QuickQuan 2.4 User Guide Version A
Xcalibur
Thermo QuickQuan
Version 2.4
User Guide
XCALI-97251 Revision A
July 2009
© 2009 Thermo Fisher Scientific Inc. All rights reserved.
TSQ and TSQ Vantage are trademarks and TSQ Quantum and Xcalibur are registered trademarks of Thermo
Fisher Scientific Inc. in the United States.
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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 errorfree 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
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Sale shall govern all conflicting information between the two documents.
Release history:
Revision A—July 2009
Software requirements:
QuickQuan 2.4, Foundation 1.0, Xcalibur 2.1, TSQ Series 2.1.1 or later, LC Devices 2.2.1 or later (includes
Thermo PAL), Microsoft Windows XP Service Pack 3, Microsoft Office, and compatible autosampler drivers
For Research Use Only. Not for use in diagnostic procedures.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
QuickQuan Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Changes in This Release . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
QuickQuan Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Chapter 2
Selecting QuickQuan Data Sources and Databases . . . . . . . . . . . . . . . . . . . . . . . .3
About the QuickQuan Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Granting Database Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Backing Up Your Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
About the Data Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Selecting a File Data Source. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Selecting a Machine Data Source. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Chapter 3
Defining the Compounds and Drug Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Defining the Compounds in the Database. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Manually Adding or Editing Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Importing Compounds Using a Text File . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Deleting Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Add Compounds Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Defining the Drug Sets in the Database. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Adding Drug Sets Manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Importing Drug Sets Using a Text File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Deleting Drug Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Add Drug Sets Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Viewing Compound and Drug Set Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Chapter 4
Optimizing Your Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Understanding the Compound Optimization Process . . . . . . . . . . . . . . . . . . . . 33
Reusing Optimization Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Specifying Optimization Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
QuickQuan 2.4 User Guide
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Contents
Setting Up the Tune Plate for Compound Optimization . . . . . . . . . . . . . . . . . 45
Losses/Adducts Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Manually Assigning Drug Sets to the Tune Plate Graphic . . . . . . . . . . . . . . . 48
Importing Tune Plate Information Using a Text File . . . . . . . . . . . . . . . . . . 54
Importing Compound, Drug Set, and Tune Plate Information Using a
Text File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Running an Optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Configuration Options Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Viewing the Optimization Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Viewing Results in the Optimization Tune Report Page . . . . . . . . . . . . . . . . 72
Viewing Results Using Adobe Acrobat Reader. . . . . . . . . . . . . . . . . . . . . . . . 77
Generating an Optimization Summary Report . . . . . . . . . . . . . . . . . . . . . . . 78
Updating SRM Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Modifying SRM Information Manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Importing SRM Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Deleting SRM Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Update SRM Information Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
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Chapter 5
Acquiring the Sample Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
Setting Up for Acquisition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Reusing Acquisition Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Creating a Generic Instrument Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Creating a Generic Processing Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Specifying Template Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Creating or Importing a Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Creating a Sequence in the Acquisition Setup Page . . . . . . . . . . . . . . . . . . . . 99
Editing a Sequence on the Acquisition Setup Page. . . . . . . . . . . . . . . . . . . . 102
Copying Sequences from Excel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Importing a Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Importing Excel and Sequence Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Creating an Excel Template for the Assay . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Creating a Sequence Template. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Importing the Excel and Sequence Templates . . . . . . . . . . . . . . . . . . . . . . . 111
Saving the QuickQuan Assay. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Running an Acquisition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Stopping an Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Exporting the Instrument and Processing Methods . . . . . . . . . . . . . . . . . . . . . 124
Export Methods Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Chapter 6
Reviewing the Quantitation Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .127
Reviewing the Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Generating an Acquisition Summary Report . . . . . . . . . . . . . . . . . . . . . . . . . . 129
How the QuickQuan Application Performs Postprocessing. . . . . . . . . . . . . . . 131
QuickQuan 2.4 User Guide
Thermo Scientific
Contents
Appendix A Configuration Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .133
Configuring Instruments without the Aria OS System . . . . . . . . . . . . . . . . . . 133
Configuring Instruments with the Aria OS System . . . . . . . . . . . . . . . . . . . . . 134
Bypassing the LC Column and the Dual-Pump, Dual-Column
Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
Appendix B Using a Macro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .137
Appendix C QuickQuan Page Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .139
Compounds Browse Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Compounds Table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Drug Set Names Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
Source Type Table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
SRM Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Optimization Setup Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Optimization Tune Report Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
Acquisition Templates Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
Acquisition Setup Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Acquisition Aria Configuration Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Acquisition Results Summary Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
Appendix D QuickQuan Menu and Toolbar Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .169
File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
Go Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Reports Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Toolbar and Status Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .175
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QuickQuan 2.4 User Guide
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P
Preface
This user guide describes how to use the QuickQuan™ 2.4 rapid optimization and
acquisition solution to perform high-throughput optimization and quantitative analysis of
your compounds.
Y To suggest changes to documentation or to Help
Complete a brief survey about this document by clicking the link below.
Thank you in advance for your help.
Related Documentation
The following QuickQuan manuals are available on the QuickQuan CD as PDF files:
• Thermo QuickQuan Installation Guide describes how to install the QuickQuan
application and register the database.
• Thermo QuickQuan User Guide describes how to use the QuickQuan application to
perform high-throughput optimization and quantitative analysis of your compounds.
• Thermo QuickQuan Quick Start describes how to use the main features of the QuickQuan
application.
• Thermo QuickQuan and Aria Quick Start describes how to use the QuickQuan
application with the Aria™ OS system.
Y To view QuickQuan manuals
From the Windows™ taskbar, choose Start > All Programs > Thermo Xcalibur >
Manuals > QuickQuan.
Y To open QuickQuan Help
From the QuickQuan window, choose Help > QuickQuan Help. To locate a particular
topic, use the Help Contents, Index, or Search panes.
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Preface
Special Notices
This guide includes the following types of special notices:
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or may contain information that is critical for optimal
performance of the system.
Note Highlights information of general interest.
Tip Highlights information that can make a task easier.
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
Y To contact Technical Support
Phone
800-532-4752
Fax
561-688-8736
E-mail
[email protected]
Knowledge base
www.thermokb.com
Find software updates and utilities to download at mssupport.thermo.com.
Y To contact Customer Service for ordering information
Phone
800-532-4752
Fax
561-688-8731
E-mail
[email protected]
Web site
www.thermo.com/ms
Y To copy manuals from the Internet
Go to mssupport.thermo.com and click Customer Manuals in the left margin of the
window.
Y 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]
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1
Introduction
The QuickQuan application can optimize the selected reaction monitoring (SRM) transitions
and tune parameters of multiple compounds, acquire chromatographic data, and generate
quantitative results in a single analytical run. The application stores the compound
optimization parameters in a database, so you can analyze the same compounds in multiple
assays. You can use the database information to automatically generate the acquisition and
postacquisition methods for multiple analytical runs.
Contents
• QuickQuan Features
• Changes in This Release
• QuickQuan Workflow
QuickQuan Features
The QuickQuan application does the following:
• Automates compound optimization and enables high-throughput compound
optimization and acquisition.
• Provides a graphical interface for the layout of tune plates for compound optimization.
• Supports the importing of compound information and acquisition sequences.
• Uses a central database that supports access by local (acquisition) workstations and remote
(analysis) workstations. The QuickQuan database can also support multiple instruments,
which allows you to run the optimization and the acquisition on separate instruments.
• Uses a Microsoft™ Excel™ worksheet to drive the acquisition, processing, and reporting of
quantitative sequences using standard methods.
• Enables using an Excel macro to automatically generate custom calculations based on the
postacquisition results.
• Requires minimal input for rerunning complex assays.
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Introduction
Changes in This Release
Changes in This Release
QuickQuan version 2.4 provides these main new features and enhancements:
• Compatibility with Thermo Xcalibur version 2.1
• Support for optimization using a Laser Diode Thermal Desorption (LDTD™)
autosampler
• Support for a loop injection optimization interface for compatible autosamplers
• Improved usability and stability for high throughput workflows
• Ability to share data optimized by either the TSQ Quantum™ or TSQ Vantage™ mass
spectrometer model, except for the tube lens or S-Lens voltages
• Navigation using keyboard shortcuts and tab stops
• Restructured menu (Acquisition changed to Go menu) and renamed icon (Go changed to
Run icon)
• Enhanced optimization result reports
QuickQuan Workflow
The first time you use the QuickQuan application, follow these procedures. On subsequent
uses, you can skip some of the steps if you plan to reuse the previous settings.
1. “Selecting QuickQuan Data Sources and Databases” on page 3
2. “Defining the Compounds and Drug Sets” on page 11
3. “Optimizing Your Compounds” on page 33 and “Viewing the Optimization Results” on
page 72
4. “Acquiring the Sample Data” on page 87
5. “Reviewing the Quantitation Results” on page 127
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2
Selecting QuickQuan Data Sources and Databases
This chapter describes how to select the QuickQuan database from a file data source.
Contents
• About the QuickQuan Database
• About the Data Source
About the QuickQuan Database
The QuickQuan application stores compound information used for both compound
optimization and data acquisition in a central database (.mdb file) that supports access by
local (acquisition) workstations and remote (analysis) workstations. Because the QuickQuan
database also supports multiple instruments, you can use separate instruments for the
optimization and acquisition runs. Upon installation, the QuickQuan application creates a
default database file, named QuickQuanCompounds.mdb, in the default database folder:
C:\Xcalibur\QuickQuan\QuickQuanDatabase\
The QuickQuan application uses drug sets, which are groups of one or more compounds, to
define which compounds to use for each sequence of samples in an assay or which compounds
to optimize. Each database contains tables of information about the compounds and drug
sets.
For each optimized compound, the application automatically writes the optimization
data—polarity, parent and product ion masses, collision energy, tube lens (for the TSQ
Quantum) or S-Lens (for the TSQ Vantage), and Q1 peak width—to the database.
For a compound optimization and acquisition run, the application uses the information
stored in the specified database to build methods for analyzing and processing the data, and
for providing analysis reports.
IMPORTANT The size limit for a Microsoft Access™ database is approximately 2 GB.
You cannot update your database when its size exceeds this limit.
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2
Selecting QuickQuan Data Sources and Databases
About the QuickQuan Database
Granting Database Permissions
If you are a restricted user and you do not have permissions to write to the database file, do
the following:
1. Log off and log back in as an administrator.
2. Use the Properties command in Windows to grant full permissions to the .mdb database
file.
a. Open the folder containing your .mdb database file. The default QuickQuan
database folder is:
C:\Xcalibur\QuickQuan\QuickQuanDatabase\
b. Right-click the .mdb file and choose Properties from the shortcut menu.
c. In the Properties dialog box, click the Security tab.
d. Under the Group or user names area, select Users (user path).
e. Under the Permissions for Users area, select the Allow check box for Full Control.
f.
Click Apply and click OK.
3. Log off and log back in as a user. You should now be able to update the data in your
database, such as compound and drug set information.
Backing Up Your Database
If you want to back up your database and start over with fresh data, do one of the following:
• If you are currently using the default QuickQuanCompounds.mdb file:
a. Make a copy of this file within your database folder and give that database backup
copy a different name. The default QuickQuan database folder is:
C:\Xcalibur\QuickQuan\QuickQuanDatabase\
b. Manually delete the data in your current QuickQuanCompounds.mdb database,
such as your compounds and drug sets, and then continue with your operations.
c. If you want to use the backup database again, register your backup database by
creating a new file data source (for details, refer to the QuickQuan Installation Guide).
Then, select that file data source (for details, see “About the Data Source” on page 5).
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Selecting QuickQuan Data Sources and Databases
About the Data Source
• If you are not using the default QuickQuanCompounds.mdb file created upon
installation, switch to this empty database file:
a. Register the QuickQuanCompounds.mdb database by creating a new file data source
(for details, refer to the QuickQuan Installation Guide). Then, select that file data
source (for details, see “About the Data Source” on page 5).
b. Retain your current database file as the backup database. If you want to use this
backup database again, select the file data source for this database (for details, see
About the Data Source).
About the Data Source
A data source is a connection to a database. Typically, you create a separate data source for
each database that you want to connect to.
A data source name (DSN) refers to the drive and other information that are required to
access data and is the logical name that the Open Database Connectivity (ODBC) application
uses.
Databases can have several general configurations. The QuickQuan database is typically
configured as a file data source. This is the most flexible format for the database and can be
used on a single computer or by several computers over a network.
