc Conc Units No The calculated concentration units.
Bkg Start No Start time in minutes for the peak background. Note that this
parameter does not affect the peak integration in any way,
however it does affect how the noise (and hence S/N) is
calculated.
Bkg End No End time in minutes for the peak background.
Expected RT No The expected retention time in minutes (from 0 to 1666).
RT Window No The retention time window in seconds (from 1 to 1000).
Algorithm No Specifies which peak-finding and integration algorithm
should be used. If present, this should be one of:
0 – Analyst Classic (TurboChrom)
1 – IntelliQuan - IQA II (Automatic)
2 – IntelliQuan – MQ III
3 – Window Summation
Note that the window summation algorithm is not available
from within the Analyst software user interface, but can be
enabled using the script.
Bunching Factor No The bunching factor for the peak (from 1 to 100) when using
the TurboChrom algorithm.
Num Smooths No The number of smooths (from 0 to 10) when using the
TurboChrom algorithm.

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Table 1-1 Text File Formats (Continued)

Column Name Required Description
Noise Threshold No The noise threshold (from 1-6 to 19) when using the
TurboChrom algorithm.
Area Threshold No The area threshold (from 1-6 to 112) when using the
TurboChrom algorithm.
Separation Width No The separation width (from 0 to 5) when using the
TurboChrom algorithm.
Separation Height No The separation height (from 0 to 1) when using the
TurboChrom algorithm.
Exp Peak Ratio No The exponential peak ratio (from 1 to 16) when using the
TurboChrom algorithm.
Exp Adjusted No The exponential adjusted ratio (from 2 to 16) when using the
Ratio TurboChrom algorithm.
Exp Valley Ratio No The exponential valley ratio (from 1 to 16) when using the
TurboChrom algorithm.
Min Height No The minimum allowed peak height (from 0 to 116) when
using the IntelliQuan algorithm.
Min Width No The minimum allowed peak width (from 0 to 116) in seconds
when using the IntelliQuan algorithm.
Smooth Width No The half-width of the Savitzky-Golay smoothing filter (from 0
to 20) when using the IntelliQuan algorithm.
MQ III Noise No The noise percentage when using the MQ III option of the
Percent IntelliQuan algorithm. This should be an integer from 0 to
100.
MQ III Baseline No The baseline subtraction window (from 0 to 10 minutes)
Sub Window when using the MQ III option of the IntelliQuan algorithm.
MQ III Peak No The peak-splitting factor (from 0 to 10) when using the MQ
Splitting Factor III option of the IntelliQuan algorithm.
MQ III Use Largest No When using the MQ III option of the IntelliQuan algorithm,
specifies whether the largest peak (within the retention time
window) or the peak whose retention time is closest to that
expected is reported. Select Yes to use the largest peak and
No to use the closest.
Summation No When using the special window summation algorithm,
Baseline Sub specifies whether the area should be integrated to the
intensity=0 line or to the intensity value of the least intense
data point within the window.

The following table shows an example text file for full-scan data. Imagine that there are tabs
between the columns and a hard return at the end of each line.
Table 1-2 Example Text File for Full-Scan Data
Peak Name First Mass Second Mass Bunching Factor
Analyte Peak 1 500.10 500.70 1

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Table 1-2 Example Text File for Full-Scan Data (Continued)

Peak Name First Mass Second Mass Bunching Factor
Analyte Peak 2 812.00 813.00 2
Analyte Peak 3 400.00 401.00 3

The following table shows one more example for MRM data. The Analyte Peak 1 will be set up to
use the specified internal standard and Analyte Peak 2 will not use an internal standard.
Table 1-3 Example Text File for MRM Data
Peak Name Is IS IS Name First Mass Second Mass
IS Peak 1 Yes 500.10 413.20
Analyte Peak 1 No IS Peak 1 600.20 382.10
Analyte Peak 2 No 400.00 312.1

The following table contains a mixture of full-scan and MRM data in different experiments:
Table 1-4 Example Text File for MRM Data
Peak Name Extraction Experiment First Mass Second Mass
Type
Analyte Peak 1 0 1 500.10 413.20
Analyte Peak 2 0 1 600.20 382.10
Analyte Peak 3 2 2 812.00 813.00
Analyte Peak 4 2 2 400.00 401.00

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DBS Settings
The DBS (Dynamic Background Subtraction™ algorithm) is a feature that ensures better
selection of precursor ions in an IDA (Information Dependant Acquisition) experiment. When
DBS is activated, IDA uses a spectrum that has been background subtracted to select the
candidate ion of interest for MS/MS analysis, as opposed to selecting the precursor from the
survey spectrum directly. DBS enables detection of species as their signal increases in intensity,
thus focusing on detection and analysis of the precursor ions on the rising portion of the LC peak,
up to the top of the LC peaks (maximum intensity).
The DBS functionality is embedded in the Analyst® software for IDA experiments. However, the
associated parameters are not accessible in the Analyst software. The hidden parameters and
their default values are as follows:
• Average number of previous spectra = 4
• Smooth before subtract: activated
• Smooth = 5 data points.
Use this script to change the default parameters to ones that are more representative of the
experimental conditions. Depending on the cycle time and chromatography, the default settings
may result in an obvious candidate ion from being omitted for dependent MS/MS analysis or the
same candidate ion may be selected for MS/MS analysis over the entire LC peak. Therefore, this
script will be useful to customers who find that the embedded default values are not appropriate
for their analysis.
After the script is installed, the DBS feature uses the settings in the script. The script will
remember the last settings used.

Prerequisites
• Analyst 1.6.2 Software installed
• Administrator rights on the computer

Use the Script

1. Activate the DBS feature by selecting the After Dynamic Background Subtraction
of Survey scan check box on the IDA – First Level Criteria tab.

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2. Although the DBS feature is activated at the method level, the DBS options are set
using the script. From the Analyst software menu, click Script > DBS Settings.

• Subtract the _ previous spectra from current spectrum: Use this field to
select the number of spectra averaged to represent the background signal.
These spectra are taken immediately before the current survey spectrum.
Typical values used are between 2 and 5.
• Smooth Before Subtract: Select to make sure that the current survey
spectrum is smoothed using a Savitzky-Golay smooth before the subtraction
step. Select the number of points to consider in the process. A typical value is
5.

Survey Scans Supported

The DBS feature can be used with any IDA survey scans currently supported: EMS, EMC,
Precursor Scan, Neutral Loss, MRM, Q3 MS and Q3 MI. DBS does not apply to the confirmation
or dependant levels.

Known Limitations and Issues

• With the exception of DBS being on or off, DBS parameters are not stored as part of
the file information. In order to recall which settings were used, the user should
document the parameters selected during the acquisition.
• DBS is meant for use during LC analysis, therefore, when performing IDA by infusion
it is recommended to have DBS deactivated.

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Define Custom Elements

Use this script to select a custom isotope pattern when working with radio-labeled compounds.
An experiment-specific element pattern is used in the data interpretation in conjunction with the
Analyst® software calculators or the Metabolite ID application.
The custom isotope patterns are stored together with the information from the periodic table
elements in the element definition file, SAElements.ini, which is located in the Analyst\bin folder.
In the element definition file, the custom elements must have a unique symbol and an atomic
number of 104 or higher.

Prerequisites
The following program is optional:
• Metabolite ID 1.3 for Analyst QS 2.0 software
When the script is launched for the first time, a backup copy of the SAElements.ini file is saved in
the API Instrument folder. If needed, the edited SAElements.ini file in Analyst\bin folder can be
replaced with this file.

Update the Element Definition File Successfully

1. Do not open the SAElements.ini file in another text editor program while using the
software.
2. Make sure the file access must be set to read/write.

Edit the Define Custom Elements Table

The custom element table cannot be edited in the dialog. After the element definition file is
updated, the custom elements can be used with the Analyst software calculators.
1. Click Script > DefineCustomEl.

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Figure 1-6 Define Custom Elements Dialog

2. In the table, click the row containing the element.

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Figure 1-7 Define Element Dialog

3. Edit the fields and then click OK.

4. To save the updated element definition file and exit the program, click OK.

View the Custom Element Symbol, Custom Element Name, and Custom Pattern
• To view the custom pattern in the mass/relative intensity graph, in the Define
Custom Elements dialog, click Show.
The Isotopic Distribution dialog opens.
The total of the individual isotope abundance for an element stored in the element
definition file must be equal to one. Therefore, the abundances entered in the Define
Element Window are rescaled before they are added to the Define Custom Elements
dialog. This Isotopic Distribution dialog cannot be edited. You can zoom in the area
of interest by dragging along the corresponding x- or y-axis region.
The application requires the gen01.wiff example file to display custom pattern. If the
gen01.wiff file is not in the Example folder in the Analyst Data\Projects folder, you will
be prompted to find this file.

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Delete Others
Use this processing script to delete all panes except for the active one.

