toxid 2.1 user guide version a - thermo fisher...

ToxID

User Guide

XCALI-97239 Revision A September 2008

© 2008 Thermo Fisher Scientific Inc. All rights reserved.

ToxID and LCquan are trademarks and Xcalibur is a registered trademark of Thermo Fisher Scientific Inc. in the United States.

Microsoft, Windows, and Excel are registered trademarks of Microsoft Corporation in the United States and other countries.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the product operation. This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this document is for reference purposes only. System configurations and specifications in this document supersede all previous information received by the purchaser.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might result from any use of this document, even if the information in the document is followed properly.

This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of Sale shall govern all conflicting information between the two documents.

Release history: Revision A released September 2008.

Software version: ToxID 2.1, Xcalibur 2.1 or earlier, LCquan 2.6 or earlier

For Research Use Only. Not regulated for medical or veterinary diagnostic use by U.S. Federal Drug Administration or other competent authorities.

Thermo Scientific ToxID User Guide iii

C

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vContacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

Chapter 1 Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1Hardware and Software Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2Installing ToxID Files and Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2Running ToxID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Chapter 2 Working with Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5Adding a Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5Adding Libraries to the Search List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7Archiving a Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Chapter 3 Setting Up ToxID Processing Configuration Files. . . . . . . . . . . . . . . . . . . . . . . . . .11Processing Configuration File Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Processing Configuration File Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 12Setting Processing Configuration File Parameters . . . . . . . . . . . . . . . . . . . . . 15

Example Processing Configuration Files and Reports . . . . . . . . . . . . . . . . . . . . 15MS2 Spectrum and Retention Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16MS2/MS3 Spectra and Retention Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20MS3 Spectrum and Retention Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24MS2 Spectrum Collected in a QED Experiment and Retention Time . . . . . . 27SRM Transitions and Ion Ratios . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Exact Mass. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Chapter 4 Configuring the ToxID User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37

Chapter 5 Running Tox ID. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41Running ToxID Using the ToxID User Interface . . . . . . . . . . . . . . . . . . . . . . . 41Running ToxID Using an Xcalibur Processing Method. . . . . . . . . . . . . . . . . . . 43Running ToxID Directly After Data Acquisition for Each Sample in the Sequence

48Using the Log File to Troubleshoot Processing Problems . . . . . . . . . . . . . . . . . 49

Contents

Thermo Scientific ToxID User Guide v

P

Preface

ToxID™ 2.1 is an automated compound identification tool that dramatically simplifies toxicology screening workflows for the clinical and forensic laboratory.

This guide describes how to install and use ToxID.

Contacting UsThere are several ways to contact Thermo Fisher Scientific for the information you need.

To contact Technical Support

Find software updates and utilities to download at mssupport.thermo.com.

To contact Customer Service for ordering information

To copy manuals from the Internet

Go to mssupport.thermo.com and click Customer Manuals in the left margin of the window.

To suggest changes to documentation or to Help

• Fill out a reader survey online at www.thermo.com/lcms-techpubs.

• Send an e-mail message to the Technical Publications Editor at [email protected].

Phone 800-532-4752Fax 561-688-8736E-mail [email protected] base www.thermokb.com

Phone 800-532-4752Fax 561-688-8731E-mail [email protected] site www.thermo.com/ms

mailto:[email protected]

http://www.thermokb.com

http://mssupport.thermo.com

http://www.thermo.com/finnigan

http://mssupport.thermo.com

http://www.thermo.com/lcms-techpubs

mailto:[email protected]

Thermo Scientific ToxID User Guide 1

1

Getting Started

ToxID is an application that provides automated compound identification from Xcalibur™ data files.

OverviewToxID identifies compounds and provides reports for the following experiments:

• Ion trap mass spectrometer experiments

− MS2 spectra and retention time

− MS2/MS3 spectra and retention time

− MS3 spectra and retention time

• Triple quadruple mass spectrometer experiments

− MS2 spectra collected in a QED experiment and retention time

− SRM transitions and ion ratios

• Hybrid mass spectrometer experiment

− Exact mass

Contents

• Overview

• Hardware and Software Requirements

• Installing ToxID Files and Components

1 Getting StartedHardware and Software Requirements

2 ToxID User Guide Thermo Scientific

Hardware and Software RequirementsIn order to run ToxID, your computer must conform to the following minimum requirements:

Installing ToxID Files and ComponentsTo install ToxID

1. Insert the ToxID installation CD and click Next.

2. To accept the license agreement terms, select the I accept the terms of the license agreement option and click Next.

3. After reviewing the hardware and software requirements, click Next.

4. To install the ToxID files:

a. Select the Program Files check box to install the ToxID application.

b. To copy the ToxID User Guide to your system, select the Manuals check box.

c. To copy the example processing configuration files to your system (recommended), select the Examples check box.

d. Click Next.

5. To start installing files, click Next.

6. Choose whether to review the saved Installation Qualification report by clicking Yes or No.

7. Click Finish.

Table 1. Hardware and software requirements

System Requirements

PC • 2.0 GHZ processor with 512 MB RAM• 75 GB hard drive (NTFS formatted)• CD-ROM drive• Display monitor resolution of 1280×1024

Software • Microsoft Windows™ XP SP2 or higher• Microsoft Office 2003 or 2007• Xcalibur 2.1 or previous versions• LCquan™ 2.6 (optional)

1 Getting StartedRunning ToxID


ToxID installs the files listed in Table 2 as well as a desktop icon.