Selecting a File Data Source
The QuickQuan application automatically opens the previously used database, unless you are
using this application for the first time. If you want to use this previous database, you can skip
the rest of this chapter and go to Chapter 3, “Defining the Compounds and Drug Sets.”
You must select a data source in the following instances:
• When you are using the QuickQuan application for the first time on your computer
You must create a file data source and register the QuickQuan database before you can use
the application for the first time. For details, refer to the QuickQuan Installation Guide.
• If you want to change the database for the current QuickQuan session
If you have not yet created a file data source to connect to the database that you want to
change to, then you must create the file data source and register that database. For details,
refer to the QuickQuan Installation Guide.
Otherwise, you have already created a file data source and registered the database that you
want to change to. You just need to select that file data source.
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Selecting QuickQuan Data Sources and Databases
About the Data Source
Y To select a file data source
1. In the QuickQuan window, choose File > Open Database. The Select Data Source
Dialog Box appears.
2. On the File Data Source page, select a file data source (see Figure 1).
3. Click OK. The ODBC Microsoft Access Setup dialog box appears.
4. In the Database area, the name of the database that is connected to your selected file data
source appears. Verify that this is the database that you want to use for this session.
If this is not the desired database, you must create a new file data source that connects to
the correct database (for details, refer to the QuickQuan Installation Guide), and then
repeat the steps in this section to select that file data source.
5. Click OK to close the ODBC Microsoft Access Setup dialog box.
Selecting a Machine Data Source
You can select or create a machine data source that is specific to the computer (machine)
hosting the QuickQuan application. The machine data source can be of the following types:
• User data source, which is specific to a single user on the computer.
• System data source, which can be used by all users or a system-wide service specific to the
computer.
Y To select a data source specific to the computer
1. In the QuickQuan window, choose File > Open Database. The Select Data Source
Dialog Box appears.
2. Click the Machine Data Source tab (see Figure 2).
3. In the Data Source Name list, select the data source you want to use.
4. Click OK. Depending on the data source selection, another dialog box, for example the
Login Dialog Box, can appear.
Y To create a new data source specific to the computer
1. In the QuickQuan window, choose File > Open Database. The Select Data Source
Dialog Box appears.
2. Click the Machine Data Source tab (see Figure 2).
3. Click New and follow the instructions in the Create New Data Source Wizard.
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Selecting QuickQuan Data Sources and Databases
About the Data Source
Select Data Source Dialog Box
Use the Select Data Source dialog box to do the following:
• Select the file data source and open a database at the first use of the QuickQuan
application, or change the file data source or database for the current QuickQuan session.
For details, see “Selecting a File Data Source” on page 5.
• Select the machine data source that is specific to your computer. For details, see “Selecting
a Machine Data Source” on page 6.
Y To open this dialog box
In the QuickQuan main window, choose File > Open Database. The Select Data Source
dialog box appears.
The Select Data Source dialog box contains these pages:
• File Data Source page: Specifies the file data source (for example, QuickQuan.dsn) for the
driver (for example, Microsoft Access Driver) that you want to use to connect to a
database. You can use any file data source that refers to an ODBC driver installed on your
computer.
Figure 1.
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Select Data Source dialog box showing File Data Source page
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About the Data Source
• Machine Data Source page: Specifies the machine data source of the type user or system. A
machine data source is specific to the computer (machine) and cannot be shared. A user
data source is specific to a user on the computer. A system data source can be used by all
users on the computer or by a system-wide service.
Figure 2.
Select Data Source dialog box showing Machine Data Source page
Login Dialog Box
The Login dialog box appears if you select a machine data source that is different from the one
currently open in the QuickQuan application. For details on how to select a machine data
source, see “Selecting a Machine Data Source” on page 6.
You provide login security information in this dialog box, if necessary, to log into a different
database.
Y To open this dialog box
1. Choose File > Open Database. The Select Data Source Dialog Box appears.
2. Click the Machine Data Source tab.
3. Click the data source in the list, for example, MS Access Database.
4. Click OK. The Login dialog box appears.
Figure 3.
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Login dialog box
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Selecting QuickQuan Data Sources and Databases
About the Data Source
The Login dialog box contains these parameters.
Parameter
Description
Data Source
(Read-only) Lists the data source, for example, MS Access
Database.
Authorization:
Login name
Type your login ID if required by your site. See your administrator
if you do not know your login ID.
If your site does not require a login ID, leave this box blank.
Authorization:
Password
Type your password if required by your site. See your
administrator if you do not know your password.
If your site does not require a password, leave this box blank.
Opens the Select Database dialog box where you navigate to and
choose a different database from the one currently open in the
QuickQuan application.
Select Database Dialog Box
Use the Select Database dialog box to select a QuickQuan database.
Y To open this dialog box
In the Login Dialog Box, click Database. The Select Database dialog box appears.
Figure 4.
Select Database dialog box
The Select Database dialog box contains these parameters.
Table 1. Select Database dialog box parameters (Sheet 1 of 2)
Parameter
Description
Database Name
Database Name
Thermo Scientific
Displays the name of the currently selected QuickQuan
database. Do not edit the text in this box. Use the
Directories list (see below) to navigate to the location of
the database you want to use.
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About the Data Source
Table 1. Select Database dialog box parameters (Sheet 2 of 2)
Parameter
Description
[Database Names List]
After you have used the Directories list to navigate to the
location of the database you want to use, this list on the
left of the dialog box displays the database files (of the
type specified in List Files of Type) in that selected
directory. Click the name of the database you want to
open. The name of the selected database then appears in
the Database Name box.
List Files of Type
Lists file types available for selection. Select
Access Databases (*.mdb) if it is not already selected.
Directories
Directories
(Read-only) Displays the location of the currently
selected database.
[Directories list]
Navigate in this list to the folder that contains the
database file you want to use.
Drives
Lists the currently selected root directory. If the database
you want to access is on a drive other than the one
currently listed, select that other drive.
Buttons/Radio Buttons
Read Only
Typically, when you are using the QuickQuan
application, you do not select this option. If you select
this option, the database opens as read-only to prohibit
any updates.
If you do not select this option, the database opens in
both read and write mode to allow updates.
Exclusive
Typically, when you are using the QuickQuan
application, you do not select this option. If you select
this option, the database opens in Exclusive mode, which
limits access to one user at a time and improves
performance.
If you do not select this option, the database opens in
Shared mode and can be accessed simultaneously by
multiple users.
Connects to a shared network location. Click this button
if you want to navigate to a database in a network
location.
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Defining the Compounds and Drug Sets
This chapter describes how to assign compounds to drug sets within the QuickQuan
database. A drug set can contain one or several compounds depending on the assay you want
to run. You can create a multicompound drug set to facilitate simultaneous optimization and
analysis of several analytes in the same sample. A cassette dosing experiment is one example of
an assay where multicompound drug sets are helpful.
Contents
• Defining the Compounds in the Database
• Defining the Drug Sets in the Database
• Viewing Compound and Drug Set Data
Defining the Compounds in the Database
The QuickQuan database must contain the information for the compounds in your
QuickQuan experiments before you can run these experiments. You use the Add Compounds
Dialog Box to manage the compound information stored in the database.
Follow these procedures to manage the compound information:
• “Manually Adding or Editing Compounds” on page 11
• “Importing Compounds Using a Text File” on page 13
• “Deleting Compounds” on page 17
Manually Adding or Editing Compounds
To add the compound information manually, use the following procedure. To import the
compound information, see “Importing Compounds Using a Text File” on page 13.
Y To manually add to or edit compounds in the QuickQuan database
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
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Defining the Compounds in the Database
2. On the Compounds Browse Page, click Add Compounds.
Figure 5.
Opening the Add Compounds dialog box
Click Add Compounds.
The Add Compounds Dialog Box appears (see Figure 8).
3. In the Compound Name box, type the new compound name.
IMPORTANT Do not use any of the following characters in a compound name:
space, period (.), double-quote (“ or ”), slash (/ or \), square bracket ([ or ]),
colon (:), semi-colon (;), vertical line (|), asterisk (*), question mark (?)
Only use underscores for spacing if needed for clarity. The QuickQuan application
uses the compound name as the file name for the sequence (.raw) file. A space in the
file name will cause the Xcalibur application to fail the submission to the sequence
queue.
The QuickQuan application prevents you from entering spaces in drug set and
compound names but it does not prevent you from manually editing the database.
If you are editing a compound, select the compound in the Database Compound List.
4. In the Charge State list, select a charge state.
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Defining the Compounds in the Database
5. In the Num Products list, select the number of product ions for the QuickQuan
application to detect.
6. In the Mass/Formula box, type the monoisotopic ion mass or the molecular formula for
the compound.
For example, if you are adding reserpine, the monoisotopic ion mass is 608.010 instead of
609.010.
7. Click Add.
Note If you use the same database for different configured mass spectrometers, when
you add or edit a compound, the QuickQuan application updates this compound
record in the database for both instruments.
8. To add or edit additional compounds, repeat steps 3 through 7.
9. Click Close.
Importing Compounds Using a Text File
You can import the compound information from a text file (.txt) instead of entering the
information manually. The text file must be in a specified format. The QuickQuan installer
provides these compound text files as examples:
\Xcalibur\QuickQuan\ImportFiles\ImportCompounds.txt
\Xcalibur\QuickQuan\ImportFiles\ImportCompoundsWithFormulas.txt
Tip To import the combined compound, drug set, and tune plate information in one step,
see “Importing Compound, Drug Set, and Tune Plate Information Using a Text File” on
page 57.
Creating a Text File for Importing Compounds
The text file can include either of the following:
• Compounds with molecular weight only
• Compounds with a formula/mass index and either a molecular formula or molecular
weight
Y To create a compound file with molecular weights only
1. Open a file in Microsoft Excel, Notepad, or any application where you can create a
tab-delimited text file (.txt).
2. In the first row of the text file, type this line:
COMPOUND_DATABASE_INFORMATION_v1
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Defining the Compounds in the Database
3. (Optional) To include a comment in the file, use a double forward slash (//) at the start of
the row. The QuickQuan application ignores any rows that begin with “//”.
IMPORTANT Do not add any commas to your comment rows. The commas cause
import problems if you open and save the file using Excel.
4. Enter a separate row for each compound. In each row, enter the following fields, and use a
tab to separate each field in the row.
• compound name
IMPORTANT Do not use any of the following characters in a compound name;
otherwise, the import process will fail:
space, period (.), double-quote (“ or ”), slash (/ or \), square bracket ([ or ]),
colon (:), semi-colon (;), vertical line (|), asterisk (*), question mark (?)
Only use underscores for spacing if needed for clarity. The QuickQuan
application uses the compound name as the file name for the sequence (.raw) file.
A space in the file name will cause the Xcalibur application to fail the submission
to the sequence queue.
The QuickQuan application prevents you from entering spaces in drug set and
compound names but it does not prevent you from manually editing the
database.
• compound molecular weight
• charge state (1 to 10)
• number of product ions to detect (1 to 10)
5. Save the compound file as a .txt file. Use a different name so that your import file does
not overwrite the following sample file provided by the QuickQuan installer:
\Xcalibur\QuickQuan\ImportFiles\ImportCompounds.txt
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Defining the Compounds and Drug Sets
Defining the Compounds in the Database
Figure 6 shows a sample file format (in Notepad) for importing compounds with molecular
weight only (no formulas).
Figure 6.
Compound file with molecular weights (no formulas)
Y To create a compound file with molecular weights and formulas
1. Open a file in Microsoft Excel, Notepad, or any application where you can create a
tab-delimited text file (.txt).
2. In the first row of the text file, type this line:
COMPOUND_DATABASE_INFORMATION_v2
3. (Optional) To include a comment in the file, use a double forward slash (//) at the start of
the row. The QuickQuan application ignores any rows that begin with “//”.
IMPORTANT Do not add any commas to your comment rows. The commas cause
import problems if you open and save the file using Excel.
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Defining the Compounds in the Database
4. Enter a separate row for each compound. In each row, enter the following fields, and use a
tab to separate each field in the row.
• compound name
IMPORTANT Do not use any of the following characters in a compound name;
otherwise, the import process will fail:
space, period (.), double-quote (“ or ”), slash (/ or \), square bracket ([ or ]),
colon (:), semi-colon (;), vertical line (|), asterisk (*), question mark (?)