Use the Script

1. With a sample file (.wiff) with multiple panes open, click a pane.
The pane becomes the active pane.
2. Click Script > DeleteOthers.
All the panes except for the active one are deleted.

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DFT Tracker
The Dynamic Fill Time (DFT) Tracker script tracks the DFT settings used during QTRAP®
instrument scans. You can use the script to determine the optimal fill time for linear ion trap (LIT)
mode to obtain high data quality over a wide dynamic range. The DFT Tracker monitors the
following LIT scan types: Enhanced MS (EMS), Enhanced Resolution (ER), Enhanced Product
Ion (EPI), and MS/MS/MS (MS3).

Use the Script

• Click Script > DFTTracker.
Figure 1-8 Dynamic Fill Time Tracker Dialog

DFT Tracker monitors the dynamic changes occurring during a real-time run.
The system dynamically calculates the time required to fill the linear ion trap. For
abundant compounds, a short fill time reduces the space charge effects by limiting
the number of ions in the ion trap; on the other hand the longer fill time increases
weak signals by allowing the ions to accumulate.

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Export IDA Spectra

Use this script to export data in a format that can be searched using a third-party application. The
Export IDA Spectra script exports every dependent product spectrum from an IDA (Information
Dependent Acquisition) LC/MS run to a series of text files. These text files can then be submitted
and searched using Sequest. The export is optimized so that any spectra in adjacent cycles with
the same precursor m/z are combined into a single spectrum. This optimization also applies to
spectra with the same precursor but which reside in different experiments, most likely using
different values of the collision energy.
The charge state of the precursor ion is a required input. Sequest tries to automatically determine
this from the isotope spacing at the precursor m/z in the IDA survey spectrum. Note that while
this determination is usually correct, it is not always so.

Use the Script

It is assumed that the first experiment of the IDA method represents the survey spectrum and
that all other experiments represent dependent product spectra. Therefore, this script cannot be
used if there are multiple survey experiments.
1. With an IDA chromatogram in an active pane, click Script > Export IDA Spectra.

Figure 1-9 Export IDA Spectra (in Sequest Format) Dialog

2. In the Mass tolerance for combining MS/MS spectra field, type the tolerance to be
used to determine if two precursor m/z values should be considered identical. If the
precursors for two sequential product spectra differ by less than this value, the
spectra are added and a single text file is exported.
3. In the MS/MS intensity threshold field, type the threshold that is applied to each
product spectrum after it is centroided. It is assumed that peaks below this threshold
are most likely noise. Type 0 in the field if you do not want to use a threshold.
4. In the Minimum number of MS/MS ions for export field, type the minimum number
of ions that must be present in a product spectrum, after centroiding and
thresholding, in order for a text file to be exported. If a spectrum does not contain the
specified number of ions, it is assumed that the quality of the spectrum is too low to
merit exporting.

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5. To separate fields in the output files with a space character, select the Separate
values in output with a space, not a tab check box; otherwise a tab character is
used. (Certain versions of Sequest require a space delimiter.)
6. To export the text files, click Go.
7. In the Save As dialog, type a location and root file name for the exported text files.
Before being exported to a text file, each of the product spectra is centroided. The
cycle number range and charge state is appended to this file for each exported
spectrum.

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Export Sample Information

Use this script to extract sample information, such as the name, sample ID, comment, and
acquisition method name for all samples in the .wiff file. You can define the information you would
like exported, and the script saves the information in an .inf file located in the same folder as the
.wiff file.

Use the Script

1. With a chromatogram or spectrum in an active pane, click Script >
ExportSampleInformationFromMultipleSampleinOneWiff while pressing the Ctrl
key.

Figure 1-10 Export Sample Information Dialog

2. Select the check boxes that correspond to the information that you want to export
and then click OK.

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Export to JCamp
You can use the Analyst® software to export graph data to a tab-delimited text file that can be
read by most applications. However, some applications require a more specific format.
With the Export to JCAMP script, you can export graph data in the JCAMP format. The script
works on both chromatograms and spectra. For chromatograms, depending on the number of
selections made, either all the spectral data of the chromatogram is exported, or the averaged
sum of the selected regions is exported. If you are using this script on a single spectrum, then
only that data is exported. This script can also be attached to a batch so that the export occurs
automatically after the sample is acquired.
Table 1-5 shows an overview of the operation of the script. When run interactively the exact
behavior depends on the active Analyst software data.
Table 1-5 Script Operation
Modes Active data Operation
Interactive Spectrum You will be prompted for the name of the JCamp file and
the active spectrum exported to it.
Interactive Chromatogram with You will be prompted for the name of the JCamp file and an
two or more averaged spectrum corresponding to each of the
selections chromatogram’s selections exported to it.
Interactive Chromatogram with You will be prompted for the name of the JCamp file and
one or no selections every spectrum for the run exported to it.
Batch N/A The name of the JCamp file is generated by appending the
sample number to the name of the .wiff file and changing
the extension to jdx. Every spectrum for the run is exported
to the JCamp file. For multiple period/experiment data, a
separate file is exported for each experiment (the period
and experiment numbers are appended to the filename).

Use the Script

1. To use the Export to JCAMP do one of the following:
• With either a chromatogram or a spectrum in an active pane, click Script >
Export to JCAMP.
• In the Batch Editor dialog, type Analyst Data \API Instrument\Processing
Scripts\Export to Jcamp.dll in the Batch Script field.

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Figure 1-11 JCAMP Options Dialog

2. To select the centroiding options, do one of the following:

• Check the Centroid Exported Spectra check box to centroid the spectra
before exporting to the JCAMP format.
• To have the JCAMP Options window appear only if the Ctrl key is pressed
when clicking the script from the Script menu, or when submitting the batch to
the queue, select the Only show this dialog again if the control key is
down check box.
3. To continue processing and to have the spectrums exported, click OK.
4. When prompted, type the file name of the exported JCAMP file. When a script is
attached to the batch, the file name is automatically generated using the following
format: [WiffFileName]_[Sample#]_[Period#]_[Experiment#].jdx

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IDA Trace Extractor

Use this script to review the survey data collected using IDA (Information Dependent Acquisition)
based on the information in the corresponding dependent data. The script searches the MS/MS
data for given neutral losses or fragments and then calculates the Extracted Ion Chromatograms
(XICs) for the precursor masses, which give the specified losses or fragments. The XICs are
overlaid in Explore mode and their peaks are labeled with the precursor mass (Figure 1-12).
Figure 1-12 Characteristic Traces in Dependent Experiment and XICs of the Survey
Experiment. The characteristic m/z 387.1 detected in negative mode was
converted to m/z 389.1 in the positive survey scan.

You can use the script to do the following:

• Specify a list of expected fragments or neutral losses, in either the positive mode
polarity, the negative mode polarity or both, in terms of fragment formula or mass.
• Save the list of masses and fragments for a compound class and load them to the
settings at a later time.
• Process just a selected time region in the chromatogram.
• Display precursor (survey scan) or fragment (dependent scan) XIC trace that yield
given fragment or neutral loss.
• From the survey scan chromatograms the user can link to any survey scan
spectra
• From the dependent scan traces the user can link to any dependent scan
spectra
• Reduce the precursor XIC traces to show just peaks that have corresponding neutral
losses (or fragments)
• Save the precursor mass list in a text file for further processing; build the list of
precursors from a set of samples
• Save the list of masses in a format that can be loaded to the XICfromTable script

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• Save the list of masses and peaks in a format that can be loaded to the
CreateQuantMethodFromText script.

Note: The script is compatible with MRM / MIM IDA data and with the Analyst® 1.6.2
software.

Note: The script supports parallel data processing from positive and negative
experiments. Multiple survey and dependent experiments of any polarity can be used.

Use the Script

Note: The Analyst software version for a specific file can be displayed in the file
properties > comments.

1. With a chromatogram of IDA data open in an active pane, click Script >
IDATraceExtractor.
You can process a full chromatogram or just a selected region (make a selection
before running the script).
Figure 1-13 IDA Trace Extractor Dialog

2. In the Options tab of the script, set the fields as required. For more information, refer
to Table 1-6 Tab and Menu Parameters on page 36.
3. To store the retention times and precursor masses found during processing, click the
Results tab, type a filename, and then select Save Precursor Information.