Running ToxIDIn order to run ToxID, you must configure the ToxID software, which consists of the following steps:

• Configuring spectra libraries. This step is required only for experiments implementing specific libraries in compound identification. See Chapter 2, “Working with Libraries,” on page 5.

• Setting up a processing configuration file to define experiment- and compound-specific parameters. See Chapter 3, “Setting Up ToxID Processing Configuration Files,” on page 11.

• Setting up the ToxID interface to specify the processing configuration file and the type of required reports. See Chapter 4, “Configuring the ToxID User Interface,” on page 37.

ToxID also produces a log file, which saves information about the processing.

Table 2. ToxID files and their folder locations

File type Description Default folder location

ToxID.exe (and related DLL files)

ToxID application \Xcalibur\system\programs

ToxID_User_Guide.pdf ToxID User Guide \Xcalibur\system\programs

library Folder for example library files

\Xcalibur\examples\ToxID\libraries

experiment type.csv Example ToxID processing configuration files

\Xcalibur\examples\ToxID

experiment type.raw Example raw files \Xcalibur\examples\ToxID


2

Working with Libraries

ToxID requires one or more spectra libraries for experiments identifying compounds based on MS2, MS3, or both MS2 and MS3 spectra. To add, configure, and archive libraries, use the following:

• “Adding a Library,” next

• “Adding Libraries to the Search List” on page 7

• “Adding Libraries to the Search List” on page 7

To see a sample library file, go to the folder:

\Xcalibur\examples\ToxID\libraries

For more detailed information about using libraries, see the Creating and Searching Libraries User Guide included in the Xcalibur documentation.

Adding a LibraryTo add a library

1. Open the Xcalibur Home Page and choose Tools > Library Manager.

The Library Manager dialog box opens with the Manage libraries page shown by default (Figure 1).

2 Working with LibrariesAdding a Library


Figure 1. Library Manager dialog box

2. Click Add.

The Add Library dialog box opens (Figure 2).

Figure 2. Add Library dialog box

3. Click Browse to locate the library you want to add.

ToxID installs libraries in the \Xcalibur\examples\ToxID\libraries folder.

4. Click OK.

The library you selected is now shown in the Source box.

2 Working with LibrariesAdding Libraries to the Search List


5. Depending on the location of the source library, select the Copy the library to the local computer or Link to the library from either a remote location or computer check box.

6. Click OK.

The File Status message box opens and reports the progress of copying the file.

7. After you receive confirmation that the library has been added, click Dismiss.

By default, the library is copied to the folder:

\Program Files\NISTMS\MSSEARCH

8. Click Exit to close the Library Manager dialog box.

Adding Libraries to the Search ListTo add a library to the search list

1. Open the Xcalibur Home Page and click Qual Browser.

The Qual Browser window opens (Figure 3).

Figure 3. Qual Browser window

2. Choose File > Open.

The Open Raw File dialog box opens (Figure 4).

2 Working with LibrariesAdding Libraries to the Search List


Figure 4. Open Raw File dialog box

3. Select an Xcalibur raw date file.

4. Click Open.

The Qual Browser spectrum window opens (Figure 5).

Figure 5. Qual Browser spectrum window

To ensure that the spectrum window is active, look for the icon. (If you see instead, click the icon to activate the window.)

5. Right-click the activated spectrum window and choose Library > Options from the shortcut menu.

2 Working with LibrariesArchiving a Library


The Search Properties dialog box opens with the Search List page shown by default (Figure 6).

Figure 6. Search Properties dialog box

6. Select the library from the Available Libraries list.

7. Click Add to include the library in the Selected libraries list.

8. Use the Top, Up, Down, and Bottom buttons to create a search order of multiple libraries.

9. Click Apply, and then click OK.

10. Right-click the activated spectrum window and choose Library > Search from the shortcut menu.

If you see some compound results in the library, then your library settings are valid and the NIST software is activated.

Archiving a LibraryArchiving a library creates a copy of the library as a backup or to use on another instrument.

To archive a library

1. Open the Xcalibur Home Page.

2. Choose Tools > Library Manager.

The Library Manager dialog box opens (Figure 7).

2 Working with LibrariesArchiving a Library


Figure 7. Library Manager dialog box

3. Select the library from the NIST libraries list.

4. Click Archive.

The Archive Library dialog box opens (Figure 8).

Figure 8. Archive Library dialog box

5. Click Browse and select the destination to archive the library.

6. Click OK.

7. After you receive confirmation that the library has been archived, click Dismiss.

8. Click Exit to close the Library Manager dialog box.


3

Setting Up ToxID Processing Configuration Files

ToxID requires experiment- and compound-specific information that you define in the processing configuration file. The processing configuration file is a .csv file that you name and save.

Processing Configuration File TemplateA read-only processing configuration (.csv) file template is provided on the CD. As part of the installation process, this template is put in the following folder:


In addition, the CD contains an example file for each type of experiment that you can analyze with ToxID, as described in “Example Processing Configuration Files and Reports” on page 15.