Only use underscores for spacing if needed for clarity. The QuickQuan
application uses the compound name as the file name for the sequence (.raw) file.
A space in the file name will cause the Xcalibur application to fail the submission
to the sequence queue.
The QuickQuan application prevents you from entering spaces in drug set and
compound names but it does not prevent you from manually editing the
database.
• formula (F) or mass (M) index
• compound molecular formula or molecular weight
• charge state (1 to 10)
• number of product ions to detect (1 to 10)
5. Save the compound file as a .txt file. Use a different name so that your import file does
not overwrite the sample file provided by the QuickQuan installer:
\Xcalibur\QuickQuan\ImportFiles\ImportCompoundsWithFormulas.txt
Figure 7 shows a sample file format (in Notepad) for importing compounds with both
molecular weights and formulas.
Figure 7.
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Compound file with both molecular weights and formulas
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Defining the Compounds in the Database
Importing the Compounds Text File
Y To import the compound file to the QuickQuan database
1. In the QuickQuan left pane, click Compounds. Or, choose Go > Browse Compounds.
On the Compounds Browse Page, click Add Compounds. The Add Compounds Dialog
Box appears (see Figure 8).
–or–
In the QuickQuan left pane, click Optimization. Or, choose Go > Optimization >
Setup. The Optimization Setup Page appears (see Figure 14 or Figure 16).
IMPORTANT If you do not have the Aria OS system installed, before you can access
the settings on the Optimization Setup page, you must first configure an autosampler.
To configure an autosampler, see “Configuring Instruments without the Aria OS
System” on page 133.
2. Click Import.
3. When the confirmation message appears, click Yes.
4. In the Open dialog box, select the file you want to import and click Open. The imported
compounds appear in the Database Compound List in the Add Compounds dialog box
or the Drug Set Selector list on the Optimization Setup page.
Note If you use the same database for different configured mass spectrometers, when
you import a compound, the QuickQuan application updates this compound record
in the database for both instruments.
5. If you are in the Add Drug Sets dialog box, click Close.
Deleting Compounds
Y To delete compounds from the QuickQuan database
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
2. On the Compounds Browse Page, click Add Compounds. The Add Compounds Dialog
Box appears (see Figure 8).
3. In the Database Compound List, select the compound and click Delete. Repeat this step
for any other compounds you want to delete.
4. When you have finished deleting compounds, click Close.
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Defining the Compounds in the Database
Note If you use the same database for different configured mass spectrometers, when you
delete a compound, the QuickQuan application deletes this compound record from the
database for both instruments.
Add Compounds Dialog Box
Use the Add Compounds dialog box to add, edit, or delete compounds. You can import the
list of compounds from a text file, or you can manually enter your changes in the dialog box.
To add a large number of compounds at a single time, see “Importing Compounds Using a
Text File” on page 13.
When you modify the list of compounds in the Add Compounds dialog box, the QuickQuan
application updates the compounds table within the database (see “Defining the Compounds
in the Database” on page 11). The application also adds a drug set with the same name as the
compound name to the database automatically.
Y To open this dialog box
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
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Defining the Compounds in the Database
2. On the Compounds Browse Page, click Add Compounds. The Add Compounds dialog
box appears.
Figure 8.
Add Compounds dialog box
The Add Compounds dialog box contains these parameters.
Table 2. Add Compounds dialog box parameters (Sheet 1 of 2)
Parameter
Description
Database Compound List
This is a read-only table that displays the contents of the database. The columns contain the
following optimization parameters for each compound:
• Compound Name
• Parent Mass
• Charge State
• Number of Product Ions
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Table 2. Add Compounds dialog box parameters (Sheet 2 of 2)
Parameter
Description
Compound Information
Compound Name
Specifies the name of the compound that you selected from the
Database Compound List, or specifies the name of a new
compound that you want to add.
Limit: 50 characters
IMPORTANT Do not use any of the following characters in a
compound name:
space, period (.), double-quote (“ or ”), slash (/ or \),
square bracket ([ or ]), colon (:), semi-colon (;),
vertical line (|), asterisk (*), question mark (?)
Only use underscores for spacing if needed for clarity. The
QuickQuan application uses the compound name as the file
name for the sequence (.raw) file. A space in the file name will
cause the Xcalibur application to fail the submission to the
sequence queue.
Charge State
Specifies the charge state of the selected compound.
Valid range: 1 to 10
Num Products
Specifies the number of product ions for the QuickQuan
application to attempt to detect for the selected compound.
Valid range: 1 to 10
Mass/Formula
Specifies the monoisotopic ion mass or the molecular formula for
the selected compound.
For example, the monoisotopic ion mass of caffeine is 194.100.
Valid range: 1 to 2000 amu; precision to 3 decimals
Buttons
Adds the compound information to the database or change the
parameter values as you specified. A new compound and its
parameters are added to the end of the current table listings. See
“Manually Adding or Editing Compounds” on page 11.
Deletes the selected compound from the database. See “Deleting
Compounds” on page 17.
Displays the Open dialog box to import compound information
into the database from a text file. See “Importing Compounds
Using a Text File” on page 13.
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Defining the Drug Sets in the Database
Defining the Drug Sets in the Database
In the QuickQuan application, you group compounds together in drug sets. The tune plate
and the acquisition assay both use drug sets to define the compounds associated with one
another for each tuning well or acquisition sequence.
Whenever you add a new compound, the application automatically adds a drug set containing
just that one compound to the database, with the same name as the new compound. You can
associate more compounds to this drug set if you wish, or delete it.
Note Up to 10 compounds can be associated with a single drug set. If you try to associate
more than 10 compounds, you receive an error message.
Use the Add Drug Sets Dialog Box to manage the drug set information stored in the database.
Follow these procedures to manage the drug sets:
• “Adding Drug Sets Manually” on page 21
• “Importing Drug Sets Using a Text File” on page 24
• “Deleting Drug Sets” on page 26
Adding Drug Sets Manually
You can create drug sets manually and edit the compounds included in that drug set.
Y To add a new drug set manually to the QuickQuan database
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
2. On the Compounds Browse Page, click Add Drug Sets.
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Defining the Drug Sets in the Database
Figure 9.
Opening the Add Drug Sets dialog box
Click Add Drug Sets.
The Add Drug Sets Dialog Box appears (see Figure 11).
3. In the Drug Set Name box, type the drug set name.
IMPORTANT Do not use any of the following characters in a drug set name:
space, period (.), double-quote (“ or ”), slash (/ or \), square bracket ([ or ]),
colon (:), semi-colon (;), vertical line (|), asterisk (*), question mark (?)
Only use underscores for spacing if needed for clarity. The QuickQuan application
uses the drug set name as the file name for the sequence (.sld) file. A space in the file
name will cause the Xcalibur application to fail the submission to the sequence queue.
The QuickQuan application prevents you from entering spaces in drug set and
compound names but it does not prevent you from manually editing the database.
4. In the Database Compounds list, select all the compounds you want to add to the new
drug set. Each selected compound is highlighted.
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Defining the Drug Sets in the Database
5. Click Add. The QuickQuan application adds the selected compounds to the drug set,
and the new drug set name appears in the Database Drug Sets list.
Note If you use the same database for different configured mass spectrometers, when
you add a drug set, the application adds this drug set record to the database for both
instruments.
6. Click Close.
Y To add compounds to an existing drug set
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
2. On the Compounds Browse Page, click Add Drug Sets. The Add Drug Sets Dialog Box
appears (see Figure 11).
3. In the Database Drug Sets list, select the drug set name.
4. In the Database Compounds list, select all the compounds you want to add to the drug
set. Each selected compound is highlighted.
5. Click Add. The QuickQuan application adds the selected compounds to your selected
drug set.
Note If you use the same database for different configured mass spectrometers, when
you add compounds to an existing a drug set, the application updates this drug set
record in the database for both instruments.
6. Click Close.
Y To remove compounds from an existing drug set
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
2. On the Compounds Browse Page, click Add Drug Sets. The Add Drug Sets Dialog Box
appears (see Figure 11).
3. In the Database Drug Sets list, select the drug set name.
4. In the Database Compounds list, select all compounds you want to remove from your
selected drug set. Each selected compound is no longer highlighted.
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Defining the Drug Sets in the Database
5. Click Add.
IMPORTANT Even though you want to delete compounds, you click Add to add a
change to your drug set. Do not click Delete or you will delete your currently selected
drug set.
The QuickQuan application removes the compounds you indicated from your selected
drug set. The newly removed compounds still remain in the Database Compounds list.
Note If you use the same database for different configured mass spectrometers, when
you remove compounds from an existing drug set, the application updates this drug
set record in the database for both instruments.
6. Click Close.
Importing Drug Sets Using a Text File
You can import the drug set information from a text file (.txt) into the QuickQuan database.
The text file must be in a specified format. The QuickQuan installer provides this drug set
text file as an example:
\Xcalibur\QuickQuan\ImportFiles\ImportDrugSetNames.txt
Tip To import the combined compound, drug set, and tune plate information in one step,
see “Importing Compound, Drug Set, and Tune Plate Information Using a Text File” on
page 57.
Creating a Text File for Importing Drug Sets
Y To create a drug set file
1. Open a file in Microsoft Excel, Notepad, or any application where you can create a
tab-delimited text file (.txt).
2. In the first row of the text file, type this line:
DRUGSET_DATABASE_INFORMATION_v1
3. (Optional) To include a comment in the file, use a double forward slash (//) at the start of
the row. The QuickQuan application ignores any rows that begin with “//”.
IMPORTANT Do not add any commas to your comment rows. The commas cause
import problems if you open and save the file using Excel.
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Defining the Drug Sets in the Database
4. Enter a separate row for each drug set. In each row, enter the drug set name followed by
up to 10 compound names, and use a tab to separate each field in the row.
IMPORTANT Do not use any of the following characters in a drug set name;
otherwise, the import process will fail:
space, period (.), double-quote (“ or ”), slash (/ or \), square bracket ([ or ]),
colon (:), semi-colon (;), vertical line (|), asterisk (*), question mark (?)
Only use underscores for spacing if needed for clarity. The QuickQuan application
uses the drug set name as the file name for the sequence (.sld) file. A space in the file
name will cause the Xcalibur application to fail the submission to the sequence queue.
The QuickQuan application prevents you from entering spaces in drug set and
compound names but it does not prevent you from manually editing the database.
5. Save the file as a .txt file. Use a different name so that your import file does not overwrite
the following sample file provided by the QuickQuan installer:
\Xcalibur\QuickQuan\ImportFiles\ImportDrugSetNames.txt
Figure 10 shows a sample file format (in Notepad) for importing drug sets.
Figure 10. Drug set text file
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Defining the Drug Sets in the Database
Y To import the drug set file
1. In the QuickQuan left pane, click Compounds. Or, choose Go > Browse Compounds.
On the Compounds Browse Page, click Add Drug Sets. The Add Drug Sets Dialog Box
appears (see Figure 11).
–or–
In the QuickQuan left pane, click Optimization. Or, choose Go > Optimization >
Setup. The Optimization Setup Page appears (see Figure 14 or Figure 16).
IMPORTANT If you do not have the Aria OS system installed, before you can access
the settings on the Optimization Setup page, you must first configure an autosampler.
To configure an autosampler, see “Configuring Instruments without the Aria OS
System” on page 133.
2. Click Import.
3. When the confirmation message appears, click Yes.
4. In the Open dialog box, select the drug set file you want to import and click Open. The
drug sets appear in the Database Drug Sets list in the Add Drug Sets dialog box or the
Drug Set Selector list on the Optimization Setup page.
Note If you use the same database for different configured mass spectrometers, when
you import a drug set, the QuickQuan application updates this drug set record in the
database for both instruments.
5. If you are in the Add Drug Sets dialog box, click Close.
Deleting Drug Sets
Y To delete drug sets from the QuickQuan database
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
2. On the Compounds Browse Page, click Add Drug Sets. The Add Drug Sets Dialog Box
appears (see Figure 11).
3. In the Database Drug Sets list, select the drug set and click Delete. Repeat this step for
any other drug set you want to delete.
4. When you have finished deleting drug sets, click Close.
Note If you use the same database for different configured mass spectrometers, when you
delete a drug set, the QuickQuan application deletes this record from the database for
both instruments.