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Figure 1-14 IDA Trace Extractor Dialog: Results Tab

4. To review or enter the mass information, click the Neutral Losses or Fragments
tab. Type the neutral losses and fragments as masses or chemical formulas. You
can also specify the polarity of the Neutral Loss or fragment spectrum experiment
where the specified neutral loss or fragment is expected to be found.
Figure 1-15 IDA Trace Extractor Dialog: Neutral Losses Tab

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Figure 1-16 IDA Trace Extractor Dialog: Fragments Tab

5. Click Extract to find the survey XIC traces that give the selected neutral loss or
fragment.
6. If the precursor information was saved, the found precursor mass/time data can be
converted to a compatible format using other scripts. To convert the data, click the
Results tab and then select the Results File. View and edit this file as required.
• To make a format for the XICfromTable script, click Make XIC Table. The
Results File will be converted into a file of the same name with the suffix _XIC.
• To make a format for the CreateQuantMethodFromText script on the
Precursor XICs dialog, click Make Quant Input. The Results File will be
converted into a file of the same name with the suffix _Peaks.
7. Click File > Save Settings as. Alternatively, previously saved settings can be used.
Click File > Load Settings to open previously saved settings.
Several functions are available in the Tools menu. You can start processing without switching to a
specific tab.
Table 1-6 Tab and Menu Parameters
Location Parameters Description
Neutral Losses Use Masses Select the required neutral loss(es) as
mass.
Neutral Losses Use Formulas Select the required neutral loss(es) as
formula.
Neutral Losses Start Low mass limit (from mass) for the
neutral loss(es).
Neutral Losses End High mass limit (to mass) for the neutral
loss(es).

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Table 1-6 Tab and Menu Parameters (Continued)

Location Parameters Description
Neutral Losses Formula Chemical formula of the neutral loss.
Neutral Losses Extract Start data processing according to the
current settings.
Neutral Losses Clear Clear all neutral losses in the settings.
Neutral Losses Polarity Select the polarity of the Neutral Loss
experiment where the specified neutral
loss is expected to be found.
Fragments Use Masses Describe the characteristic fragment(s) in
terms of their m/z.
Fragments Use Formulas Describe the characteristic fragment(s) in
terms of their formulas.
Fragments Start Low mass limit (from mass) for the
fragment m/z window.
Fragments End High mass limit (to mass) for the
fragment m/z window.
Fragments Formula Chemical formula of the fragment
(protonated/ deprotonated form).
Fragments Extract Start data processing according to the
current settings.
Fragments Polarity Select the polarity of the fragment
spectrum experiment where the specified
fragment is expected to be found.
Fragments Clear Clear all fragments in the settings.
Options From Time (min) Start of time region to be processed.
Options To Time (min) End of time region to be processed.
Options Trace Width (Da) Width of XIC traces in resulting survey
scan and dependent scan
chromatograms and mass tolerance
window for processing in case that the
neutral losses or fragments are specified
as chemical formulas.
Options Remove Unconfirmed Review all peaks in the survey XIC traces
Peaks and retain only those that were validated
based on the data in corresponding
dependent scan.
Options Spectrum Peaks > Minimum size of diagnostic peak in
dependent scan in terms of signal to
noise (lowest measurable signal).
Options Label Peaks > Peak label threshold applied to resulting
survey and dependent scan
chromatograms (note that just the largest
peak in each trace is labeled).

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Table 1-6 Tab and Menu Parameters (Continued)

Location Parameters Description
Options Show Survey Scan Display XICs (original or filtered) from the
Chromatograms survey scan that correspond to parent
masses yielding specified fragment or
neutral loss.
Options Show Dependent Display neutral loss traces (one for each
Chromatograms neutral loss) reconstructed from
dependent scan data.
Options Subtract Peaks Present in Remove peaks that can be found in the
Control Sample control sample XICs from the survey
scan chromatograms.
Results Result File Select Results file (containing identified
peak times and masses will be saved).
Results Save Precursor Write processing results (list of found
Information peaks - times and masses) to selected
results file.
Results XIC Peaks > Minimum size of the peak in survey scan
to be stored in the results file.
Results Append Results to an Do not overwrite existing results file.
Existing File
Results View Open the selected results file.
Results Make XIC Table Use the selected results file to prepare
settings file for XIC from Table script.
Results Make Quant Input Use the selected results file to prepare an
input for CreateQuanMethodFromText
script.
File Menu Load Settings… Load previously saved script settings to
the interface.
File Menu Save Settings As… Save current script settings for future
use.
File Menu Set Results File… See Results/Result File
Tools Menu Extract Fragments See Fragments/Extract
Tools Menu Extract Neutral Losses See Neutral Losses/Extract
Tools Menu Clear Fragments See Fragments/Clear
Tools Menu Clear Neutral Losses See Neutral Losses/Clear
Tools Menu Make XIC Table See Results/Make XIC Table
Tools Menu Make Quant Input See Results/Make Quant Input

Table 1-7 Related Scripts

Script Name Description
Export to JCamp Converts spectra from .wiff format to JCamp format.

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Table 1-7 Related Scripts (Continued)

Script Name Description
MSMS Methods from MW Allows lists of molecular weights obtained from text files to be used
Lists as the basis for creating a series of MS/MS acquisition methods.
Multiple Batch Scripts Allows multiple batch acquisition scripts to be used at the same time
Script (the Batch Editor only allows a single batch script to be specified).
Unit Conversion Converts from one set of concentration units to another.
Wiff To MatLab Converts the data from a data file from the ‘.wiff’ format to MatLab
(.mat) format.

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Label Selections
Use this script to add missing labels to the selected peaks in the active graph or to remove them.
The script can be run when a pane containing a spectrum or a chromatogram is active in Explore
mode, and there are one or more selections in the active pane. If neither peak mass (spectrum)
nor peak retention time (chromatogram) is available, the data will be marked with information for
the selection maximum.

Note: Only font type and label color are synchronized with the automatic labels. For
the best performance, synchronize the other font attributes manually in the Appearance
Options dialog.

Note: Labeling spectra with centroid mass/charge state appends just the centroid
mass. Labeling chromatograms with base peak ion mass or base peak ion intensity is
not supported.

Use the Script

• Do one of the following:
• To add labels to selections in active graph, click Script > LabelSelections.
• To view the script description and add the labels to an active Explore pane,
hold the Shift key down while clicking the script.

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Label XIC Traces

Use this script when a pane containing one or more XIC traces is active in Explore mode. There
may be a time region selected in a trace. If there is no selection, a complete chromatogram will
be considered for processing. The script labels the largest peak in each XIC trace with mass.
XIC traces with a maximum point of less than 5% of the most intense trace will not be labeled.
Other types of traces (TIC, ADC) in the overlay will be ignored.

Note: No user settings are required for this script.

Use the Script

• Do one of the following:
• Click Script > LabelXICs.
• To view the script description, and add the labels to an active Explore pane,
hold the Shift key down while clicking the script.

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Make Exclusion List from Spectrum

Use this script to create a text file containing all of the peaks from the currently active spectrum.
The text file is in a format that can be directly imported into the Analyst® software IDA
(Information Dependent Acquisition) exclusion list.

Use the Script

If the spectrum has been previously manually centroided, the resulting peak list is exported
directly to the exclusion text file. Otherwise, the script will first centroid the spectrum.
1. With a spectrum in an active pane, click Script > Make Exclusion List from
Spectrum.

Figure 1-17 Make Exclusion List from Spectrum Dialog

2. In the Exclusion List File Name field, type the name and path of the text file.
3. If required, in the Threshold field, type the threshold that will be applied to the
centroided spectrum so Threshold field that small noise peaks are not included in
the exclusion list. Type 0 in the to not use a threshold.
4. Click Export to export the exclusion list using the specified parameters.

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Make Subset File

Use this script to manipulate data files by transferring samples to another data file, unpacking all
samples in a data file to their own data file, and decomposing a single sample into many
samples.

Use the Script

Section 1: General
This section describes how to select a data file to work on.
1. Click Script > MakeSubsetFile.
Figure 1-18 Make Subset File Dialog

2. By default, all the files in the current project data folder are loaded. To add another
file to this list, click File > Open and then navigate to the file.
3. Click the file.
4. To exit the program, click File > Exit.

Section 2: Transfer
This section describes how to transfer samples from one data file to another.
1. Click the Transfer tab.
All the samples in the current working data file will automatically appear in the
Samples to Transfer list.
2. To exclude a sample from the transfer, select it from the list and then click >>.
The unwanted sample is shown in the Samples to Exclude list.
3. To include an excluded sample in the transfer, select it from the Samples to
Exclude list and then click <<.
4. To exclude all the samples, click the Remove All type the full path and the file name
of the file in which the sample will extract, or navigate to a file. If the file does not
exist, the Make Subset File script will create it.
5. To start the transfer, click Extract.

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Section 3: Unpack
This section describes how to unpack every sample in one data file into its own data file.
1. Click the Unpack tab.
2. In the Destination Directory group, the location of the current working data file is
shown. Use this tree to select the location for the unpacked data files.
3. To create a new directory, right-click the directory tree. You will be prompted to type
the new folder name and set the active folder.
4. In the Output File Name text field, type the output file name. Each sample
unpacked from the working data file will begin with this name followed by the sample
number in parentheses. Do not give an extension to this file (for example, do not
include “.wiff”), because the Make Subset File program will automatically append
this.
5. To begin unpacking the samples, click Extract.