Use Microsoft Excel™ to edit ToxID .csv processing configuration files. Note the following about editing the processing configuration files with Excel:

• NEVER add, remove, or rearrange columns or rows above row 20 in a processing configuration file. ToxID cannot process the analysis if any information is missing or moved.

• Changes you make to a .csv processing configuration file, such as enlarging or shrinking columns or rows, are lost when you save the file.

• Always save the edited processing configuration file as a .csv file. You cannot run ToxID using Excel (.xls) files.

Contents

• Processing Configuration File Template

• Example Processing Configuration Files and Reports

Note If you have a processing configuration file from ToxID 1.0, you can open the processing configuration file template on the ToxID 2.1 CD and save it with a new name. You then copy information from the ToxID 1.0 configuration file into the copy of the ToxID 2.1 configuration processing file you saved in step 1.

3 Setting Up ToxID Processing Configuration FilesProcessing Configuration File Template


The ToxID processing configuration file (name.csv) supplied on the ToxID CD is shown in Figure 9.

Figure 9. Processing configuration file

Processing Configuration File Parameters

A ToxID processing configuration file contains three sections:

• Global parameters at the top of the file define your company name, logo, and laboratory name that appear at the top of all reports.

• Experiment-specific parameters define items that relate to specific experiments.

• Compound-specific parameters are located in line 20 and below. These parameters are also screening experiment specific.

The global parameters as they appear in the file are shown in Figure 10 and described in Table 3.

Figure 10. Global parameters



The experiment-specific parameters, shown in Figure 11 and defined in Table 4, contain the information needed for specific experiments.

Figure 11. Experiment-specific parameters

Table 3. Global parameters

Parameter Description

m/z window The m/z variability window.

RT window in secs Retention time variability window.

Laboratory Name of laboratory.

Company name Name of company.

Company logo Location of the logo file for the company. For example: C:\logo.jpg

Table 4. Experiment-specific parameters


Ion Ratio Window(%) The ion ratio variability window.

MS2 Search Library The name of the library to search MS2 spectra. If no library name is specified, ToxID searches all the libraries defined in Qual Browser. To specify multiple libraries, put the library name in the columns to the right. There is no limit on the number of libraries you can specify.

MS3 Search Library The name of the library to search MS3 spectra. If no library name is specified, no search takes place.

Exact Mass Window (ppm)

Specifies the exact mass variability window.



The compound-specific parameters, are shown in Figure 12 and defined in Table 5.

Figure 12. Compound-specific parameters

Table 5. Compound-specific parameters (Sheet 1 of 2)


Compound Name Name of the compound. If a spectra library is implemented, this name must match the library compound name. Compound names are required for all screening experiments.

Parent Ion m/z Parent ion mass-to-charge ratio. This parameter is required for all experiments.

Analyte Type Specifies a parent, metabolite, or other analyte type, as appropriate. The first letter of an analyte type name is posted in the report. This parameter is required for all experiments.

The Code column in the reports refers to the information in the Analyte Type column: P for Parent, M for Metabolite, or I for Internal Standard.

Expected RT Expected retention time. This parameter is required for all experiments.

MS2 Product Ion For MS2 and MS2/MS3experiments, specifies the most intense or most specific fragment in MS2 spectra. The m/z value for this fragment is used to reconstruct the chromatogram.

For MS3experiments, it specifies the MS2 fragment ion for which an MS3spectrum was collected.

For QED MS2 experiments, this parameter is optional.

Product ion Intensity Threshold

For MS2 and MS2/MS3 experiments, a search hit is only reported if the signal intensity for the most intense or most specific fragment in the MS/MS spectra is equal to or above this value.

For QED MS2 experiments, a search hit is only reported if the intensity of the fragment ion collected in an SRM scan event is equal to or above this value.

For other types of experiments, a hit is reported if the TIC signal intensity is equal to or above this value.

SI Specifies the minimum search index value for the reported hits. This parameter is required for the MS2 spectra, MS2/MS3spectra, MS3spectra, and MS2 QED experiments.

3 Setting Up ToxID Processing Configuration FilesExample Processing Configuration Files and Reports


Setting Processing Configuration File Parameters

To set the ToxID processing configuration file parameters

1. Do one of the following:

• Open Excel and then open the ToxID processing configuration file for the experiment you want to perform.

• Double-click the ToxID processing configuration file for the experiment you want to perform.

2. Set the global parameters as shown in Table 3 on page 13.

3. Set the compound-specific parameters as shown in Table 5 on page 14.

4. Save the file with a new name in a location of your choice.

Example Processing Configuration Files and ReportsIn addition to the default processing configuration file template, six example processing configuration files are provided on the ToxID CD, one for each type of experiment you can analyze. These sample files are located in the following folder:


The following sections describe each example processing configuration file and provide an example of both the summary and long reports that each file generates:

• “MS2 Spectrum and Retention Time” on page 16

• “MS2/MS3 Spectra and Retention Time” on page 20

• “MS3 Spectrum and Retention Time” on page 24

• “MS2 Spectrum Collected in a QED Experiment and Retention Time” on page 27

RSI Specifies the minimum reverse search index value for the reported hits. This parameter is required for the MS2 spectra, MS2/MS3 spectra, MS3 spectra, and MS2 QED experiments.