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Defining the Compounds and Drug Sets
Defining the Drug Sets in the Database
Add Drug Sets Dialog Box
Use the Add Drug Sets dialog box to add, delete, or edit the drug sets. To add a large number
of drug sets at a single time, you can import a list of drug sets from a text file (see “Importing
Drug Sets Using a Text File” on page 24). The QuickQuan application stores any drug set
additions, deletions, or changes in the drug set table within the database (see “Defining the
Drug Sets in the Database” on page 21).
The application uses the concept of a drug set to group compounds together. The tune plate
and the acquisition assay both use drug sets to define the compounds associated with one
another for each tuning vial or acquisition sequence.
You can assign compounds to drug sets within the database, enabling you to perform cassette
dosing experiments.
Y To open this dialog box
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
2. On the Compounds Browse Page, click Add Drug Sets. The Add Drug Sets dialog box
appears.
Figure 11. Add Drug Sets dialog box
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Defining the Drug Sets in the Database
The Add Drug Sets dialog box contains these parameters.
Table 3. Add Drug Sets dialog box parameters (Sheet 1 of 2)
Parameter
Description
Drug Set Name
Specifies the name of the drug set that you are adding or editing.
For the procedure, see “Defining the Drug Sets in the Database”
on page 21.
The drug set names appear in alphabetical order in the Database
Drug Sets list.
IMPORTANT Do not use any of the following characters in a
drug set name:
space, period (.), double-quote (“ or ”), slash (/ or \),
square bracket ([ or ]), colon (:), semi-colon (;),
vertical line (|), asterisk (*), question mark (?)
Only use underscores for spacing if needed for clarity. The
QuickQuan application uses the drug set name as the file name
for the sequence (.raw) file. A space in the file name will cause
the Xcalibur application to fail the submission to the sequence
queue.
Database Compounds
Lists all the compounds in the database.
You select the compounds from this list to include in a drug set. A
compound can be associated with more than one drug set. You
can assign a maximum of 10 compounds to a drug set.
To add more compounds to the list, see “Defining the
Compounds in the Database” on page 11.
Database Drug Sets
Lists all the drug sets in the database.
Select a drug set name in this list to view the compounds assigned
to that drug set, which are highlighted in the Database
Compounds list.
Note When you add a new compound to the database, the
QuickQuan application automatically creates a new drug set
with the same name as the added compound and associates that
compound with that drug set in the database.
Buttons
Adds the new drug set or your edits to a pre-existing drug set. See
“Adding Drug Sets Manually” on page 21.
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Viewing Compound and Drug Set Data
Table 3. Add Drug Sets dialog box parameters (Sheet 2 of 2)
Parameter
Description
Deletes the selected drug set name from the database. See
“Deleting Drug Sets” on page 26.
Note The drug set name is deleted from the database when you
click Delete, but the compounds that were associated with that
drug set remain in the database (and in the Database
Compounds list).
Displays the Open dialog box to import drug set information into
the database from a text file (.txt). See “Importing Drug Sets
Using a Text File” on page 24.
Viewing Compound and Drug Set Data
Use the Compounds Browse Page to view the contents of the database tables for the currently
opened QuickQuan database. You can also enter SQL query commands to filter the data in
the tables.
Y To view compounds with the Compound Browse page
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
The Compounds Browse Page appears.
2. In the Table list, for the TSQ Quantum mass spectrometer, select [COMPOUNDS], or
for the TSQ Vantage mass spectrometer, select [COMPOUNDS_VANTAGE]. The
Compounds table appears (see Figure 12).
3. (Optional) If the table contains many rows and you want to move up and down in the
table without having to scroll row by row, click
(first set of rows),
(previous set),
(next set), and
(last set) to change the view in the table.
4. (Optional) To use an SQL statement to filter the data, type the statement in the
Compound box and click Query to filter the data.
For example, to list only the information for one compound, type the name of that
compound; to list all compounds, type *; to list all compounds whose names contain a
specific character or characters, type the exact characters. When you have entered the
appropriate filter statement, click Query.
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Defining the Compounds and Drug Sets
Viewing Compound and Drug Set Data
Figure 12. Compounds table on the Compounds Browse page
Y To view drug sets with the Compounds Browse page
1. In the Table list, select [DRUGSETNAME]. The Drug Set table appears. See Figure 13.
2. (Optional) If the table contains many rows and you want to move up and down in the
table without having to scroll row by row, click
(first set of rows),
(previous set),
(next set), and
(last set) to change the view in the table.
3. (Optional) To use an SQL statement to filter the data, type the statement in the
Compound box and click Query to filter the data.
For example, to list only the information for one drug set, type the name of that drug set;
to list all drug sets, type *; to list all drug sets whose names contain a specific character or
characters, type the exact characters. When you have entered the appropriate filter
statement, click Query.
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Defining the Compounds and Drug Sets
Viewing Compound and Drug Set Data
Figure 13. Drug Set table on the Compounds Browse page
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Optimizing Your Compounds
This chapter describes how to automatically optimize the tune and SRM parameters for all
the compounds defined in the tune plate.
Contents
• Understanding the Compound Optimization Process
• Reusing Optimization Settings
• Specifying Optimization Settings
• Setting Up the Tune Plate for Compound Optimization
• Running an Optimization
• Viewing the Optimization Results
• Updating SRM Information
Before you set up the optimization information, add compounds and drug sets to your
selected database as described in “Defining the Compounds and Drug Sets” on page 11.
Understanding the Compound Optimization Process
To run compound optimization, assign drug sets to the wells in the tune plate. The
QuickQuan application monitors the status of each compound within the assigned drug sets
during the optimization, and then adds the data returned from the optimization to the
database.
The optimization data for each compound includes the following:
• polarity
• precursor ion mass
• product ion masses
• collision energy
• Q1 peak width
• tube lens voltage (for the TSQ Quantum) or S-Lens voltage (for the TSQ Vantage)
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Understanding the Compound Optimization Process
• product ion intensity
• ion source type
You can share the data optimized by either the TSQ Quantum and TSQ Vantage mass
spectrometer models, except for the tube lens or S-Lens voltages. The QuickQuan application
obtains the values for these voltages in the tune file of the acquisition instrument method (see
“Creating a Generic Instrument Method” on page 88).
For example, if you configure the TSQ Vantage, you can use the data previously optimized by
the TSQ Quantum to run an acquisition, except for the tube lens voltage that the application
obtains from the tune file. Conversely, if you configure the TSQ Quantum, you can use the
data previously optimized by the TSQ Vantage, except for the S-Lens voltage that the
application obtains from the tune file.
You can run acquisitions on either model without having to optimize your compounds twice.
For acquisition, when creating the instrument method using optimization results from the
database, the QuickQuan application automatically selects the Use Tuned Tube Lens Value or
Use Tuned S-Lens Value check box in the Xcalibur Instrument Setup window (see Figure 39).
During acquisition, the application uses the tube lens or S-Lens value defined in the tune file
of the acquisition instrument method.
If a compound is not optimized by your currently configured model but is optimized by
another model as recorded in the database, the QuickQuan application considers this
compound as optimized, and does not submit an optimization for this compound, unless you
clear the Use Optimization Database for Existing Compounds option in the Configuration
Options Dialog Box.
Tip Instrument methods for optimization differ from those for acquisition. If your system
includes a Thermo PAL autosampler with multiple injection ports, multiple valves, and a
stream selector, you can bypass the chromatography (LC) column, speeding up the
optimization process. See “Bypassing the LC Column and the Dual-Pump, Dual-Column
Configuration” on page 134.
To set up for optimization, follow one or both of these procedures:
• Reuse settings from a previous optimization run. See “Reusing Optimization Settings.”
• Enter or modify the optimization settings manually. See the following sections:
• “Specifying Optimization Settings” on page 35
• “Setting Up the Tune Plate for Compound Optimization” on page 45
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Reusing Optimization Settings
Reusing Optimization Settings
Instead of entering the tune and method files and optimization settings manually, you can
reuse the settings from a previous assay file (.aql file) that you created in the QuickQuan
application. The .aql file contains the configuration settings, acquisition settings, compound
optimization information, assay layout, and template information.
Y To reuse the settings in an .aql file
1. In the QuickQuan window, choose File > Open.
2. In the Open dialog box, select the .aql file and click Open. For example, open this file:
\Xcalibur\examples\QuickQuan\SampleSet\optimization template.aql
3. Verify the optimization settings on the Optimization Setup Page. For details, see
“Specifying Optimization Settings” on page 35 and “Setting Up the Tune Plate for
Compound Optimization” on page 45.
IMPORTANT If you are using the TSQ Vantage mass spectrometer and you select an .aql
file created by a QuickQuan version that does not support TSQ Vantage, make sure to
update your template tune and instrument method files to work appropriately for this
instrument.
Specifying Optimization Settings
Specify the tune and method files, output path, optimization, and tune plate settings on the
Optimization Setup Page.
IMPORTANT If you do not have the Aria OS system installed, before you can access the
settings on the Optimization Setup page, you must first configure an autosampler. To
configure an autosampler, see “Configuring Instruments without the Aria OS System” on
page 133.
Even if you configure an LDTD autosampler, you must have the correct TSQ and LDTD
driver versions before the Optimization Setup page is available.
Y To display the Optimization Setup page
In the QuickQuan left pane, click Optimization, and then click the Setup icon,
.
–or–
Choose Go > Optimization > Setup.
The Optimization Setup page appears.
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Specifying Optimization Settings
Note The Optimization Setup page contains different fields in the Tune and Method
Files area, depending on whether you are running the QuickQuan application with
the Aria OS system (see Figure 14) or without it (see Figure 15, Figure 16, or
Figure 17).
The Optimization Setup page contains an additional check box in the Optimization
Settings area when your configured autosampler supports both injection-based or
infusion-based optimization (see Figure 16).
The Optimization Setup page contains different fields in the Optimization Settings
and Plate Setup areas, depending on whether you are using a non-LDTD autosampler
(see Figure 14, Figure 15, or Figure 16), or an LDTD autosampler (see Figure 17).
If you reuse optimization settings from an .aql file (see “Reusing Optimization
Settings” on page 35) and the .aql file contains optimization setup data previously
imported from a text file instead of entered manually, then some fields do not appear
or are not selectable. See the Optimization Setup Page for details.
Figure 14, Figure 15, Figure 16, and Figure 17 show the Optimization Setup page with
various settings.
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Specifying Optimization Settings
Figure 14. Optimization Setup page when using the Aria OS system
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Specifying Optimization Settings
Figure 15. Optimization Setup page without the Aria OS system and for non-LDTD autosampler supporting either injection or
infusion
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Specifying Optimization Settings
Figure 16. Optimization Setup page without the Aria OS system and for non-LDTD autosampler supporting both injection and
infusion
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Specifying Optimization Settings
Figure 17. Optimization Setup page for LDTD autosampler supporting optimization
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Specifying Optimization Settings
Y To specify the tune and method files, output path, optimization, and tune plate settings
1. In the Tune and Method Files area, type the file path, or click
desired location for each of the following:
and navigate to the
a. In the Tune File box, specify a generic tune file. For example:
C:\Xcalibur\QuickQuan\Templates\tune template.TSQTune (for the TSQ
Quantum)
–or–
C:\Xcalibur\QuickQuan\Templates\tune template_Vantage.TSQTune (for the TSQ
Vantage)
The QuickQuan installer provides these generic tune files.
IMPORTANT Tune parameters are instrument parameters that affect the intensity
of the ion signal. You must specify a generic tune file that corresponds to the type
of experiment you are performing, for example ESI high-flow. During tune
optimization, QuickQuan determines additional settings, such as polarity, tube
lens/S-Lens voltage, parent and product ion masses, Q1 peak width, and collision
energy. These settings, which maximize the ion signal for your compounds, are
added to the settings in the generic tune file.
b. In the Instrument Method box, specify the method file that contains the instrument
settings for tune optimization. For example:
C:\Xcalibur\QuickQuan\Templates\Tune_LC_Pos.meth (for the TSQ Quantum)
–or–
C:\Xcalibur\QuickQuan\Templates\Tune_LC_Pos_Vantage.meth (for the
TSQ Vantage)
The QuickQuan installer provides these generic method files.
c. If you plan to use the Aria OS system, then in the Aria AS Method and Aria LC
Method boxes, specify the method files that contain the AS and LC settings for tune
optimization.
Note The Optimization Setup page displays the Aria AS Method and Aria LC
Method boxes only if you have the Aria OS system installed.