Section 4: Decompose
This section describes how to decompose a sample into different samples.
1. Click the Decompose tab.
2. To use the Make Subset File script default values, select the Use Defaults check
box.
3. To provide threshold values, deselect the Use Defaults check box and then type the
values in the fields.
• The Noise field contains the noise threshold value. This value indicates when
a sub-sample begins and ends. If the intensity value exceeds this threshold,
then it is considered a new sample. After an intensity value falls below this
threshold, the sub-sample is considered complete and it is sent to the file.
• The Width field contains the width threshold value. This value is used to
prevent short periods of loud noise. If noise exceeds the noise threshold value
for a short period of time (that is, have a small width) then without the width
threshold this noise will be considered a new, sample. Only detected samples
with a width that exceeds the width threshold will be exported to the file.
4. In the Decompose To field, type the full path and the file name of the file in which
the sample will be decomposed, or navigate to a file. If this file does not exist, then
the Make Subset File program will create it.
5. To start decomposing the sample, click Extract.

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Manually Integrate
The Analyst® software has various peak-finding algorithms that determine and integrate peaks
and then show the results in the peak list. If required, you can also use the Manually Integrate
script to integrate a selected region of a graph because the software may not have detected the
peak or perhaps because only a portion of the peak is of interest.
Use the script to draw a line on a chromatogram and have the area above the line integrated.
The integrated area is highlighted in the chromatogram, and the calculated area of the region can
be pasted on the graph. The results are displayed in the script window, which can also be added
to the graph or exported to a text file for storage.

Use the Script

1. With a chromatogram opened, click Script > Manually Integrate.
The fields in the Result group are modifiable from the Options button.

Figure 1-19 Manual Integration 1 Dialog

2. In the Text File Exporting group, click Select to navigate to a text file.
3. Do one of the following:
• Select Automatically export after each selection to automatically export the
results to the specified text file.
• Click Export Now to export the current results.
4. To remove the last exported results from the text file, click Remove Last Entry.
5. To populate the fields in the Result group, highlight a section of the graph. The
values are calculated using the selected area of the graph.
6. To change the manual integration options, click Options.

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Figure 1-20 Manual Integration Options

7. If required, in the Mode group, do one of the following:

• Click Add area as caption to graph, then quit to paste the area of a single
selection on the graph and then exit the program.
• Click Add area as caption to graph and stay open to display the area on the
graph as well as in the program.
• Click Don’t add caption to graph (and stay open) to only display the results
in the program and to leave the graph unaltered.
8. Select the following as required:
• In the Display Format group, select how the results will be displayed in the
Manual Integration 1 dialog.
• Select the Show integrated area in graph check box to display the integrated
area in the active chromatogram.
• Select the Force zero intensity baseline check box to force the integrated
area to start from the intensity=0 baseline. In this case, the starting and ending
times from the manual selection are used, but the y-positions are ignored.
• Select the Report ‘raw’ peak height check box to report the peak height as
the intensity of the largest point comprising the peak. If the check box is
cleared, then the usual software algorithm is used to calculate the peak height
(a parabola is fitted to the three largest data points and the peak height is set
to the y-value of the parabola’s apex).
• Select the Report centroid Retention Time check box to report the retention
time using a centroid calculation. If the check box is cleared, then the usual
software algorithm is used to calculate the retention time (a parabola is fitted
to the three largest data points and the retention time is set to the x-value of
the parabola’s apex).

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• The Fixed RT width: _ sec option is for MALDI workflows only. If selected, the
total width of the resulting peak is fixed at the specified value and is centered
at the apex retention time.
9. To save changes and return to the Manual Integration 1 dialog, click OK.
10. On the Manual Integration 1 dialog, click Close

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Mascot
Use this script to send either the active spectrum or all product spectra contained in the active
sample, or all samples in the active data file, to the Mascot protein search engine. The script was
co-developed with Matrix Science Limited, the creators of Mascot.
When sending only the active spectrum, the script can work with either MS or MS/MS data; in the
first case a peptide mass fingerprint search is conducted. When sending all spectra, the script
works with data acquired using two distinct types of acquisition methods: either a multiple period
/ multiple experiment method containing any number of product experiments or an IDA
(Information Dependent Acquisition) method. In the former case, the script calculates one
spectrum for each experiment by averaging all spectra acquired for the experiment. In the latter
case, the script uses all dependent product spectra, combining adjacent spectra with the same
parent mass and charge state.

Use the Script

If you are planning to send just one spectrum to Mascot, make sure that a centroided spectrum is
active in the Analyst® software before running the script. If you are planning to send all spectra
contained in a sample, the TIC for the sample should be active.
1. With a centroided spectrum in an active pane, click Script > Mascot.
The File, Sample, Periods, and Scan type IDA data fields are read-only and show
information about the active sample.

Figure 1-21 Mascot Search Dialog

2. In the Search group, you can do one of the following:

• If the active pane is a centroided spectrum (either MS or MS/MS), click The
current spectrum to search this spectrum on its own. You can select this
option only if the spectrum was centroided using the Centroid command on
the Explore menu.
• If the active pane contains MS/MS data, click All MS-MS spectra for current
sample to perform a single search using all spectra for the sample.
• If the active pane contains MS/MS data and also contains a selected region,
click All MS-MS spectra from selected region in TIC to perform a single
search using only the spectra from this region. This can be particularly useful
to speed the generation of the search input if only a portion of the run is known
to contain useful data.

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• If the active pane contains MS/MS data and the associated data file contains
more than one sample, click All MS-MS spectra from all samples for
current file to perform a single search using all MS/MS spectra from all
samples in the data file.
3. To open the Mascot search form and populate it with the appropriate information,
click Search. If you are searching all product spectra contained in the sample, this
may take some time (a progress bar will appear). After the Web form shows, click
Start Search.
4. To set the various search options, click Options.
Figure 1-22 Mascot Search-Options Dialog

Tip! To display the Mascot search form defaults Web page, click Set
default parameters.

5. To set where the text file used as input to Mascot is located, click Set search file
location, select one of the following options and then click OK.

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Figure 1-23 Search File Location Dialog

• To place the file in the Windows temporary folder with a random but unique file
name, click In the Windows ‘Temp’ folder with a random filename.
• To always write to a specific file, overwriting the file for every search, click
Always to the following file. To navigate to the folder, click Set.
• To create the file with a random but unique filename in the specified directory,
click To the following directory with a random filename. To navigate to the
folder, click Set.
• To be prompted to save every time a search is performed, click Prompt me
each time for the location.
6. In the Default precursor charge states group when searching only the current
spectrum, values here are not available; the precursor charge state should be set
manually using the resulting Mascot web form. When searching product spectra for
an IDA run, the charge state is automatically determined by the script—the values
specified here are not used unless the charge state could not be automatically
determined or the Try to determine charge state from survey scan check box is
not selected. When searching product spectra for a multiple period or multiple
experiment LC/MS run, the specified charge states will always be considered for
each product spectrum.
This option is only required for those using an older Mascot software version that
does not accept charge states greater than 5. If you are using one of these older
versions, make sure that in the Default precursor charge states group, the Discard
ions with charge of 5+ or higher check box is selected. Some versions of the Mascot
search engine cannot accept ions with a charge state of 5 or higher and show a
warning for each ion exceeding this limit.
7. To use the default precursor charge states as is, clear the Try to determine charge
state from survey scan check box. Otherwise, it will attempt to determine the
charge state by examining the isotope spacing in the survey spectrum, and for
Analyst TF 1.5 software data, it will use the charge state determined by the MS
Acquisition Engine, which is saved to the data file. If this check box is selected but
the charge state determination fails, the default charge states are used.
8. In the MS/MS averaging of IDA dependents group, edit the parameters that pertain
to the calculation of the product ion spectra for an IDA run.

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• The Precursor mass tolerance for grouping field is used to potentially

combine adjacent product spectra into a single spectrum. If two spectra have
precursors with the same charge state and the same MW within this tolerance,
they will be combined.
• In the Max. number cycles between groups field, spectra are not combined
if the number of cycles between spectra with the same m/z and charge state is
greater than the specified value. Use this option if you do not want to combine
spectra with significantly different retention times.
• In the Min. num cycles per group field, type the minimum number of spectra
that need to be combined in order for the result to be kept.

Note: If you have used the dynamic exclusion IDA option, set this value to
1.

9. In the MS/MS data processing group, select parameters that pertain to the filtering
of product ion spectra.
• Remove peaks if intensity < _ — Removes peaks that are either less than a
specific count or a specific percent of the maximum peak intensity of the
spectrum.
• To centroid the MS/MS spectra before sending them to Mascot for searching,
select the Centroid all MS/MS data check box. It is highly recommended that
you enable the centroid option.
• If the centroid option is used, indicate whether isotope peaks should be
removed from the MS/MS spectra before sending them to Mascot by selecting
the De-isotope MS/MS data check box. It is recommended that you enable
this option.
• Report peak area (otherwise intensity)—If selected, the script uses the area
of the peak. Otherwise it uses the intensity at the apex.
• Reject spectra if less than ‘n’ peaks —If a spectrum contains unreasonably
few peaks after combining adjacent spectra (if used) and centroiding (if used),
the spectrum can be eliminated.
• Remove peaks within ‘n’ Da of precursor m/z— Sets a window around the
precursor ion m/z and then removes any peaks within that window.
10. In the Other group, select Use original format for query titles if you are using a
third-party protein quantitation application and you would like to use the original title
format.
11. To display the Mascot search form defaults Web page, click Set default
parameters. You can edit the various defaults so that you do not need to reset them
manually every time before submitting a search. After changing the parameters, click
Save defaults as cookie to close the Web page.