SRM Fragment Ions Specifies the fragment and, in parentheses, the relative intensity of each fragment ion. Separate each ion entry with a semicolon (;), for example: 191.3(25);245.2(100);345.9(67). This parameter is required for the SRM and QED. The SRM fragment ions input must match with the SRM scans, or else it does not return a hit.

Table 5. Compound-specific parameters (Sheet 2 of 2)




• “SRM Transitions and Ion Ratios” on page 30

• “Exact Mass” on page 33

ToxID saves all reports in the raw file folder using the following format for the report file name:

raw_file_name_date_timestamp_report type

where:

raw_file_name is the name of the source file;

date is the date when ToxID generated the report (using the format yyyymmdd where yyyy is the year, mm is the month, and dd is the day of the month);

timestamp is the time (using the format hhmmss where hh is the hour, mm are the minutes, and ss are the seconds). The timestamp ensures that all report files are unique and never overwritten;

report type is S (Summary Report) or L (Long Report). The spreadsheet file has no report type.

Example: DrugXRawFileFolder\DrugX_20070605_100935_S

ToxID produces two types of reports:

• Summary Report: Lists all detected compounds and provides related chromatograms.

• Long Report: Provides one page of detailed information for each compound.

MS2 Spectrum and Retention Time

Use the MS2_spectra.csv processing configuration file in screening experiments that identify compounds based on MS2 spectrum and retention time. You can view the processing configuration file in Figure 13, a sample summary report in Figure 14, and a sample long report in Figure 15.



Figure 13. MS2 spectrum and retention time processing configuration file (MS2_spectra.csv)



Figure 14. MS2 spectrum and retention time sample summary report

Your Company NameToxID 2.1.0 Summary Report

Raw File Name: C:\XCalibur\examples\ToxID\MS2\MS2_Test.RAWConfig File Name: C:\XCalibur\examples\ToxID\MS2\ConfigFile_MS2_Test.csvSample Name:Laboratory: Your Lab NameAcquistion Start Time: 3/27/2008 6:48:33 PM

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1.30 1.81 2.254.73

4.774.704.80

4.66 4.87 5.515.40

5.455.345.495.30 5.90

4.15

4.204.114.26

3.323.28

3.353.453.25

3.853.88

3.913.814.39

4.164.10

4.214.05 4.625.295.25

5.215.355.16 5.77

NL: 3.51E4m/z= 147.8-148.4 F: ITMS + c ESId w Full ms2 [email protected][55.00-255.00]








Page 1 of 1

PeakNumber

Compound Name Code SI RSI m/z ExpectedRT

Real RT Intensity Library Name

1 Albuterol P 958 959 240.10 1.40 1.40 35119 MS2_Test2 Alprenolol P 885 887 250.20 4.80 4.73 120657 MS2_Test3 Amitriptyline P 912 912 278.20 5.40 5.40 283564 MS2_Test4 7-Amino-Flunitrazepam M 883 884 284.10 4.20 4.15 29260 MS2_Test5 6-Acetylmorphine P 866 867 328.20 3.30 3.32 25831 MS2_Test6 Acebutolol P 880 884 337.30 3.90 3.85 103888 MS2_Test7 6-Acetylcodeine M 862 863 342.30 4.20 4.16 60872 MS2_Test8 Haloperidol-D4 I 883 883 380.30 5.30 5.29 170724 MS2_Test



Figure 15. MS2 spectrum and retention time sample long report (page for hit number 1)

Your Company NameToxID 2.1.0 Long Report


Page 1 of 8

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1 Albuterol P 958 959 240.10 1.40 1.40 35119 MS2_Test

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MS2/MS3 Spectra and Retention Time

Use the ms2_ms3_spectra.csv processing configuration file in screening experiments that identify compounds based on MS2 and MS3 spectra and retention time. You can view the processing configuration file in Figure 16, a sample summary report in Figure 17, and a sample long report in Figure 18 and Figure 19.

Figure 16. MS2/MS3 spectra and retention time processing configuration file (MS2_MS3_spectra.csv)



Figure 17. MS2/MS3 spectra and retention time sample summary report (first page)


Raw File Name: C:\XCalibur\examples\ToxID\MS2_MS3\MS2_MS3_Test.RAWConfig File Name: C:\XCalibur\examples\ToxID\MS2_MS3\ConfigFile_MS2_MS3_Test.csvSample Name:Laboratory: Your Lab NameAcquistion Start Time: 3/27/2008 6:34:32 PM

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4.834.874.68 5.343.965.38

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NL: 2.11E3TIC F: ITMS + c ESI d w Full [email protected]@cid37.00 [55.00-255.00]








Page 1 of 2

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Compound Name Code MSOrder

SI RSI m/z ExpectedRT


1 * Albuterol P 3 889 895 240.10 1.40 1.12 2111 MS3_Test2 * Albuterol P 2 976 976 240.10 1.40 1.11 35817 MS2_Test3 * Alprenolol P 3 830 830 250.20 4.80 4.79 18413 MS3_Test4 * Alprenolol P 2 895 897 250.20 4.80 4.78 64106 MS2_Test5 * Amitriptyline P 2 929 929 278.20 5.40 5.38 266839 MS2_Test6 * Amitriptyline P 3 877 878 278.20 5.40 5.39 62546 MS3_Test7 * 7-Amino-Flunitrazepam M 3 830 833 284.10 4.20 4.18 5544 MS3_Test8 * 7-Amino-Flunitrazepam M 2 868 871 284.10 4.20 4.18 25081 MS2_Test