The QuickQuan installer provides the following template files:
C:\Xcalibur\QuickQuan\Templates\Optimization.tmt
C:\Xcalibur\QuickQuan\Templates\Optimization.htc
The Aria OS installer provides the following template files:
C:\Aria Data\AS Methods\QuickQuan Opt Template.tmt
C:\Aria Data\LC Methods\QuickQuan Opt Template.htc
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Specifying Optimization Settings
Tip Start with a template file and update the method as appropriate for your
system. For details on how to update AS/LC methods, refer to the Aria OS User
Guide. Use a different name to save the updated method files, before you specify
them in the Aria AS Method and Aria LC Method boxes.
d. In the PDF/RAW Files Output Path box, specify the path for the output folder. For
example:
C:\Xcalibur\QuickQuan\
This folder (or your previously set folder) is the default output folder for
optimization. The PDF and raw files resulting from the optimization run are stored
under this output folder.
2. In the Ion Source list, select the ion source: ESI, APCI, APPI, or H-ESI.
Note If you are using an LDTD autosampler then the Ion Source list is not selectable
because the only applicable ion source is ESI.
If some wells in the tune plate already have drug set assignments, then when you
change the ion source, if the highlight color of the well is not red, the highlight color
might change according to your ion source selection. For more information on the
various highlight colors, see section “Manually Assigning Drug Sets to the Tune Plate
Graphic” on page 48.
3. In the Intensity Threshold box, type the minimum intensity threshold for the product
ions. If the intensity resulting from optimization is less than this threshold value, the
QuickQuan application considers that the optimization run has failed.
4. (Optional) Select the H-SRM check box to specify tuning for H-SRM (precursor ion
peak width = 0.2 amu).
Note If you are using an LDTD autosampler, QuickQuan uses the H-SRM setting to
calculate the Max. Desorptions Needed value (see Figure 21). For LDTD
optimization, after you apply a drug set to the tune plate (see “Manually Assigning
Drug Sets to the Tune Plate Graphic” on page 48), import from a text file (see
“Importing the Tune Plate Information File” on page 56), or reuse an .aql file
containing imported optimization data (see “Reusing Optimization Settings” on
page 35), the QuickQuan application disables the H-SRM check box on the
Optimization Setup page.
To enable this setting again, click Clear Plate to clear all well assignments in the tune
plate.
5. In the Polarity list, select the polarity: Positive, Negative, or Both. The polarity you select
applies to the entire tune plate.
If you select Both, the TSQ™ application determines the best polarity (positive or
negative) during optimization.
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Specifying Optimization Settings
Note After you apply a drug set to the tune plate (see “Manually Assigning Drug Sets
to the Tune Plate Graphic” on page 48), the QuickQuan application disables this
polarity list because the same setting applies to all drug set assignments on the tune
plate and the application uses this setting to calculate the Max. Desorptions Needed
value (see Figure 21).
If you import the tune plate data from a text file (see “Importing the Tune Plate
Information File” on page 56), or reuse an .aql file containing imported optimization
data (see “Reusing Optimization Settings” on page 35), the polarity set in the import
file for each drug set overrides this polarity setting. As a result, after these instances,
the QuickQuan application hides the Polarity list on the Optimization Setup page.
To enable the polarity setting again, click Clear Plate to clear all well assignments in
the tune plate.
6. If you are using a non-LDTD autosampler:
a. In the Injection Volume (ul) box, type the sample amount to inject for each
compound.
b. If your configured autosampler supports both infusion- and injection-based
optimization:
• To indicate infusion-based optimization, select the Use Autosampler Infusion
During Optimization option.
• To indicate injection-based optimization, clear the Use Autosampler Infusion
During Optimization option.
IMPORTANT Make sure that the instrument method you selected in step b
contains the correct infusion or injection settings for the autosampler, to match
this infusion or injection option selection. Otherwise, you might encounter
unexpected results with errors.
For example, if you are using the Thermo PAL and you select the Use
Autosampler Infusion During Optimization option for infusion-based
optimization, make sure that the instrument method is set to infusion for the
autosampler. Conversely, if you clear this option to indicate injection-based
optimization, make sure that the instrument method is set to injection for the
autosampler. If necessary, use the Thermo Xcalibur Instrument Setup window to
modify your instrument method.
c. In the Plate Type list, select the autosampler plate type to use for this optimization.
There are two choices for the plate type:
• 96-well plate
• 384-well plate
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Specifying Optimization Settings
d. In the Autosampler Tray Name list, select the name of the autosampler tray to use for
this optimization.
Otherwise, if you are using an LDTD autosampler:
a. In the Desorptions Per Well box, specify the number of times that sample desorption
can occur with adequate intensity for each well. The number you enter applies to the
entire tune plate.
Note After you apply a drug set to the tune plate (see “Manually Assigning Drug
Sets to the Tune Plate Graphic” on page 48), the QuickQuan application disables
this field because the same setting applies to all drug set assignments on the tune
plate.
If you import the tune plate data from a text file (see “Importing the Tune Plate
Information File” on page 56), or reuse an .aql file containing imported
optimization data (see “Reusing Optimization Settings” on page 35), the
desorptions number set in the file overrides the number in the Desorptions Per
Well box. As a result, after these instances, the QuickQuan application disables
the Desorptions Per Well box on the Optimization Setup page.
To enable this setting again, click Clear Plate to clear all well assignments in the
tune plate.
b. In the Wells Per Drug Set box, specify the number of wells that you plan to set up in
the tune plate for each drug set. The number you enter applies to the entire tune
plate.
Tip You can divide the highest calculated Max. Desorptions Needed number for
your drug sets by the Desorptions Per Well number to best determine the Wells
Per Drug Set number for the tune plate. For more information on the Max.
Desorptions Needed number, see “Manually Assigning Drug Sets to the Tune
Plate Graphic” on page 48.
Note After you apply a drug set to the tune plate (see “Manually Assigning Drug
Sets to the Tune Plate Graphic” on page 48), the QuickQuan application disables
this field because the same setting applies to all drug set assignments on the tune
plate.
If you import the tune plate data from a text file (see “Importing the Tune Plate
Information File” on page 56), or reuse an .aql file containing imported
optimization data (see “Reusing Optimization Settings” on page 35), the number
of wells set in the file for each drug set overrides the number in the Wells Per
Drug Set box. As a result, after these instances, the QuickQuan application hides
the Wells Per Drug Set box on the Optimization Setup page.
To enable this setting again, click Clear Plate to clear all well assignments in the
tune plate.
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Setting Up the Tune Plate for Compound Optimization
c. In the Plate Serial Number box, type the 6-digit serial number for the LazWell plate
used for this optimization run.
If you enter less than six digits for the serial number, the leftmost missing digits
autofill with zeros.
7. Each time you assign a drug set to the tune plate, if you want to automatically highlight
the well or wells horizontally by row order, then select Row for the Order By option.
Otherwise, to highlight vertically by column order, select Column for the Order By
option. The setting you select applies to the entire tune plate.
Note After you apply a drug set to the tune plate (see “Manually Assigning Drug Sets
to the Tune Plate Graphic” on page 48), the QuickQuan application disables this
option because the same setting applies to all drug set assignments on the tune plate.
If you import the tune plate data from a text file (see “Importing the Tune Plate
Information File” on page 56), or reuse an .aql file containing imported optimization
data (see “Reusing Optimization Settings” on page 35), the order set in the file
overrides the Order By option setting. As a result, after these instances, the
QuickQuan application disables the Order By option on the Optimization Setup
page.
To enable this setting again, click Clear Plate to clear all well assignments in the tune
plate.
Setting Up the Tune Plate for Compound Optimization
The QuickQuan application uses the compound information specified in a drug set to
optimize all the compounds within the drug set. You assign the drug sets to the wells of the
tune plate, one drug set at a time. The tune plate can represent hundreds of compounds, with
each compound optimized individually. You can arrange the drug sets within the tune plate in
any desired layout.
The application submits the entire tune plate for optimization as one sequence so that no
other optimizations or acquisitions can interleave with the current optimization run. If a
single compound is found on the plate more than once, the application optimizes only one
instance of this compound, the one in the well of the earliest drug set assignment.
Y To set up the tune plate for compound optimization
1. Specify the drug sets in the tune plate by doing one of the following:
• Use the tune plate graphic (see Figure 19) to assign drug sets one at a time to the
wells. See “Manually Assigning Drug Sets to the Tune Plate Graphic.”
• Import the tune plate information from a text file. See “Importing Tune Plate
Information Using a Text File” on page 54.
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Setting Up the Tune Plate for Compound Optimization
• Import the tune plate information from a combined text file. See “Importing
Compound, Drug Set, and Tune Plate Information Using a Text File” on page 57.
2. (Optional) To select adducts or to disallow product ion losses that are not specific
enough, click Losses/Adducts on the Optimization Setup Page. In the Losses/Adducts
Dialog Box, select the adducts to include and the product ion losses you want to disallow,
and click OK.
Note If you are using an LDTD autosampler, the QuickQuan application uses the
losses/adducts settings to calculate the Max. Desorptions Needed value (see
Figure 21). For LDTD optimization, after you apply a drug set to the tune plate (see
“Manually Assigning Drug Sets to the Tune Plate Graphic” on page 48), import from
a text file (see “Importing the Tune Plate Information File” on page 56), or reuse an
.aql file containing imported optimization data (see “Reusing Optimization Settings”
on page 35), the QuickQuan application disables the Losses/Adducts button on the
Optimization Setup page.
To enable the losses/adducts settings again, click Clear Plate to clear all well
assignments in the tune plate.
Losses/Adducts Dialog Box
You can select adducts or disallow product ion losses for optimization. See “Setting Up the
Tune Plate for Compound Optimization” on page 45. Use the Losses/Adducts dialog box to
set these parameters:
• Disallow product ion losses that are not specific. The choices are H20, NH3, CH3, and
two user-definable losses.
• Select adducts. For positive ions, the choices are M+H, M+Na, M+NH4, and
three user-definable adducts. For negative ions, the choices are M-H, M-COO, and three
user-definable adducts.
Y To open this dialog box
1. In the QuickQuan left pane, click Optimization, and then click the Setup icon,
.
–or–
Choose Go > Optimization > Setup.
2. On the Optimization Setup page, click Losses / Adducts. The Losses/Adducts dialog box
appears.
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Setting Up the Tune Plate for Compound Optimization
Figure 18. Losses/Adducts dialog box
The Losses/Adducts dialog box contains these parameters.
Parameter
Description
Disallow Loss of
Select the check boxes to specify the product ion losses
you want to disallow. The choices are
• H20
• NH3
• CH3
• User: User-defined losses 1 to 2
Positive Ions
Select the check boxes to specify which adducts to use for
positive ions. The choices are:
• (M+H)+
• (M+Na)+
• (M+NH4)+
• (M+User)+: User-defined adducts 1 to 3
Negative Ions
Select the check boxes to specify which adducts to use for
negative ions. The choices are:
• (M-H)• (M-COO)• (M-User)-: User-defined adducts 1 to 3
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Setting Up the Tune Plate for Compound Optimization
Manually Assigning Drug Sets to the Tune Plate Graphic
Use the tune plate graphic on the Optimization Setup Page to assign drug sets manually, one
at a time.
Y To display the Optimization Setup page
In the QuickQuan left pane, click Optimization, and then click the Setup icon,
.
–or–
Choose Go > Optimization > Setup.
Y To assign drug sets using the tune plate graphic
1. Select a well position in the tune plate graphic. See Figure 19.
Figure 19. Tune plate graphic
You must manually select the first well position. Afterward, the QuickQuan application
automatically advances to select the next well position, or you can select a different well
position. The application highlights the next well position by row or column order
depending on your setting of the Order By option.
The position of the currently selected or highlighted well shows under Current Well:
[Compound: Mass] on the right side of the Optimization Setup page (see Figure 20).
If this well is already assigned to a drug set, then the drug set name also appears (see
Figure 21). If this drug set contains only one compound, then the compound name and
mass also appear.
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Setting Up the Tune Plate for Compound Optimization
2. Select a drug set in the Drug Set Selector area on the right side of the Optimization Setup
page. See Figure 20.
Figure 20. Current Well and Drug Set Selector for non-LDTD autosampler
Note If your database contains a large number of drug sets, when you enter the
Optimization Setup page, the Drug Set Selector area shows the first group of drug sets
from the database. The QuickQuan application loads the next group of drug sets each
time you scroll down to the bottom of the previous group. This might take a few
seconds.