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Mass Defect Filter

The identification of drug metabolites in biological fluids with low concentrations from a total ion
chromatogram (TIC) is challenging because of significant interferences from endogenous
species. A technique of filtering the data based on the mass defect of the parent drug and a small
tolerance value has been used to decrease the amount of interference. Using this technique aids
in the identification of phase I and phase II metabolites.
The Mass Defect Filter script filters either a TIC or a spectrum using this technique. Only those
data points in the spectrum whose centroid mass is within the tolerance range of the parent ion’s
mass defect applied at that nominal mass will be retained. All other points are excluded.
Summing the intensity for each of the spectra generates the TIC. A further filtering based on
absolute mass can also be applied.
A new graph of the filtered TIC or spectrum will appear below the current graph.

Use the Script

1. With either a spectrum or a TIC active, click Script > Mass Defect Filter.

Figure 1-24 Mass Defect Filter Settings Dialog

2. In the Parent Formula field, type the formula for the parent ion. The Mass Defect
and Nominal Mass fields are automatically updated.
3. If the parent formula is unknown, then type values in the Nominal Mass and Mass
Defect fields.
4. In the Mass Defect Tolerance (+-) field, type the tolerance value.
5. If required, type a value in the Resolution Factor field. The Resolution Factor
further filters the data by keeping only the centroid values whose resolution is
greater than or equal to it.

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6. If required, to allow the mass defect to be applied differently at each nominal mass in
the spectrum, click the Use Dynamic Mass Defect Calculation check box. If you
deselect the check box, a constant value of the mass defect is added to each
nominal mass.
7. In the Mass Range Parameters group, select the Use Mass Range Filter check
box to set the mass range parameters. Only masses in the spectrum between Start
Mass and Stop Mass inclusively will be retained.
8. Click OK to start processing.

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Merge MRM
Use this script to add all experiment data from the method to be merged to the base method.
Both methods should have only one period and one experiment. The script does not limit the
number of mass ranges in an experiment. All mass ranges are saved to the base method.
This script can be used to merge multiple final methods created by Compound Optimization.
After you have merged the methods, the LC information can be modified if necessary to reflect
the analysis conditions.

Use the Script

1. Click Script > Merge MRM.
Figure 1-25 Merging MRM methods Dialog

2. To navigate to the original acquisition method file or template, click the button to the
right of Original method.
3. To specify the name and location of the merged acquisition method file, click the
button to the right of New Method, type the name of the method, and then click
Open.
4. To add an acquisition method to the list of methods to be merged, click Add to the
right of Methods to be merged. To remove a method from the list, click Remove.
5. (Optional) If both methods were created using Compound Optimization, select the
Update MRM compound ID from the file name check box to populate the
compound ID column with the compound name in the merged method.
6. To add all the mass ranges from the selected methods, click Go.

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MRM3 Optimization Script

Use this script for quantitation on the QTRAP® systems in order to provide increased specificity
and, therefore, improved detection when quantifying analytes in complex matrices. This script is
designed to generate an optimal MS3 acquisition method on any QTRAP system with any source
and at any flow using infusion. The script performs the following optimization steps:
• Confirm precursor mass
• Optimize transmission to collision cell
• Determine the major fragment ions
• Optimize the Collision Energy (CE) for each fragment ions
• Perform MS3 scans on each fragment ion
• Optimize Excitation Energy (AF2) for all MS3 scans
• Generate a report
• Save all data and acquisition methods
The script can also be used in qualitative applications to generate collections of MS/MS and MS3
spectra for compounds in a semi-automated way (that is, one compound at a time).

MRM3 Optimization Window Overview

You can use the controls in the MRM3 Optimization window to navigate through the script. The
window also displays the optimization results as they are generated. The following is an overview
of the various sections in this window.
• Status Window: When the script is first started, this window displays the current
optimization settings that will be used for optimization. When the optimization is
started, spectral information is displayed in this window.
• Log File: Displays the results found during optimization in text format. Each entry
found in this section is also added to the generated Log.txt file.
• Overall Progress: This is a visual display of the overall optimization progress.
• Main Controls: Contains all of the main functions associated with the setting and
execution of the optimization process.
• After the optimization is completed, a Results.txt file is automatically
generated and saved. If you click View Results, you can open and review it
with Microsoft Notepad.
• Click Settings to open a window where you can type compound information
required for the optimization process.
• Click Start to initiate the optimization process. During optimization, this button
is renamed to Abort, which you can click to stop the optimization process.

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Figure 1-26 MRM3 Optimization Window

Item Description
1 Status Window
2 Log File
3 Main Controls
4 Overall Progress

Set the Preferences

When the script is run for the first time, the Settings dialog opens automatically. Otherwise, the
MRM3 Optimization window opens, displaying the last values and information used for
optimization.
1. Click Browse to navigate to the starter acquisition method. This method
predominantly contains the source conditions to be used for the optimization.
2. In the Compound Name field, type a descriptive compound name. This name is
used as a prefix to all of the acquisition methods and data files generated.
3. In the Q1 Resolution field, select a Q1 Resolution to be used for MS/MS and MS3.
4. In the Polarity group, click a polarity, which may differ from the starter method. The
Both Polarity option is currently not supported.
5. In the Expected m/z (amu) field, type the expected mass-to-charge (m/z) ratio for
the compound. If you do not know the m/z of the compound, then click Calculate
from chemical formula to calculate it from the chemical formula of the compound.
Refer to Calculate m/z on page 57.
6. To modify some of the settings used by the optimization process, click Advanced.
Refer to Use the Advanced Settings Dialog on page 58.
7. To verify and use the updated settings, click OK.

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Use the Script

1. Build a starter acquisition method if one does not already exist. The starter method
should be a Q1 acquisition method created in Manual Tune and should contain the
source conditions required for the tuning process because these are not optimized
by the script.
2. Save the method in the Acquisition Methods folder of the required project where all
generated files will be saved.
3. Click Script > MRM3 Optimization.
Figure 1-27 Settings Dialog

4. Enter the compound information required for the optimization process and then click
OK on the Settings dialog.
5. To initiate the optimization process, click Start in the MRM3 Optimization window.

Calculate m/z
The m/z calculator is accessed through the Settings dialog.
1. In the MRM3 Optimization window, click Settings.
2. In the Settings dialog, click Calculate from chemical formula.

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Figure 1-28 Calculate m/z Dialog

3. In the Chemical Formula field, type the chemical formula of the compound. Use
capital letters for elements. The chemical formula for peptides is also entered into
this dialog. You can obtain the chemical formulas for peptides by typing the peptide
sequence into the New Protein Sequence window in the BioAnalyst™ Software.
4. In the Num of charges field, click the number of charges.
5. To calculate the m/z for the entered chemical formula and charge, click Calculate.
6. To close the calculator and update the Expected m/z (amu) field in the Settings
dialog with the calculated m/z, click Use m/z.

Use the Advanced Settings Dialog

In this dialog, a description for each of the optimization steps is provided. You can also modify
some of the settings in order to customize the optimization.
1. In the MRM3 Optimization window, click Settings.
2. In the Settings dialog, click Advanced.

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Figure 1-29 Advanced Settings Dialog

3. In the Scan Rate fields in the Enhanced Resolution, Enhanced product Ion and MS/
MS/MS groups, select a scan rate for ER, EPI, and MS3.
4. In the Q1 Multiple Ion group, in the DP Ramp fields, type the declustering potential
(DP) range for optimization. The range is expressed in absolute values and the
appropriate polarity is automatically applied based on the selection made in the
Settings dialog.
5. In the Enhanced Product Ion group, do the following:
• In the 2nd Precursors field, type the maximum number of second precursors
(fragment ions) used for MS3 optimization. Type a number between 1 and 10.
• In the Enhanced Product Ion group, in the Mass range field, type a mass
range for the second precursors that will be selected for MS3 optimization.
• In the CE field, type a collision energy value and in the CES field, type a
collision energy spread (CES) value that will provide a good MS/MS spectrum
from which fragment ions can be selected.
6. To generate all of the final MS3 methods for each second precursor and the optimal
MS3 method for quantitation, in the Generate Final Methods group, click Save All
Final Methods. Click Save Optimal Method Only to save only the optimal MS3
method (most sensitive for quantitation).
7. Click OK to accept the updated Advanced Settings.