Figure 18. MS2/MS3 spectra and retention time sample long report (first page of MS3 spectrum for hit number 1)



Page 1 of 16

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1 * Albuterol P 3 889 895 240.10 1.40 1.12 2111 MS3_Test

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Figure 19. MS2/MS3 spectra and retention time sample long report (second page of MS2 spectrum for hit number 1)

Your Company Name ToxID 2.1.0 Long Report


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2 * Albuterol P 2 976 976 240.10 1.40 1.11 35817 MS2_Test

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NL: 3.58E4m/z= 147.8-148.4F: ITMS + c ESI d wFull [email protected][55.00-255.00]

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Library Structure



MS3 Spectrum and Retention Time

Use the ms3_spectra.csv processing configuration file in screening experiments that identify compounds based on MS3 spectrum and retention time. You can view the processing configuration file in Figure 20, a sample summary report in Figure 21, and a sample long report in Figure 22.

Figure 20. MS3 spectrum and retention time processing configuration file (MS3_spectra.csv)



Figure 21. MS3 spectrum and retention time sample summary report



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4.834.64 5.285.38

5.44

5.33 5.51 5.924.15

4.204.09 4.28

3.333.29

3.373.26 3.48 4.24

3.833.88

3.923.78 4.37

4.14

4.214.07 4.655.26

5.315.21

5.395.17









Page 1 of 1

PeakNumber



1 Albuterol P 829 835 240.10 1.40 1.42 2156 MS3_Test2 Alprenolol P 837 837 250.20 4.80 4.76 21707 MS3_Test3 Amitriptyline P 860 871 278.20 5.40 5.38 51929 MS3_Test4 7-Amino-Flunitrazepam M 819 819 284.10 4.20 4.15 5435 MS3_Test5 6-Acetylmorphine P 827 827 328.20 3.30 3.33 8505 MS3_Test6 Acebutolol P 888 891 337.30 3.90 3.83 75901 MS3_Test7 6-Acetylcodeine M 841 841 342.30 4.20 4.14 29648 MS3_Test8 Haloperidol-D4 I 871 871 380.30 5.30 5.26 19816 MS3_Test



Figure 22. MS3 spectrum and retention time sample long report (page for hit number 1)



Page 1 of 8

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1 Albuterol P 829 835 240.10 1.40 1.42 2156 MS3_Test

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1.351.50

1.531.31 1.65

1.871.27 2.39

NL: 2.16E3TIC F: ITMS + c ESId w Full [email protected]@cid37.00[55.00-255.00]

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Library Structure



MS2 Spectrum Collected in a QED Experiment and Retention Time

Use the ms2_spectra_QED.csv processing configuration file in screening experiments that identify compounds based on MS2 spectrum collected in a QED experiment and retention time. You can view the processing configuration file in Figure 23, a sample summary report in Figure 24, and a sample long report in Figure 25.

Figure 23. MS2 spectrum collected in a QED experiment processing configuration file (MS2_spectra_QED.csv)



Figure 24. MS2 spectrum collected in QED experiment sample summary report


Raw File Name: C:\XCalibur\examples\ToxID\MS2_QED\MS2_QED.RAWConfig File Name: C:\XCalibur\examples\ToxID\MS2_QED\ConfigFile_MS2_QED.csvSample Name:Laboratory: Your Lab NameAcquistion Start Time: 6/18/2007 6:32:54 AM

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3.63 4.380.63 1.584.75

5.170.53 4.571.15 6.542.37 7.454.30

7.401.15 2.05 3.66 5.58 7.785.67

6.11 6.67 7.87

NL: 5.54E5TIC F: + c ESI sid=10.00 SRM [email protected] [134.192-134.202]



NL: 3.47E5TIC F: + c ESI sid=10.00 SRM [email protected] [165.005-165.015,240.976-240.986]

NL: 8.26E5TIC F: + c ESI sid=10.00 SRM [email protected] [122.199-122.209,223.112-223.122]

Page 1 of 1

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1 Phenylpropanolamine p 999 999 152.000 2.50 2.65 553531 MS2_Test2 Methcathinone p 999 999 164.000 3.30 3.42 1474860 MS2_Test3 Methaqualone p 999 999 251.100 4.80 4.75 3639669 MS2_Test4 4-Hydroxynordiazepam p 999 999 287.100 4.30 4.30 347148 MS2_Test5 Ibogaine p 999 999 311.200 5.50 5.67 826397 MS2_Test



Figure 25. MS2 spectrum collected in QED experiment sample long report (page for hit number 1)


Raw File Name: C:\XCalibur\examples\ToxID\MS2_QED\MS2_QED.RAWConfig File Name: C:\XCalibur\examples\ToxID\MS2_QED\ConfigFile_MS2_QED.csvSample Name:Laboratory: Your Lab NameAcquistion Start Time: 6/18/2007 6:32:54 AM

Page 1 of 5

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1 Phenylpropanolamine p 999 999 152.000 2.50 2.65 553531 MS2_Test

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NL: 5.54E5TIC F: + c ESI sid=10.00SRM [email protected][134.192-134.202]

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Library Structure



SRM Transitions and Ion Ratios

Use the ion_ratio.csv processing configuration file in screening experiments that identify compounds based on single SRM transitions and retentive ion ratios and retention time. You can view the processing configuration file in Figure 26, a sample summary report in Figure 27, and a sample long report in Figure 28.