You must manually select the first drug set. Afterward, the QuickQuan application
automatically advances to select the next drug set down the list, or you can select a
different drug set.
If you are using an LDTD autosampler, then the application automatically calculates the
maximum number of times sample desorption is needed to optimize the selected drug set.
The calculation is based on the parent mass and product ion of the selected drug set, as
well as the H-SRM (see step 4), polarity (see step 5), and adduct (see Losses/Adducts
Dialog Box) selections. The application displays the calculated number in the Max.
Desorptions Needed field on the right side of the Optimization Setup page.
See Figure 21.
Figure 21. Current Well, Drug Set Selector, and Maximum Desorptions Needed for an LDTD
autosampler
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Setting Up the Tune Plate for Compound Optimization
When you set up the tune plate for an LDTD autosampler, you can view this calculated
number to best determine how many wells per drug set you need, depending on the
number of times that sample desorption can occur efficiently in each well.
Note If you import the tune plate data from a text file instead of entering the data
manually (see “Importing the Tune Plate Information File” on page 56), or reuse an
.aql file containing imported optimization data (see “Reusing Optimization Settings”
on page 35), the QuickQuan application uses the imported data to calculate the Max.
Desorptions Needed value. After these instances, the application hides the Max.
Desorptions Needed field on the Optimization Setup page.
To enable this field again, click Clear Plate to clear all drug set assignments in the
tune plate.
3. Click Apply to assign the selected drug set to a well or to a group of wells in the tune
plate.
Note If you import the tune plate data from a text file instead of entering the data
manually (see “Importing the Tune Plate Information File” on page 56), or reuse an
.aql file containing imported optimization data (see “Reusing Optimization Settings”
on page 35), the QuickQuan application uses the imported data for the drug set
assignments. As a result, after these instances, the application disables the Apply
button on the Optimization Setup page.
To enable this button again, click Clear Plate to clear all drug set assignments in the
tune plate.
The assigned well positions in the tune plate graphic correspond to these color-coded
highlights:
•
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Red: At least one compound in the well (drug set) is not optimized.
•
Orange: At least one compound in the drug set is not optimized by the currently
configured mass spectrometer model but is optimized by another model, and at least
one compound is not optimized by the currently selected ion source but is optimized
by another ion source.
•
Yellow: All compounds in the drug set are optimized by the currently configured
mass spectrometer model, and at least one compound is not optimized by the
currently selected ion source but is optimized by another ion source.
•
Dark Green: All compounds in the drug set are optimized by the currently
selected ion source, and at least one compound is not optimized by the currently
configured mass spectrometer model but is optimized by another model.
•
Light Green: All compounds in the drug set are optimized by the currently
configured mass spectrometer model and the currently selected ion source.
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For wells with orange or dark green highlight colors that contain at least one compound
optimized by a mass spectrometer model other than the currently configured model, the
letter for the other model also appears.
For example, when you use the TSQ Vantage, a “Q”,
, appears in the wells containing
at least one compound not optimized by the TSQ Vantage but optimized by the
TSQ Quantum. Conversely, when you use the TSQ Quantum, a “V”,
, appears in
the wells containing at least one compound not optimized by the TSQ Quantum but
optimized by the TSQ Vantage.
Well position A1 is red in the tune plate (see Figure 22), which indicates at least one
unoptimized compound in that well.
Figure 22. Well position A1 is red
If you are using an LDTD autosampler, then the following occur when you assign a
drug set:
• If the number you set for Wells Per Drug Set is sufficient (it is ≥ the result from the
calculated Max. Desorptions Needed shown in Figure 21 divided by the number you
set for Desorptions Per Well), then the QuickQuan application highlights in the
appropriate color the group of wells assigned to the selected drug set. The number of
wells in the group is equal to the Wells Per Drug Set number, the highlight order by
row or by column is based on your setting of the Order By option, and the selected
well becomes the first well in the new group.
Otherwise, if the number you set for Wells Per Drug Set is not sufficient, the
QuickQuan application cancels your assignment of the drug set and prompts you to
increase the Wells Per Drug Set number.
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Note You must click Clear Plate to clear all well assignments on the tune plate
before you can change the Wells Per Drug Set number.
For example, your optimization settings are the following:
• Desorptions Per Well = 2
• Order By = Column
• Wells Per Drug Set = 3
• Drug set = Drug_set1
• Selected well position = A1
• Calculated Max. Desorptions
Needed number for Drug_set1 = 6
Because the Wells Per Drug Set (3) is equal to Max. Desorptions Needed (6) divided
by Desorptions Per Well (2), the QuickQuan application determines that the Wells
Per Drug Set number is sufficient and highlights wells A1, B1, and C1 for the group
of wells assigned to drug set Drug_set1. The optimization sequence is A1, B1, C1,
A1, B1, C1 because there are two desorptions for each well.
• If any well in the group of wells for your drug set is already assigned to another drug
set, the QuickQuan application prompts you to override the previous drug set
assignment with the new assignment.
If you select Yes, the application clears all wells in the group assigned to that previous
drug set before assigning the new drug set to its group of wells. The application also
clears any adjacent wells occupying the same positions as the group of wells for your
new drug set assignment. If you select No, the application does not make any changes
and cancels your new drug set assignment.
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• A marker appears indicating the end of the group of wells assigned to each drug set.
Figure 23 shows two groups of wells ordered by row.
Figure 23. Group of wells when ordered by row, for an LDTD autosampler
Marker for each group of wells
Figure 24 shows two groups of wells ordered by column.
Figure 24. Group of wells when ordered by column, for an LDTD autosampler
Marker for each group of wells
4. Repeat steps 1 through 3 for each drug set assignment.
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5. To clear all of the wells on the plate and cancel all drug set assignments, click Clear Plate.
If some fields on the Optimization Setup Page were previously hidden or disabled,
clicking Clear Plate activates all of these fields so that you can select them.
6. To clear a specific well and cancel its drug set assignment, select the well and click Clear
Well.
If you are using an LDTD autosampler, then when you click Clear Well, the QuickQuan
application prompts you to also clear all related wells in the same group. If you click Yes,
the application clears all wells in the group assigned to the same drug set as the selected
well. If you click No, the application cancels your clear well action.
7. When you are done setting up the tune plate, choose File > Save to save the tune plate
information in an .aql file.
Importing Tune Plate Information Using a Text File
You can import a text (.txt) file that contains all the tune plate information that you would
otherwise enter manually by using the tune plate graphic on the Optimization Setup Page.
When you import this file, the QuickQuan application adds the tune plate information to the
database. The text file must be in a specified format. The data set in the file overrides the
manual settings on the Optimization Setup page.
The QuickQuan installer provides these tune plate template files as examples:
\Xcalibur\QuickQuan\ImportFiles\ImportTunePlate.txt (for non-LDTD autosampler)
\Xcalibur\QuickQuan\ImportFiles\LDTDImportTunePlate.txt (for LDTD autosampler)
Tip To import the combined compound, drug set, and tune plate information in one step,
see “Importing Compound, Drug Set, and Tune Plate Information Using a Text File” on
page 57.
Creating a Text File for Importing Tune Plate Information
Y To create a tune plate information file
1. Open a new file in Microsoft Excel, Notepad, or any application where you can create a
tab-delimited text file (.txt).
2. If you are using a non-LDTD autosampler, in the first row of the text file, type this line:
TUNE_DATABASE_INFORMATION_v1
Otherwise, for an LDTD autosampler, type this line:
TUNE_DATABASE_INFORMATION_LDTD_v1
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3. In another row of the text file, type this line:
ORDER_BY = ROW (to highlight the wells in the tune plate by row order)
–or–
ORDER_BY = COLUMN (to highlight the wells in the tune plate by column order)
4. If you are using an LDTD autosampler, in another row of the text file, type this line:
DESORPTIONS_PER_WELL = number
5. (Optional) To include a comment in the file, use a double forward slash (//) at the start of
the row. The QuickQuan application ignores any rows that begin with “//”.
IMPORTANT Do not add any commas to your comment rows. The commas cause
import problems if you open and save the file using Excel.
6. In each of the remaining rows, enter the following fields. Use a separate row for each drug
set assignment in the tune plate, and use a tab to separate each item in the row.
• well/vial positions
If you are using a non-LDTD autosampler, enter only one well position for each drug
set.
Otherwise, for an LDTD autosampler:
–
If only one well is assigned to the drug set, enter the one well position.
–
Otherwise, enter the starting and ending positions of the continuous group of
wells assigned to the drug set, separating these two positions with “-”.
• polarity (0=positive, 1=negative, 2=both)
• scan width
• drug set name
7. Save the tune plate information file as a .txt file. Use a different name so that your import
file does not overwrite the template files provided by the QuickQuan installer:
\Xcalibur\QuickQuan\ImportFiles\ImportTunePlate.txt (for non-LDTD autosampler)
\Xcalibur\QuickQuan\ImportFiles\LDTDImportTunePlate.txt (for LDTD autosampler)
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Figure 25 shows a sample file format (in Notepad) for importing tune plate information when
you are using a non-LDTD autosampler.
Figure 25. Tune plate import text file when using a non-LDTD autosampler
Figure 26 shows a sample file format (in Notepad) for importing tune plate information when
you are using an LDTD autosampler.
Figure 26. Tune plate import text file when using an LDTD autosampler
Importing the Tune Plate Information File
Y To display the Optimization Setup page
In the QuickQuan left pane, click Optimization, and then click the Setup icon,
.
–or–
Choose Go > Optimization > Setup.
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Y To import the tune plate information file
1. On the Optimization Setup Page, click Import.
2. When prompted to have the imported file overwrite the vial information for existing vial
positions, click Yes. The Open dialog box appears.
3. In the Open dialog box, select the tune plate information file (.txt), and click OK. The
QuickQuan application imports the information and the tune plate graphic displays
color-coded highlights for the imported wells.
Note After import, the application hides the Polarity list and disables the Order By
option and the Apply button on the Optimization Setup Page. If you are using an
LDTD autosampler, the application also hides the Wells Per Drug Set and Max.
Desorptions Needed fields, and disables the H-SRM, Desorptions Per Well, and
Losses/Adducts items.
To enable any of these fields again, click Clear Plate to clear all drug set assignments
in the tune plate.
4. To save the tune plate information in an .aql file, choose File > Save.
Importing Compound, Drug Set, and Tune Plate Information Using a Text File
You can import a text file (.txt) that contains all the compound, drug set, and tune plate
information that you would otherwise enter manually or import individually. When you
import this file, the QuickQuan application adds all the compound, drug set, and tune plate
information to the database in one step. The text file for import must be in a specified format.
The data set in the file overrides the manual settings on the Optimization Setup page.
The QuickQuan installer provides these combined import text files as examples:
\Xcalibur\QuickQuan\ImportFiles\CombinedImports.txt (for a non-LDTD
autosampler)
\Xcalibur\QuickQuan\ImportFiles\LDTDCombinedImports.txt (for an LDTD
autosampler)
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Creating a Text File for Importing Combined Information
Y To create a combined compound, drug set, and tune plate information file
1. Open a new file in Excel, Notepad, or any application where you can create a
tab-delimited text file (.txt).
2. Add the compound, drug set, and tune plate information to the file, as follows:
• Enter the compound portion in the format described in “Creating a Text File for
Importing Compounds” on page 13.
• Enter the drug set portion in the format described in “Creating a Text File for
Importing Drug Sets” on page 24.
• Enter the tune plate portion in the format described in “Creating a Text File for
Importing Tune Plate Information” on page 54.
Note You can add the combined portions in any order to the text file as long as each
compound, drug set, or tune plate portion follows its correct format.
3. Save the combined information file as a .txt file. Use a different name so that your import
file does not overwrite the sample files provided by the QuickQuan installer:
\Xcalibur\QuickQuan\ImportFiles\CombinedImports.txt (for non-LDTD autosampler)
\Xcalibur\QuickQuan\ImportFiles\LDTDCombinedImports.txt (for LDTD
autosampler)
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Figure 27 shows a sample file format (in Notepad) for importing combined information when
you are using a non-LDTD autosampler.
Figure 27. Combined information text file when using a non-LDTD autosampler
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Figure 28 shows a sample file format (in Notepad) for importing combined information when
you are using an LDTD autosampler.