Optimization in Progress
When the optimization is started, Manual Tune in the Analyst® software is automatically stopped.
While the script is running, all of the functions in the software can still be used. A Log.txt file is
also updated as each part of the optimization procedure is completed. To stop the script at any
time, click the Abort button. Examples of the script in progress are shown in the Figure 1-30 on

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page 60 and the Figure 1-31 on page 61. In the Overall Progress section, the Checklist images
and text fonts represent different statuses that are described in the following section.

Task not performed yet – text is black

Task in progress – text is blue and italic
Task will not be performed – text is grey
Task completed (hyperlink) – text is blue and underlined
Task completed (no link) – text is blue
Part of task completed (hyperlink) – text is blue, underlined, and italic

When the text is underlined, you can click it like a web page hyperlink and the corresponding
spectrum or chromatogram is displayed. The text found under MS/MS/MS also displays the MS3
scan number that is being performed because it is possible to have between 1 and 10 scans. The
Overall Progress section also includes a Message area. In this area, a progress bar displays the
current step progress. Above the progress bar, various messages are displayed such as the time
and other statuses for the current optimization step.
Figure 1-30 MRM3 Optimization Window after EPI Scan

Item Description
1 Checklist
2 Message

In the spectral status window, the previously generated spectrum or chromatogram is displayed.
When one of the checklist items is selected, the corresponding graph is displayed. The scan type
name indicates which scan is currently being displayed. For each completed step, it is possible to
open the acquisition method (.dam) or data file (.wiff) associated with the graph displayed. If an
MS/MS/MS scan is displayed, you can use the buttons to cycle through the different MS3 scans.

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Figure 1-31 MRM3 Optimization Window during MS3 Scan

1 2 3

Item Description
1 Scan type
2 Buttons to cycle through different MS3 scans
3 Links

Optimization Complete
When the quantitative optimization for MS3 is completed or stopped, a Results.txt file is
generated. This file is automatically opened in Microsoft Notepad. You can also view the file by
clicking View Results from the MRM3 Optimization window. The various parts of the Results.txt
file are described as follows.
• Time and Duration: Displays the date and time duration of optimization.
• User Starting Conditions: Displays the settings and Advanced Settings in this
section.
• Optimization Conditions Found: Displays the optimal conditions found during the
ER and Q1MI scans.
• MS3 Fragments Found and Associated Losses: Displays the fragments and
optimal conditions (collision energy and excitation energy) as well as associated
losses found for the EPI scan and MS3.

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Figure 1-32 Optimization Report

3 4

Item Description
1 Time and Duration
2 User Starting Conditions
3 Optimization Conditions Found
4 MS3 Fragments Found and Associated Losses

All of the generated acquisition methods have a descriptive file name in the format [supplied
compound name] + [scan type] + [m/z] + .dam. These methods are saved in the same folder as
the starter acquisition method.
All of the data, Log.txt, and Results.txt files are saved into a Data sub-folder that is created in the
same project as the starter acquisition method. The sub-folder has the format [supplied
compound name] + OptMS3 + ([date], [time]). The data files have the format [supplied compound
name] + [scan type] + [m/z] + .wiff.

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Detailed Description of Script Logic

This section describes each phase of the optimization process. All scans are performed with the
number of scans to sum set to 3.

Initialization
Before performing any optimization scans, the MRM3 Optimization script first performs the
following initialization steps. If an error occurs during any of these steps, the script will stop the
optimization process.
1. Ensure that the Analyst software is running.
2. Load the starter acquisition method to see if it is valid and check the device type.
3. Create a new Data sub-folder to store the .wiff files.
4. Create the Log.txt file.

Enhanced Resolution Scan

This step confirms the mass of the ion used for optimization. The ER scan is performed for 20
cycles at the specified scan rate. The most intense peak within ±1 amu of the expected first
precursor m/z is then selected. Similar to the Analyst software, this scan is performed with a 30
amu mass range around the specified m/z. For multiply charged species, the C12 ion is
determined in this step.

Q1 Multiple Ion Scan

This step optimizes transmission of the ion of interest up to the collision cell. This is performed
using a Q1MI scan. The script first optimizes the DP parameter by performing the scan at the
specified DP ramp. Optimize the EP parameter by ramping it from 1 V to 12 V (-12 V to -1 V for
negative mode), with 0.5 V step. If the optimal EP is less than 10 V (greater than -10 V for
negative mode), then DP is re-optimized. If the instrument is not a 4000 QTRAP instrument, the
CEP parameter is also optimized by ramping from 0 to 100 V (-100 to 0 V for negative mode) with
2 V step. In determining the optimal voltage, graphs are smoothed two times and the voltage
yielding the greatest ion count is used. Dwell Time for each scan is set to 100 ms.

Enhanced Product Ion Scan

This step selects the fragment ions that will be used for MS3 optimization. This is performed
using an EPI scan for three cycles at the selected scan rate. You can specify an optimal CE for
the compound to be analyzed. If the optimal CE is unknown, then you can specify a Collision
Energy Spread (CES) value such that a range of CE settings are used. The most intense second
precursor peaks are then found, excluding any peaks within ±2.5 amu window of first precursor.
The number of second precursors to use is selected in the Advanced Settings. The mass range
from which the second precursors are selected is specified by the user.

Multiple Reaction Monitoring Scan

This step optimizes the collision energy for each of the fragment ions selected from the EPI scan.
This is performed using MRM scans. Use CE ramps of 5 to 130 V (-130 to -5 V in negative mode)

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with 2 V step and Dwell Time of 50 ms. Each overlaid graph is then smoothed two times and the
voltages yielding the greatest ion count are used as the optimal CE values.

MS/MS/MS Scan
The script performs an MS3 scan for each chosen second precursor at the specified scan rate
and with an AF2 ramp of 0 to 100 V with 2 mV step (or 0 to 0.4 V with 0.01 V step on QTRAP®
5500 system) for both polarities. The fill time of the scan is set, and Q0Trapping can be turned on
for maximum sensitivity if required. The lower limit of the mass range for the MS/MS/MS scan
can be specified, and the upper limit is second precursor + 5 amu.
The generated graphs are smoothed twice and the optimal AF2, as shown in the Figure 1-33
How AF2 is Determined, is obtained when the residual intensity of the second precursor (based
on XIC) is at 5% of its maximum intensity. The spectrum at this AF2 value is then used to find the
two most intense second generation fragment ions, excluding peaks within ±1 amu of the second
precursor. If the second precursor m/z is greater than 10% of the total ion count, no fragments
from that spectrum will be used. This condition exists because if the second precursor m/z is
greater than 10%, there is insufficient fragmentation.
Figure 1-33 How AF2 is Determined

Generate Final Methods

After the optimization scans are performed, the script generates the final MS3 methods. If the
Save Optimal Method Only option is clicked in the Advanced Settings dialog, only an optimal
MS3 method with ±10 amu around the most intense second generation fragment ion is created. If
the Save All Final Methods option is clicked, then the optimal method as well as an MS3 method
for each of the top second precursors are created using a mass range from the user-defined
lower limit to an upper limit of (second precursor + 5) amu.

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MS3 Quant Optimization Script

The MS3 Quant Optimization script has been replaced by the MRM3 Optimization script. Users
who have upgraded from the Analyst 1.5.2 to 1.6 to 1.6.1 software versions may still have this
script installed. The MS3 Quant Optimization has not been tested with the Analyst 1.6.2 software,
therefore, users should use the MRM3 Optimization script instead.

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Multiple Batch Scripts

Use this script to attach multiple acquisition scripts to a single batch that is submitted to the
queue. These acquisition scripts are used to immediately process the data either after a sample
completes or after the batch finishes. Using the Analyst® software, you can submit only one
script with the batch, but sometimes it is convenient to run two or more scripts to perform two or
more different types of processing.

Use the Script

1. When creating a batch, in the Batch Script field, navigate to the script.
After submitting the batch to the queue, the following dialog opens in which you can
attach the additional acquisition scripts.
Figure 1-34 Multiple Batch Scripts Script Dialog

2. To attach an additional script to this batch, click Add Script to navigate to the
acquisition script.
3. To remove a script, click the script and then click Remove Selected.
4. Select the Only show this dialog again if the control key is down check box if
you want the dialog to appear when submitting the batch.
5. Click Run to attach all of the acquisition scripts to the batch.

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Open in Workspace
Use this script to open a sample in a previously created workspace. This script loads the
previous workspace and displays the sample in the same layout as specified in the saved
workspace. It is not possible to create a workspace that specifies pane arrangements so that any
sample can be loaded into it. For more information on workspaces, refer to the online Help.

Use the Script

1. Click Script > OpeninWorkspace.
The Open in Workspace dialog is shown with the current working project data folder
loaded into the Data Files list.

Figure 1-35 Open in Workspace Dialog

2. To select a data file from another project, click File > Open Data File.
3. In the Data files list, click a data file.
All the samples in the selected data file appear in the Available Samples list
4. After choosing the sample, select a workspace in the Available workspaces list. To
select a different workspace, click Workspace > Open Workspace.
5. To set a default workspace to be used each time this script is run, select the Set
Selected Workspace As Default check box.
6. To open the sample, click Open Sample in Workspace.