Figure 26. SRM transitions and ion ratios processing configuration file (ion_ratio.csv)



Figure 27. SRM transitions and ion ratios sample summary report


Raw File Name: X:\ToxID\Sample Files\SRM_3Segs.rawConfig File Name: X:\ToxID\ToxID_config_Sample.csvSample Name:Laboratory: Your Lab NameAcquistion Start Time: 08/29/2007 04:35:51 PM

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4.02 4.23 5.984.693.42 5.150.43 2.571.53 5.611.010.58 2.751.85 2.243.67

3.27 4.00 4.43 4.620.85 4.992.88 5.821.97 5.260.26 2.530.62 1.761.05 2.284.51

4.73 5.053.66 5.303.48 5.903.850.78 4.162.011.180.24 2.37 2.611.56 3.11

NL: 1.32E7m/z=139.7-140.3+164.7-165.3+207.7-208.3 F:+ c ESI SRM ms2 [email protected][140.099-140.101, 164.999-165.001,207.999-208.001]



Page 1 of 1

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Compound Name Code m/z ExpectedRT

Real RT Intensity Ion Ratio

1 SomethingA p 271.000 3.82 3.82 13188079 Pass2 Compound,C p 325.000 3.67 3.67 12920907 Fail3 SomeCompoundB p 388.000 4.51 4.51 46736434 Fail



Figure 28. SRM transitions and ion ratios sample long report (page for hit number 1)


Raw File Name: X:\ToxID\Sample Files\SRM_3Segs.rawConfig File Name: X:\ToxID\ToxID_config_Sample.csvSample Name:Laboratory: Your Lab NameAcquistion Start Time: 08/29/2007 04:35:51 PM

Page 1 of 3

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Compound Name Code m/z ExpectedRT

Real RT Intensity ExpectedIon Ratio

Ion Ratio

1 SomethingA p 271.000 3.82 3.82 13188079 PassIon 1 140.100 100.0 100.0Ion 2 165.000 60.0 69.8Ion 3 208.000 80.0 74.5

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Exact Mass

Use the exact_mass.csv processing configuration file in screening experiments that identify compounds based on exact mass and retention time. You can view the processing configuration file in Figure 29 a sample summary report in Figure 30, and a sample long report in Figure 31.

Figure 29. Exact mass processing configuration file (exact_mass.csv)



Figure 30. Exact mass sample summary report


Raw File Name: C:\Xcalibur\examples\ToxID\Exact_Mass\Exact_Mass_Test.RAWConfig File Name: C:\Xcalibur\examples\ToxID\Exact_Mass\ConfigFile_Exact_mass.csvSample Name:Laboratory: Your Lab NameAcquistion Start Time: 3/24/2008 4:46:43 PM

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5.364.12 10.151.533.57

3.493.130.87 3.80 12.50

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Page 1 of 1

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Compound Name Expectedm/z

Detectedm/z

Delta(mDa)

Delta(ppm)

ExpectedRT

Real RT Intensity

1 Albuterol 240.1594 240.1594 -0.0 -0.0 2.58 2.58 1994852 Alprenolol 250.1804 250.1804 -0.0 -0.0 4.50 4.66 126044993 Amitriptyline 278.1906 278.1906 0.0 0.0 5.00 5.19 117697554 6-Acetylmorphine 328.1543 328.1543 0.0 0.1 3.30 3.57 21120135 6-Acetylcodeine 342.1702 342.1703 0.1 0.4 4.10 4.18 45933066 Acebutolol 337.2124 337.2125 0.1 0.2 3.80 3.98 9077282



Figure 31. Exact mass sample long report (page for hit number 1)


Raw File Name: C:\Xcalibur\examples\ToxID\Exact_Mass\Exact_Mass_Test.RAWConfig File Name: C:\Xcalibur\examples\ToxID\Exact_Mass\ConfigFile_Exact_mass.csvSample Name:Laboratory: Your Lab NameAcquistion Start Time: 3/24/2008 4:46:43 PM

Page 1 of 6

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1 Albuterol 240.1594 240.1594 -0.0 -0.0 2.58 2.58 199485

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2.121.990.880.78 2.84 4.163.06

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4

Configuring the ToxID User Interface

Use the procedure in this chapter to specify a processing configuration file, screening method, ion ratio calculation method, report type, and print option for your ToxID search results.

To configure the ToxID user interface

1. Double-click the ToxID shortcut on your Windows desktop.

The ToxID dialog box opens (Figure 32).

Figure 32. ToxID dialog box

2. In the Processing Configuration File box, browse to locate the processing configuration file you want to use.

Note Do not select a file in the Source File box. You select a source file when you run ToxID to process a single raw file or sequence, as described in “Running ToxID Using the ToxID User Interface” on page 41.