Figure 28. Combined information text file when using an LDTD autosampler
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Importing the Combined Information File
Y To display the Optimization Setup page
In the QuickQuan left pane, click Optimization, and then click the Setup icon,
.
–or–
Choose Go > Optimization > Setup.
Y To import the combined information file
1. On the Optimization Setup Page, click Import.
2. When prompted to have the imported file overwrite the vial information for existing vial
positions, click Yes. The Open dialog box appears.
3. In the Open dialog box, select the combined information file (.txt), and click OK.
4. When prompted to confirm that the file contains more than a single type of import
information, click Yes. The QuickQuan application imports the information and displays
the imported data on the Compounds Browse Page and in the tune plate graphic.
Note After import, the application hides the Polarity list and disables the Order By
option and the Apply button. If you are using an LDTD autosampler, the application
also hides the Wells Per Drug Set and Max. Desorptions Needed fields, and disables
the H-SRM, Desorptions Per Well, and Losses/Adducts items on the Optimization
Setup Page.
To enable any of these items again, click Clear Plate to clear all drug set assignments
in the tune plate.
5. To save the compound, drug set, and tune plate information in an .aql file, choose
File > Save.
Running an Optimization
After you set up an optimization, you can do either of the following:
• Acquire the data for an assay with real-time compound optimization. In this case, see
“Acquiring the Sample Data” on page 87.
• Run only the optimization according to the next procedure.
In either case, you can choose to use the optimization information already stored in the
database or force the compound optimization to update the database.
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Y To display the Configuration Options dialog box
In the QuickQuan left pane, click Optimization, and then click the Run icon,
.
–or–
Choose Go > Run.
The Configuration Options Dialog Box appears.
Y To run the optimization only
1. In the Configuration Options Dialog Box, select the Compound Optimization Only
option. See Figure 29, Figure 30, or Figure 31.
2. (Optional) If you want to use the Aria OS system, select the Aria check box.
Note The Aria check box is available only if you have the Aria OS system installed.
Figure 29. Configuration Options dialog box with the Aria OS system installed
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Figure 30. Configuration Options dialog box with Thermo PAL configured and without the
Aria OS system
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Figure 31. Configuration Options dialog box with LDTD configured and supporting
optimization
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3. (Optional) To use optimization information that is already in the database, select the
Use Optimization Database for Existing Compounds check box. The QuickQuan
application optimizes only the compounds in the tune plate that are considered not
tuned.
If you clear this check box, the application optimizes all compounds that are in the
tune plate and overwrites the database with new information for these compounds.
4. In the Instrument Settings area, verify the following:
a. The Instrument column lists only the required instruments:
• If you are using the Aria OS system, then the Instrument column should list only
the mass spectrometer.
• If you are not using the Aria OS system, then the Instrument column should list
the mass spectrometer, LC pump, and autosampler (if you are using a
non-LDTD autosampler); or the mass spectrometer and autosampler (if you are
using an LDTD autosampler).
If the required instruments do not appear, see “Configuring Instruments without the
Aria OS System” on page 133, or if you are running with the Aria OS system, see
“Configuring Instruments with the Aria OS System” on page 134. You must
configure the instruments before performing the following steps.
b. For each required instrument, click the corresponding cell in the In Use column to
turn on the Yes value.
c. (If not using the Aria OS system) For the start instrument selected to initiate the run,
click the corresponding cell in the Start Instrument column to turn on the Yes value,
and to turn off the Yes value for the other instruments.
Note Typically, you select the autosampler to be the start instrument because it
controls when a run starts. In this case, the In Use column displays Yes for all
instruments to be used for the sequence submission, including the autosampler.
This means the instruments are awaiting a contact closure event to start
operation. When all instruments used in the run report that they are waiting for
contact closure, the start instrument initiates the run.
5. To set the devices to standby after the acquisition has finished, select the Put Instrument
into Standby After Batch check box.
6. Prepare to run the optimization.
a. Open the Xcalibur application to the Real Time Plot view.
b. In the Xcalibur application, verify that the instrument status is Ready to Download,
and make sure the initial system parameters are within the acceptable ranges.
c. Verify that the vessel holding the compounds for tuning is ready and in position.
Verify the same for assay plates.
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7. In the Configuration Options dialog box, click OK. The QuickQuan application starts
the optimization and displays the Optimization Status page.
Tip You can also view the status of the run in the Xcalibur Real Time Plot view.
If you are running an optimization with the Aria OS system, then the QuickQuan
application launches the Aria OS application automatically if it is not already open. After
initialization, the QuickQuan application submits the optimization setup data directly to
the Aria OS system. For more information on the Aria OS windows, refer to the
QuickQuan and Aria OS Quick Start and the Aria OS User Guide.
Note After you start the optimization run, you can launch other instances of the
QuickQuan application if you want to submit other sequences for optimization or
acquisition. Each new instance places the optimization or acquisition sequence into
the queue to be processed in the order of submission. Each QuickQuan instance
continues processing until the sequence analysis from that instance is complete or you
cancel the run.
8. After the optimization completes, click the Setup icon,
, to go to the
Optimization Setup page and verify that the compounds were optimized successfully. If
successful, the color of the wells is light green in the tune plate graphic.
Figure 32 shows the tune plate graphic with successfully optimized compounds.
Figure 32. Tune plate graphic showing optimized compounds
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Configuration Options Dialog Box
Use the Configuration Options dialog box to run an optimization or acquisition.
For details, see one of the following sections:
• “Running an Optimization” on page 61
• “Running an Acquisition” on page 115
You can select specific configured devices to use for the acquisition of an assay. You can also
specify to run postacquisition processing, generate reports, and put devices into Standby
mode at the completion of the acquisition.
Y To open this dialog box
In the QuickQuan left pane, click Optimization, and then click the Run icon,
.
–or–
In the QuickQuan left pane, click Acquisition, and then click the Run icon,
.
–or–
Choose Go > Run.
The Configuration Options dialog box appears. The elements on this dialog box vary,
depending on whether or not you have the Aria OS system installed and the type of
autosampler you are using. See Figure 29, Figure 30, Figure 52, Figure 53, or Figure 55.
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The Configuration Options dialog box contains these parameters.
Table 4. Configuration Options dialog box parameters (Sheet 1 of 5)
Parameter
Description
Run-time settings
Compound Optimization and
Acquisition
Select this mode to run an analytical experiment with
real-time compound optimization. In this mode, the
QuickQuan application proceeds in one of two ways:
• If you do select the Use Optimization Database for
Existing Compounds check box:
For each compound in the assay acquisition
sequence, the QuickQuan application checks the
database for its optimization information. If it finds
the information in the database, it builds the method
files based on the optimization information and then
acquires the data for that compound. Otherwise, it
checks the tune plate for the compound. If the
compound is in the tune plate, the application runs
the optimization and then builds the methods and
acquires the data for that compound. Otherwise, it
displays an error message and cancels the run.
• If you do not select the Use Optimization Database
for Existing Compounds check box:
The QuickQuan application clears the database of
optimization information for all compounds in the
assay. Next, it optimizes the compounds that are in
the tune plate, and then stores the information in the
database.
The application builds method files based on the
optimization information for each compound and
acquires the data for that compound. If the
application attempts to optimize a compound for the
assay and that compound is not in the tune plate, it
displays an error message and cancels the run.
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Table 4. Configuration Options dialog box parameters (Sheet 2 of 5)
Parameter
Description
Compound Optimization Only Select this mode to run an optimization session only. In
this mode, the QuickQuan application proceeds in one of
two ways:
• If you do select the Use Optimization Database for
Existing Compounds check box:
The application optimizes only the compounds in
the tune plate that are not already optimized in the
database.
• If you do not select the Use Optimization Database
for Existing Compounds check box:
The application deletes any optimized entries in the
database for compounds that exist in the tune plate
and then optimizes all the compounds in the tune
plate.
Aria
(Available only if Aria OS application is installed and not
using LDTD autosampler) Select this check box to use
the Aria OS system.
Use Optimization Database
for Existing Compounds
Select this check box to use optimization information
already in the database so that the QuickQuan
application optimizes only these compounds:
• (Compound Optimization Only run) Compounds in
the tune plate that have not been optimized
• (Compound Optimization and Acquisition run)
Compounds that are in both the assay and the tune
plate that have not been optimized
Clear this check box if you want the QuickQuan
application to optimize these compounds:
• (Compound Optimization Only run) All compounds
in the tune plate
• (Compound Optimization and Acquisition run) All
compounds that are in both the assay and the tune
plate
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Table 4. Configuration Options dialog box parameters (Sheet 3 of 5)
Parameter
Description
Instrument Settings
Instrument
Displays all the instruments configured for operation as
QuickQuan devices.
If an instrument that you want to use is not on this list,
click Cancel to close the Configuration Options dialog
box. If you are not running with the Aria OS system,
follow the instructions in “Configuring Instruments
without the Aria OS System” on page 133 to configure
your instrument. Otherwise, follow the instructions in
“Configuring Instruments with the Aria OS System” on
page 134 to configure your instrument.
In Use
Indicates if the instrument is in use (Yes) or not in use
(blank space).
A “Yes” must appear in the In Use column for all
instruments to be used for the sequence you are about to
submit. If you do not want to use an instrument for the
current sequence, click the “Yes” to change it to a blank
space. A blank space indicates an instrument is not
available for the current sequence.
Start Instrument
Indicates which instrument, if any, is the start
instrument. To select a start instrument, click the Start
Instrument cell to display a “Yes”.
Note This list can display either one “Yes” or all blanks.
The autosampler is usually the start instrument because it
controls when a run starts. A “Yes” must appear in the In
Use column for all instruments, including the
autosampler, that are used for the sequence submission.
This means that the instruments are awaiting a contact
closure event to start the operation. When all of the
in-use instruments report that they are waiting for contact
closure, then the start instrument initiates the run.
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Table 4. Configuration Options dialog box parameters (Sheet 4 of 5)
Parameter
Description
Processing Settings
Number of Quan Masses
(Enabled for compound optimization and acquisition
only) Specifies the number of masses to use for
postacquisition.
If you enter 2 or 3, then in addition to using the first
(100%) mass, the QuickQuan application also uses the
second and third masses for postacquisition, but only if
the second and third masses meet or exceed the
Threshold % of the first mass.
Range: 1 to 3
Threshold %
(Enabled for compound optimization and acquisition
only) Specifies the percentage of the first mass intensity
that the second and third masses must achieve.
All the Num Quan Masses selected for postprocessing
must meet the specified percentage threshold of the
highest intensity ion.
Range: 0 to 100
Mass Window Width
(Enabled for compound optimization and acquisition
only) Specifies the mass window width used to set the
mass range in the processing method.
If the mass window width is 1.0 ± 0.01, then the mass
range is the same as the product ion mass. Otherwise, the
mass range is the product ion mass ± (mass window
width / 2).
Default: 1
Put Instrument Into Standby
After Batch
Puts the devices in Standby mode after the acquisition has
finished.
Do Post Processing After
Acquisition
(Enabled for compound optimization and acquisition
only) Specifies that the QuickQuan application perform
postprocessing after acquisition.
Note If you do not select this check box, the
application does not perform the postprocessing.
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Table 4. Configuration Options dialog box parameters (Sheet 5 of 5)
Parameter
Description
Generate Excel Summary
(Selectable only if you select the Do Post Processing After
Acquisition option) Generates an Excel summary report
for each sequence if the data has been completely
postprocessed. The report is saved in the output path that
you specify on the “Acquisition Templates Page” on
page 155.
Run User Defined Macros
(Selectable only if you select the Do Post Processing After
Acquisition option) Select this check box if you want to
use a custom Excel macro automatically for data
reduction after data acquisition and postprocessing have
finished.
To create the macro, you can customize the provided data
reduction Excel template file
C:\Xcalibur\QuickQuan\Templates\Data_Reduction.xls
For more information, see “Using a Macro” on page 137.
Note In addition to selecting the Run User Defined
Macros check box, you must select the processing
macro template on the Acquisition Templates Page to
perform the data reduction.
Viewing the Optimization Results
Once optimization completes, you can view the optimization results using any of the
following procedures:
• “Viewing Results in the Optimization Tune Report Page” on page 72
• “Viewing Results Using Adobe Acrobat Reader” on page 77
• “Generating an Optimization Summary Report” on page 78
Viewing Results in the Optimization Tune Report Page
The tune reports for each compound are stored in the database and also stored as PDF files in
the output folder that you specified on the Optimization Setup page (see “Specifying
Optimization Settings” on page 35). The QuickQuan application generates a tune report for
optimizations that passed as well as those that failed, as long as the optimization created a raw
file. The main title of the report indicates whether the optimization passed or failed for the
selected compound. The tune report consists of two pages.