Known Issues and Limitations

The Open in Workspace script is for the presentation of graphs only. The script cannot handle
data lists that are saved in the workspace and a Type Mismatch error will be displayed. You must
save your workspaces with the graphs only first and then, after loading the workspace, create the
necessary data lists.

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Peak List from Selection

Use this script to determine the peak data for a selected region or regions in the chromatogram.
The %area and %height listed relate just to peaks in the selection. The peaks are listed in a text
pane below the active chromatogram. The peak definition is shown in the chromatogram. For
more information, refer to Figure 1-36 Data Processing with the PeakListFromSelection Script.

Use the Script

• Do one of the following:
• To run the script, click Script > PeakListFromSelection.
• To view the script description, and get the peak list, hold the Shift key down
while clicking the script.
• To process the data, make one or more selections in the chromatogram and
then select the script from the drop-down menu.
Figure 1-36 Data Processing with the PeakListFromSelection Script

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Regression Calculator
Use this script to calculate the slope, y intercept, and r values for each mass/speed dependent
parameter.

Use the Script

1. Click Script > Regression Calculator.
Figure 1-37 Regression Calculator Dialog

2. Type data in pairs of x and y co-ordinates.

3. After entering two or more pairs, to get the Slope, Intercept, and R2 value, click
Calc.
4. To delete the values for x and y co-ordinates, click Clear.
5. To exit the application, click OK.

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Remove Graph Selections

Use this script to clear a selected area in the graph. For example, you can clear the graph
selection line from the graph.

Use the Script

• To remove selections from the graph, click Script > RemoveGraphSelections.

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Repeat IDA Method

Use this script on an acquisition workstation. It opens the acquisition method for the data file and
updates the exclusion list with the masses and times that have been acquired. The method is
saved under the same name.

Use the Script

1. In Explore mode, open an IDA data file.
2. Click Script > RepeatIDAMethod.
3. To keep the previous exclusion list, press the Ctrl key while clicking the script.

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Savitzky-Golay Smooth
Using the Analyst® software, you can smooth a graph in Explore mode using two different
algorithms. When you are using the IntelliQuan integration algorithm in Quantitate mode, a third
smoothing algorithm, the Savitzky-Golay smooth, is available. The active graph in the Analyst
software will be replaced by the smoothed graph.
The Savitzky-Golay Smooth script smooths the current active graph using the Savitzky-Golay
smoothing algorithm. The IntelliQuan algorithm in Quantitate mode performs the smoothing
process.

Use the Script

1. With the peaks of interest selected in the active spectrum, click Script > Savitzky-
Golay Smooth.

Figure 1-38 Savitzky-Golay Smooth Dialog

2. Use the Smoothing Half Width drop-down list to set the half-width for smoothing
the data. The total width will be twice this value plus one. This parameter is the same
as the smoothing parameter used with the IntelliQuan algorithm in the Analyst
software.
3. To perform the smoothing, click OK.

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Selection Average and Standard Deviation

Use this script to calculate the average intensity and standard deviation of a selection in a graph
for both spectral and chromatographic data. The graph is labeled with both the average and
standard deviation of the selection.

Use the Script

• Select either an active spectrum or active chromatogram, and click Script >
Selection Average and StdDev script.
The graph will be labeled with the average and standard deviation of the selection.

Known Issues and Limitations

This script will work only once for each graph. Use the following procedure if you want to run the
script on the same graph more than once.

Calculate the Average and Standard Deviation of a Graph More than Once
1. Copy the graph into a new pane. Click Explore > Duplicate Data > Same Window.
2. Make a selection in the new graph pane and run the Selection Average and
StdDev script again.

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Send to ACD SpecManager

This script is similar to the Export to JCamp script. However, instead of prompting for the name of
the JCamp file, the spectra are exported to a temporary file and then sent directly to the ACD
SpecManager application. There is no need to open this temporary file directly.

Prerequisites
You must have the SpecManager software installed.

Use the Script

The first time you run the script, you are prompted to locate SpecManager. You will not be
prompted again unless you press the Ctrl key while clicking the script.

Note: This script cannot be used with batch acquisition.

1. With either a chromatogram or a spectrum in an active pane, click Script > Send to
ACD SpecManager.
The following figure shows the options dialog that opens when you run either of the
scripts to process chromatographic data. If you are interactively processing a single
spectrum active in the Analyst® software, these options do not apply.

Figure 1-39 JCamp Options Dialog

2. To centroid the exported spectra, select the Centroid Exported Spectra check box.
This option reduces the size of the exported JCamp file.
3. To select the threshold that will be applied to the exported spectra, in the Threshold
field, type a value. If you do not want to use a threshold, type 0 in the Intensity
Threshold field.
4. Select the Only show this dialog again if the control key is down check box to
have the JCAMP Options dialog appear if the Ctrl is pressed when selecting the
script from the Script menu or when submitting the batch to the queue.

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5. Click OK to continue processing and to have the spectra exported. These values are
used as defaults until you change them again.
6. To close the dialog without making any changes, click Cancel. In the case of
interactive use, canceling the dialog will also stop the export operation. However, in
the case of batch operation, the batch will still be acquired and JCamp files will be
exported using the original parameters.

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Signal-to-Noise Using Peak-to-Peak

The Analyst® software calculates the signal-to-noise ratio by taking the standard deviation of all
the chromatographic data points between the specified background start and background end
times.
Use this processing script to calculate the signal-to-noise ratio for the active chromatogram. The
script first subtracts the average background signal from the selected peak and then divides the
subtracted signal by the peak-to-peak noise level. It then differentiates the noise and peak
regions based on the maximum intensities of each region. Upon completion, the active
chromatogram is labeled with the signal-to-noise ratio.

Use the Script

• With a noise region and the peak of interest selected in the active chromatogram,
click Script > S-to-N.
The signal-to-noise ratio is calculated and the graph is labeled.

Tip! To remove the labels, press the Ctrl key while clicking the script.

Related Scripts
S_NstdDevQS: Calculates the signal-to-noise value with a method that uses the noise regions
standard deviation.

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Signal-to-Noise Using Standard Deviation

Use this script to calculate the signal-to-noise ratio of chromatographic peaks and label them.
The script requires two regions to be selected on the chromatogram: a selection/region
containing the noise region and a selection/region containing the peak of interest. The script will
automatically determine which region contains the peak and the noise based on maximum
intensities in each selection. It subtracts the average background signal intensity from the peak
signal intensity and then divides the subtracted signal by a user-specified factor times the
standard deviation of the noise region.

Use the Script

1. With a noise region and the peak of interest selected in the active chromatogram,
click Script > S_NstdDevQS.
Figure 1-40 S/NxstdDev Dialog

2. To erase any labels current on the active chromatogram, click Erase Labels.
3. To calculate the signal-to-noise ratio and label the graph, click Go.

Related Scripts
S-to-N using Peak-to-PeakS: Calculates the signal-to-noise for an active chromatogram. The
background subtracted signal is divided by the peak-to-peak noise level.

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Split Graph Script

Use this script to split a spectrum or chromatogram into a specified number of panes. Each
resulting pane displays a proportional fraction of the total mass (or time) range. For example, if a
spectrum displaying a mass range of 100 to 400 amu is split into three, the original spectrum will
display a range of 100 to 200 amu, the second (new) spectrum will display 200 to 300 amu, and
the third (new) spectrum 300 to 400 amu. The intention is to allow the maximum possible number
of peaks to be labeled for subsequent printout.

Use the Script

1. With either a chromatogram or a spectrum in an active pane, click Script >
SplitGraph.

Note: Make sure that the mass (or time) range for splitting is displayed. If
necessary, dock the graph to make sure that the whole graph can be seen.

2. Do one of the following:

• The current version of XICfromTable script can handle a maximum of 25 XIC
mass ranges. If you press the Ctrl key while clicking the script, a dialog opens
prompting you to select the number of panes to create. The preset value is
four.
• If the Ctrl key is not pressed, then the last number typed in the dialog is used.

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Subtract Control Data from Sample Data

Use this script when the sample data of interest are in the active graph. The data may be any
spectrum, TIC, or ADC trace. The script determines the data type, retrieves the corresponding
data from the control file, and then displays the subtracted data in a graph.
You may select to overlay the subtracted data with sample data or control data.

Use the Script

1. To process the data with current preferences, click Script > SubtractControlData.
2. Do one of the following:
• To view the script description, set the processing preferences, and get the
subtracted data, hold down the Shift key when clicking the script.
• To update the processing preferences and get the subtracted data, press the
Ctrl key when clicking the script.

Figure 1-41 Subtract Control Data QS Preferences Dialog

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Unit Conversion
Use this processing script to convert from one set of concentration units to another.