4 Configuring the ToxID User Interface


For more information about the processing configuration file, see “Processing Configuration File Template” on page 11.

3. Select a compound screening method from the Screening Method list, which allows you to choose from the following:

• Auto Detect

• Based on Full MS2 scans

• Based on SRM and MS2 scans

• Based on MS2 and MS3 scans

• Based on MS3 scans

• Based on accurate mass scans

• Based on SRM scans

4. In the Ion Ratio Calculation Method (In SRM Experiment) area, select Use Scan at Peak Apex or Use Average Scan.

• Use Scan at Peak Apex—ion ratio is calculated based on peak apex scan spectrum.

• Use Average Scan—ion ratio is calculated based on average scan spectrum over the range of the peak’s half height.

5. In the MS2, MS3, MS/MS3 Experiments area, select the Use Full MS Scan to Confirm check box if you want to confirm library search results with parent ion peak detection in the full scan event.

6. Select the type of report you want to produce:

• Summary Report—Lists all detected compounds and provides related chromatograms.

• Long Report—Provides one page of detailed information for each compound.

For examples of both the summary and long reports produced by each configuration file, see “Example Processing Configuration Files and Reports” on page 15.

Note Auto Detect is the screening method by default. With it, ToxID can identify the screening experiment implemented in the acquired data file.

Note Make sure the relative intensity in the configuration file is using the selected scan method.

Note All reports are saved as both .pdf and .csv files. You can open and print the .pdf file, or import the .csv file into a database.

4 Configuring the ToxID User Interface


\c

7. Choose what type of report output you want:

• Print—Prints the report on your default printer and also saves the report as a .pdf file.

• View—Displays the report. You can view and print the report later because it is always saved as a .pdf file in the raw file folder.

8. Click Save Settings.

Note You can choose BOTH Summary Report and Long Report. Both reports are saved as .pdf files and not displayed or printed unless you choose those options as well.

Note ToxID still saves the reports, even if you do not choose Print or View.

Note Do not click Process. You click Process when you run ToxID to process a single raw file or sequence, as described in “Running ToxID Using the ToxID User Interface” on page 41.


5

Running Tox ID

After configuring ToxID, you can run ToxID:

• Using the ToxID user interface to process a single data file or sequence

• Performing post-acquisition processing on an entire sequence or on selected data files using an Xcalibur processing method

• During sample sequence acquisition as the acquisition of each sample is completed

A log file keeps records of any problems ToxID encounters during the analysis or when creating the reports.

Running ToxID Using the ToxID User InterfaceUse this method to process a single data file or sequence.

To run ToxID on a single data file or sequence

1. Double-click the ToxID shortcut on your Windows desktop.

The ToxID dialog box opens (Figure 33).

Contents

• “Running ToxID Using the ToxID User Interface,” next

• “Running ToxID Using an Xcalibur Processing Method” on page 43

• “Using the Log File to Troubleshoot Processing Problems” on page 49

5 Running Tox IDRunning ToxID Using the ToxID User Interface


Figure 33. ToxID dialog box

2. Click next to the Source File box and browse to locate the raw data file or sequence file you want to use.

3. Click next to the Processing Configuration File box and browse to locate the configuration file you want to use.

For more information about the configuration file, see “Processing Configuration File Template” on page 11.

4. Select a compound screening method from the Screening Method list, which allows you to choose from the following:

• Auto Detect

• Based on Full MS2 scans

• Based on SRM and MS2 scans

• Based on MS2 and MS3 scans

• Based on MS3 scans

• Based on accurate mass scans

• Based on SRM scans

Note Auto Detect is the screening method by default. With it, ToxID can identify the screening experiment implemented in the acquired data file.

5 Running Tox IDRunning ToxID Using an Xcalibur Processing Method


5. In the Ion Ratio Calculation Method (In SRM Experiment) area, select Use Scan at Peak Apex or Use Average Scan.

• Use Scan at Peak Apex—ion ratio is calculated based on peak apex scan spectrum.

• Use Average Scan—ion ratio is calculated based on average scan spectrum over the range of the peak’s half height.

6. In the MS2, MS3, MS/MS3 Experiments area, select the Use Full MS Scan to Confirm check box if you want to confirm library search results with parent ion peak detection in the full scan event.

7. Select the type of report you want to produce:

• Summary Report—Lists all detected compounds and provides related chromatograms.

• Long Report—Provides one page of detailed information for each compound.

For examples of both the summary and long reports produced by each configuration file, see “Example Processing Configuration Files and Reports” on page 15.

\c

8. Choose what type of report output you want:

• Print—Prints the report on your default printer and also saves the report as a .pdf file.

• View—Displays the report. You can view and print the report later because it is always saved as a .pdf file in the raw file folder.

9. Click one of the following:

• Save Settings—To save your settings.

• Process—Processes the source and configuration files you select, and prepares the type of report you select and your choice of output.

Running ToxID Using an Xcalibur Processing MethodTo process an entire sequence or selected rows in the sequence, create a processing method and then reprocess the sequence or selected data files.

Note Make sure the relative intensity in the configuration file is using the selected scan method.

Note All reports are saved as both .pdf and .csv files. You can open and print the .pdf file, or import the .csv file into a database.