Use the Script

1. Click Script > Unit Conversion.
Figure 1-42 Unit Conversion Dialog

2. In the Convert from field, type the concentration and units to be converted.
3. If the conversion is from a weight-based concentration (for example, g/L) to a molar-
based concentration (for example, mol/L), then in the MW field, type the molecular
weight of the component.
4. In the Convert to field, type the unit.
5. To perform the conversion, click Convert.
The calculated values will be displayed in the Convert to field.
6. To retrieve these values, press Ctrl +C to select and copy them to the clipboard.
These values can then be pasted into another application.

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Wiff to MatLab
Use this script to extract the data from a .wiff file and creates the following matrices in a MatLab
file: Data, Masses, Wavelengths, Scans, and Filename. For more information about these
matrices, refer to Table 1-8 Matrix Definitions on page 83. This MatLab file can then be included
in a MatLab script and used to compute and display the results.
Although you can use the Analyst® software to perform various data manipulations, you may use
this specialized script, Wiff to MatLab, for data computations. The Analyst software cannot
extract data from a .wiff file and then store it in a file that can be read and interpreted by MatLab.
In addition to exporting the mass spectral data, this script can also export data from a diode array
detector (DAD).
The script will create a single MatLab .mat file for each sample to be translated. Depending on
the type of mass spectra data and the user options, the script can create data in two different
formats:
• The first format saves the intensities in a matrix of size (number of masses) x
(number of scans). There is thus an entry in the matrix for every mass that was
scanned and every spectrum. This is the default format for quadrupole spectra and
the format that is always used for diode array data.
• The second format is sparse or compressed and allows data points that have an
intensity of zero to be omitted; depending on the number of such data points in the
original .wiff sample, this can potentially greatly reduce the size of the MatLab file.
This format uses a matrix of size 2 x (total number of (mass, intensity) pairs). The
first row represents masses and the second row the intensities. A given number of
initial columns corresponds to the first spectrum, a given number of following ones to
the second spectrum, and so forth. Each (sparse) spectrum is essentially stored
end-to-end.
A separate vector is written, which you can use to determine the starting and ending position of
any given spectrum in this matrix. This vector contains the one-based index of the start of a given
spectrum. The end for a given spectrum can be determined by subtracting one from the start of
the following spectrum (except for the very last spectrum, which is determined by the size of the
above-mentioned matrix).
The first format is the default format for quadrupole spectra and is always used for diode array
data. The second (sparse) format is always used for TOF (time-of-flight) data and can optionally
be used for quadrupole data.
The actual names of the various matrices are specified using the Options dialog described later
in this document.

Use the Script

1. With a chromatogram in an active pane, click Script > Wiff to MatLab. Alternatively,
this script can be attached to a batch; select this script using the Batch Editor.
If the chromatogram is associated with mass spectral data (TIC, XIC) then MS data
is exported to the MatLab file; if the chromatogram is associated with diode array
data (TWC, XWC) then DAD data is exported.
2. To change the conversion options, open the Wiff to MatLab Conversion Options
dialog by pressing the Ctrl key while clicking the script. Otherwise, the options
previously specified are used.

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Figure 1-43 Wiff to MatLab Conversion Options Dialog

3. In the Matrix Names fields, type the names of the matrices that the script produces.
It is recommended that you keep these names as their default values.
4. In the Threshold for sparse format field, type a value that will be used to reduce
the size of the output MatLab file. For the sparse format only, only (mass, intensity)
pairs with intensity larger than the specified value will be written.
5. If the Save original filename as matrix field is selected, then the script will create
and populate the Filename matrix.
6. To have the quadrupole spectra saved in the sparse format, select the Use sparse
format for quadrupole data check box. Note that TOF spectra are always saved in
the sparse format and that diode array data is always saved in the non-sparse
format.
7. If the Save scan times (not scan numbers) field is cleared, then the script will
populate the Scans matrix with the time in seconds for each scan. Otherwise, the
Scans matrix is populated with the scan numbers.
8. In the Use fixed step size field, type the step size of the data to extract. If this field is
cleared, then the acquisition step size is used.
9. To populate the wavelengths matrix with the DAD data when the script is attached to
a batch, select Save DAD data in batch mode (if available).
10. To save these settings and continue processing the data, click Save.
11. To discard any changes made to the settings, click Don’t Save. Data processing will
continue after you click this button.

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12. To automatically generate a MatLab file for every sample submitted as part of a
batch run in the Batch Editor, click Select Script to select the script before
submitting the batch to the queue. The script should be located in the Processing
Scripts subproject of the API Instrument project.
A MatLab file is created for every different experiment for each sample in the batch.
The MatLab files are placed in the same location as the data files and will have the
same names with the .wiff extension replaced by .mat; however, the index of the
sample within the .wiff file will be appended. In addition, for samples acquired using
acquisition methods containing more than one experiment, the period and
experiment number will be appended to the MatLab filename.
For example if a data file is called test.wiff and contains two samples, the MatLab
files will be called:
• test-1.mat
• test-2.mat
If the acquisition method contained one period and two experiments, four MatLab
files would be generated (two for each sample):
• test-1(1,1).mat
• test-1(1,2).mat
• test-2(1,1).mat
• test-2(1,2).mat.
If the data file contains diode array data and the Save DAD data check box is
selected, then an additional file with the sample index and (DAD) is created. For the
previous example, files called test-1(DAD) and test-2(DAD).mat are created.

Known Issues and Limitations

When attaching this script to a batch, make sure that the Acquisition Queue window is opened
before submitting the batch. This window must be open until the acquisition has completed to
make sure that the script is working properly.

Related Scripts
Export to JCamp: Converts spectra from .wiff format to JCamp format.
Table 1-8 Matrix Definitions
Matrix Dimensions Type Descriptions
Data Number of Float The raw intensities for all of the spectra.
masses (or
wavelengths) x
number of scans
SparseData 2 x total number Double The raw masses (first row) and intensities
of (mass, (second row) for all spectra. This matrix is
intensity) pairs used only with the sparse format.
Masses Number of Float The actual m/z values scanned by the
masses x 1 instrument. This matrix is only present when
exporting MS data.

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Table 1-8 Matrix Definitions (Continued)

Matrix Dimensions Type Descriptions
Wavelengths Number of Float The actual wavelengths acquired by the
wavelengths x 1 diode array detector. This matrix is present
only when exporting DAD data.
Index 1 x number of Long
scans
Scans 1 x number of Float The retention times (in seconds) or the scan
scans numbers for the spectra.
Filename 1 x length of Text This optional matrix specifies the filename
filename of the original data file.

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XIC from BPC

Use this script to retrieve the list of base peak masses and overlay the corresponding extracted
ion chromatograms in an Explore pane below the active pane. Run the XIC From Base Peak
Masses script after selecting a time region of interest in a chromatogram. The largest peak in
each XIC trace will be labeled with its mass if it is greater than 5% of the most intense XIC peak.

Use the Script

You may optionally select to overlay the XIC traces with an ADC trace. The ADC trace will be
normalized to the most intense XIC trace.
1. To process the data with current preferences, click Script > XIC from BPC
2. Do one of the following:
• To view the script description, set the processing preferences, and get the
overlaid XIC traces, hold the Shift key down while clicking the script.
• To update the processing preferences and get the overlaid XIC traces, press
the Ctrl key while clicking the script.
Figure 1-44 XIC From Base Peak Masses Dialog

When processing is started, a progress bar indicates the current step. When
finished, a new pane with overlaid XIC traces is the active pane in the Analyst®
software document. If you want to use the Cycle Overlays feature and it is
unavailable, switch the active pane in the Analyst software to another one and then
reselect the overlaid XIC pane.

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XIC from Table

Use this script to create and read start and stop masses from a file. The file will have two
columns separated by a tab. The first column contains the start mass and second column
contains the stop mass.
When working with full scan data, the Analyst® software can show an Extracted Ion
Chromatogram (XIC) for a subset of the scanned mass range. If the subsets are repeatedly used
on different data, it is often convenient to store the subsets of the mass range, consisting of a
start and stop mass, in an external file and have the Analyst software generate an XIC based on
this file.
The script generates the requested XICs either as one XIC per pane or all the XICs overlaid in
one pane from the current Total Ion Chromatogram (TIC).

Use the Script

1. With a TIC open in an active pane, click Script > XIC_from_table.
Figure 1-45 XIC Preferences Dialog

2. Using the grid in the dialog, type the mass ranges to be extracted into an XIC. To
populate the grid from a text file, click File > Open and then navigate to the text file.
3. To save the current information in the grid to a file, click File > Save As.

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4. To clear the grid of all entries, click Table > Clear.

5. To overlay all XICs, into a single pane, select Overlay XICs check box.
6. To create all the specified XICs, click Extract.
7. To close the dialog and close the script, click Cancel.

Known Issues and Limitations

• When not loading XIC start/stop masses from a file, the maximum number of mass
pairs you can type is 25. However, when loading from a text file, an unlimited number
of start/stop mass pairs can be specified.
• Due to limited space on the screen, you may have to select the Overlay XICs check
box when creating more than six XICs.

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