Note You can choose both Summary Report and Long Report and both are saved as .pdf files and not displayed or printed unless you choose those options as well.

Note ToxID still saves the reports, even if you do not choose Print or View.



To create a processing method

1. Open the Xcalibur Home Page and choose GoTo > Processing Setup.

The Processing Setup dialog box opens with the Identification page displayed by default (Figure 34).

Figure 34. Processing Setup dialog box

2. If the left View bar is not visible, select View > View Bar.

3. In the left View bar, click .

The Programs view opens (Figure 35).



Figure 35. Programs view

4. Double-click the first available text box in the Enable column and select the check box that appears in that column.

5. In the Sample type area (see Figure 35), select the sample type you want (only one type can be selected):

• Std: Standard

• QC: Quality Control

• Unk: Unknown

• Other

6. In the Action column, select Run Program.

7. Double-click the Program or Macro Name column.

The Browse for Program dialog box opens (Figure 36).

Sample types



Figure 36. Browse for Program dialog box

8. Select the location of the ToxID program.

ToxID is installed in the \Xcalibur\system\programs folder. Use the full path name for ToxID and select the ToxID.exe file.

9. Click Open.

The Browse for Program dialog box closes and the ToxID path is shown in the Program or Macro Name column.

10. In the Sync column, click to select the check box that appears in that column.

11. In the Parameters column, type “%R”.

For an example of how the run information appears, see Figure 37.



Figure 37. Sample list with ToxID defined as program to run

12. Click OK.

Whenever you run a sequence, ToxID automatically processes the sequence.

13. Save the file.

To reprocess the sequence or selected data files

1. Go to the Sequence View in the Home Page.

2. Go to the . sld file directory by choosing File > Open > Xcalibur > examples > methods.

3. Make sure to select the .sld file for the created processing method.

4. In the sequence, select the range of row numbers (samples) you want to reprocess.

5. Choose Actions > Batch Reprocess.

The Batch Reprocess Setup dialog box opens (Figure 38).

5 Running Tox IDRunning ToxID Directly After Data Acquisition for Each Sample in the Sequence


Figure 38. Batch Reprocess Setup dialog box

6. Select the Programs check box.

7. Click OK.

ToxID processes the samples you selected.

Running ToxID Directly After Data Acquisition for Each Sample in the Sequence

Use this method to process a single data file with ToxID after data acquisition is completed for each sample in the sequence. The data acquisition system, Xcalibur, automatically invokes ToxID to process the raw file.

To run ToxID after data acquisition completes for each sample in a sequence

1. In the Sequence Setup window, choose Actions > Run Sequence.

The Run Sequence dialog box opens (Figure 39).

5 Running Tox IDUsing the Log File to Troubleshoot Processing Problems


Figure 39. Run Sequence dialog box

2. In the Programs area, for the Post Acquisition box, click Browse and select the full path name for ToxID.

3. Append “%R” to the ToxID file name.

4. Under Run Synchronously, select the Post Acquisition check box.

5. Click OK.

ToxID processes each sample in the sequence after the data acquisition is complete.

Using the Log File to Troubleshoot Processing ProblemsToxID provides a log file to help you resolve any problems that arise if the data file appears not to have been processed correctly.

To troubleshoot a problem, first confirm the following:

• The processing configuration file contains the information necessary to process the data file you selected. For information about what a processing configuration file contains, see “Processing Configuration File Template” on page 11.

Note NEVER add, remove, or rearrange columns or rows above row 20 in a processing configuration file. ToxID cannot process the analysis if any information is missing or moved.

5 Running Tox IDUsing the Log File to Troubleshoot Processing Problems


• If you used one of the example processing configuration files, you chose the file appropriate for the data file you are processing. See “Example Processing Configuration Files and Reports” on page 15 for more information.

• You did not add, remove, or rearrange columns or rows in the processing configuration file. See “Processing Configuration File Template” on page 11 for the correct structure for a processing configuration file.

To view the log file

Go to the folder that contains the raw data file and open the ToxID.log file.

Thermo Scientific ToxId User Guide 51

I

AAdd Library dialog box 6Archive Library dialog box 10

BBatch Reprocess Setup dialog box 48

Cconfiguration file 11

editing 11parameters 12setting 15template 11

Eexamples

processing configuration file 15Excel 11, 11experiments

hybrid mass spectrometer 1ion trap mass spectrometer 1triple quadruple mass spectrometer 1

Llibraries 5

adding 5adding to the search list 7, 7archiving 9

Library Manager dialog box 6, 10log file 49

viewing 50

OOpen Raw File dialog box 8

Pparameters

compound-specific 12configuration file 12experiment-specific 12global 12setting configuration 15

Processing Setup dialog box 44

QQual Browser spectrum window 8Qual Browser window 7

Rreports

Long 16Summary 16

Run Sequence dialog box 49

SSearch Properties dialog box 9spectra

MS2/MS3 20spectrum

MS2 16MS3 24

TToxID v

configuring user interface 37dialog box 37files and their folder locations 3hardware and software requirements 2installing files and components 2running 41

Index

52 ToxId User Guide Thermo Scientific

Index: X

XXcalibur Home Page 5, 7, 9

toxid 2.1 user guide version a - thermo fisher...

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