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Page 1 contains the following items in graphical format, numbered in the order they appear
on the page from top to bottom and from left to right:
1. An averaged normal MS spectrum
The subtitle above the spectrum indicates the maximum intensity value.
2. An averaged MS/MS product ion spectrum
The subtitle above the spectrum indicates the maximum intensity value.
3. The tube lens offset curves (if the compound was optimized by the TSQ Quantum) or
S-Lens offset curves (if the compound was optimized by the TSQ Vantage) for each
polarity, as required
The report can show up to three offset curves, depending on your selected polarity and
adducts. For example, when you select Both as the polarity for optimization, use multiple
adducts, and an adduct other than the lowest adduct is the most intense, then the report
shows three offset curves (two for positive polarity and one for negative, or vice versa).
Except for the optimized curve, the title and subtitle above each curve indicate the tune
mass, polarity, and maximum intensity for that curve. For the optimized curve, the title
and subtitle indicate the tune mass, polarity, optimal value of the tube lens/S-Lens
voltage, and optimal intensity. A vertical, light green line also shows in the optimized
curve at the location of the optimal voltage and intensity.
4. A breakdown curve
The title and subtitle above the curve indicate the tune mass, polarity, and maximum
intensity value.
If any spectrum, curve graphic, or tube lens/S-Lens offset on Page 1 is not available, the report
indicates “Not Available” in its place.
Page 2 contains the tune status information in text format. If you select Both as the polarity
for optimization, the page shows only the intensity of the chosen polarity.
You can view the tune report in the Optimization Tune Report page. In addition to viewing
the tune report, you can also open the Xcalibur Qual Browser to see the display of raw data
results for the selected compound.
Y To display the Optimization Tune Report page
In the QuickQuan left pane, click Optimization, and then
click the Tune Report icon,
.
–or–
Choose Go > Optimization > Tune Report.
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Viewing the Optimization Results
Y To view a tune report
1. On the Optimization Tune Report page, select a compound from the list on the left. The
QuickQuan application automatically displays the latest tune report for the compound.
See Figure 33 and Figure 34.
If the optimization failed but the compound raw file is available, or if the maximum
intensity is below the threshold you specified in the Configuration Options Dialog Box, a
red crossmark, , shows next to the compound name in the list. In this case, the tune
report might be missing some information because the optimization run did not
complete successfully.
If the compound was not optimized by your currently configured mass spectrometer
model but is optimized by another model, a dark green checkmark, , shows next to the
compound name in the list.
If the compound was optimized by your currently configured mass spectrometer model,
a light green checkmark, , shows next to the compound name in the list.
Note Only the compounds associated with raw files stored in the database (and most
likely tune reports as well) appear in the compound list.
If the compound was optimized by the TSQ Quantum mass spectrometer, the tune
report shows the tube lens information. If the compound was optimized by the TSQ
Vantage mass spectrometer, both pages of this report show the S-Lens information
instead of the tube lens information.
2. To display the details from the raw sample data collected for the selected compound, click
QualBrowser. Xcalibur Qual Browser opens and displays the raw data.
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Figure 33. Optimization Tune Report page, showing page 1 of the tune report (compound optimized by the TSQ Quantum)
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Figure 34. Optimization Tune Report page, showing page 2 of the tune report (compound optimized by the TSQ Quantum)
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Viewing Results Using Adobe Acrobat Reader
Use Adobe™ Acrobat Reader™ to view the tune results as PDF files. If needed, you can install
Acrobat Reader from the QuickQuan CD. The QuickQuan application creates the PDF files
upon the completion of each compound optimization and stores these files in the output
folder that you specified on the Optimization Setup page (see “Specifying Optimization
Settings” on page 35).
Y To view the tune results as PDF files
1. Start Adobe Acrobat Reader.
2. Open the PDF files for a specific set of tune results, for example, caffeine.pdf.
Note If the compound was optimized by the TSQ Quantum mass spectrometer, the
PDF file shows the tube lens information. If the compound was optimized by the
TSQ Vantage mass spectrometer, both pages of this PDF file show the S-Lens
information instead of the tube lens information.
Figure 35. Optimization Tune Report PDF (compound optimized by the TSQ Vantage)
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Viewing the Optimization Results
Generating an Optimization Summary Report
Y To generate the optimization summary report
In the QuickQuan window, choose Reports > Optimization Summary Report.
The QuickQuan application generates the report and displays it in an Excel spreadsheet. If
your optimization sequence contains some compounds that are optimized by your currently
configured mass spectrometer model, as well as some compounds that are not optimized by
your configured model but are optimized by another model, the report shows the summary
data for both sets of compounds. The report also shows information for compounds that
failed the optimization.
Note If you are using the TSQ Quantum mass spectrometer, the optimization summary
report shows the Tube Lens column. If you are using the TSQ Vantage mass spectrometer,
this report shows the S-Lens column instead of the Tube Lens column. If a compound was
optimized by both models, the QuickQuan application displays the data only for the
model you are currently using.
For compounds optimized by the mass spectrometer model you are using, the Tube Lens
or S-Lens column displays the value for your model and the Status column displays
TUNED. For compounds not optimized by your current mass spectrometer model but
optimized by a different model, the Tube Lens or S-Lens column displays N/A and the
Status column displays TUNED-model name. For compounds not optimized, the
corresponding rows of data appear in red and the Status column displays NOT TUNED.
If you are using a non-LDTD autosampler, the Vial # column shows only one well
position. For an LDTD autosampler, this column might show a range of well positions for
the group of wells assigned to a particular drug set.
Figure 36 shows a sample optimization summary report (in Excel).
Figure 36. Optimization summary report
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Updating SRM Information
Updating SRM Information
You can update the SRM transitions found during optimization using either of these
procedures:
• “Modifying SRM Information Manually” on page 79
• “Importing SRM Information” on page 79
Modifying SRM Information Manually
Y To modify SRM information
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
2. On the Compounds Browse page, click Update SRM Info. The Update SRM
Information Dialog Box appears (see Figure 38).
3. In the Compound Name list, select a compound.
The QuickQuan application displays the SRM information for compounds optimized by
your currently configured mass spectrometer model.
Note If you configured the TSQ Quantum mass spectrometer, the Update SRM
Information dialog box shows the Tube Lens column and value. Otherwise, if you
configured the TSQ Vantage mass spectrometer, this dialog box shows the S-Lens
column and value instead of Tube Lens.
4. In the Compound SRM Information table, edit the information as required.
Note The value in the Width field is the scan width of the product ion used during
optimization, not the peak width.
5. Click Update to update the SRM information.
6. Click Close.
Importing SRM Information
You can import the SRM information from a text (.txt) file into the QuickQuan database.
The text file must be in a specified format. The QuickQuan installer provides this SRM text
file as an example:
\Xcalibur\QuickQuan\ImportFiles\ImportSRMinfo.txt
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Y To create an SRM information file for importing
1. Open a file in Microsoft Excel, Notepad, or any application where you can create a
tab-delimited text file (.txt).
2. In the first row of the text file, type this line:
SRM_DATABASE_INFORMATION_v1
3. (Optional) To include a comment in the file, use a double forward slash (//) at the start of
the row. The QuickQuan application ignores any rows that begin with “//”.
IMPORTANT Do not add any commas to your comment rows. The commas cause
import problems if you open and save the file using Excel.
4. Enter a separate row for each SRM item. In each row, enter the following information,
and use a tab to separate each field in the row.
• compound name
IMPORTANT Do not use any of the following characters in a compound name;
otherwise, the import process will fail:
space, period (.), double-quote (“ or ”), slash (/ or \), square bracket ([ or ]),
colon (:), semi-colon (;), vertical line (|), asterisk (*), question mark (?)
Only use underscores for spacing if needed for clarity. The QuickQuan
application uses the compound name as the file name for the sequence (.raw) file.
A space in the file name will cause the Xcalibur application to fail the submission
to the sequence queue.
The QuickQuan application prevents you from entering spaces in drug set and
compound names but it does not prevent you from manually editing the
database.
• F = formula or M = mass
• molecular formula or nominal mass (molecular weight)
• ion source: 1 = ESI, 2 = APCI, 3 = APPI, 4 = H-ESI, or 5 = SIM
• polarity: POS or NEG
• Q1 peak width: H-SRM = 0.2, other modes = 0.7
• product ion mass
• collision energy
• tube lens offset (if you are using the TSQ Quantum) or S-Lens offset (if you are using
the TSQ Vantage)
• scan width
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• maximum intensity
• tune method file
• tune PDF file
• tune raw file
5. Save the file as a .txt file. Use a different name so that your import file does not overwrite
the sample file provided by the QuickQuan installer:
\Xcalibur\QuickQuan\ImportFiles\ImportSRMinfo.txt
Figure 37 shows a sample file format (in Notepad) for importing SRM information.
Figure 37. SRM information text file
Y To import the SRM information file
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
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2. On the Compounds Browse page, click Update SRM Info. The Update SRM
Information Dialog Box appears (see Figure 38).
3. Click Import.
4. When the confirmation message appears, click Yes.
5. In the Open dialog box, select the file you want to import and click Open. The
QuickQuan application imports the compounds and SRM transitions into the database.
6. Click Update and then click Close.
Deleting SRM Information
Y To delete SRM information from the QuickQuan database
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
2. On the Compounds Browse page, click Update SRM Info. The Update SRM
Information Dialog Box appears (see Figure 38).
3. In the Compound Name list, select the compound whose SRM information you want to
delete, and then click Delete.
The QuickQuan application removes all of the data in the Compound SRM Information
table for the selected compound as well as the ion source, tune file, tune PDF file, and
tune raw file data. The application also resets the polarity to Negative by default.
Repeat this step for any other compound whose SRM information you want to delete.
4. When you have finished deleting, click Update and then click Close.
Note If you use the same database for two different mass spectrometer models, when you
delete SRM data, the QuickQuan application deletes the SRM record from the database
for the currently configured model.
Update SRM Information Dialog Box
During compound optimization, the QuickQuan application determines the best SRM
transitions for each compound in the assay. Use the Update SRM Information dialog box to
modify these SRM transitions for each compound in the database. See “Updating SRM
Information” on page 79.
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Y To open this dialog box
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
2. On the Compounds Browse page, click Update SRM Info. The Update SRM
Information dialog box appears.
Figure 38. Update SRM Information dialog box
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The Update SRM Information dialog box contains these parameters.
Table 5. Update SRM Information dialog box parameters (Sheet 1 of 2)
Parameter
Description
Compound Information
Compound Name
Name of the compound.
Ion Source
Ion source type for tuning the compound. The
options are
• ESI
• APCI
• APPI
• H-ESI
Polarity
Polarity of the compound: Positive or Negative.
H-SRM
Select this check box to specify tuning for H-SRM
(parent ion peak width = 0.2 amu).
Clear this check box to specify tuning for unit resolution
(parent ion peak width = 0.7 amu).
Parent Mass
Parent mass of the compound.
Tune File
Temporary .TSQTune file that contains the parameters
used during optimization. The QuickQuan application
places the file in a temporary folder that it creates.
Tune PDF File
Temporary PDF file that contains the resulting tune
report. The QuickQuan application places the file in a
temporary folder that it creates.
Tune RAW File
Temporary raw file that contains data collected during the
compound optimization. The QuickQuan application
places the file in a temporary folder that it creates.
Compound SRM Information
Product Ion
Detected product ion mass.
Col Energy
Optimal collision energy of the product ion mass.
Tube Lens or S-Lens
Optimal tube lens offset (if selected compound was
optimized by the TSQ Quantum) or S-Lens offset (if
selected compound was optimized by the TSQ Vantage).
Note If the selected compound was optimized by both
mass spectrometer models, the QuickQuan application
displays the SRM information only for the model you
are currently using.
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Table 5. Update SRM Information dialog box parameters (Sheet 2 of 2)
Parameter
Description
Width
Scan width used during optimization.
Default: 0.1
Max Intensity
Maximum intensity of the product ion.
Buttons
Displays the Open dialog box to import an SRM
information text file (.txt). See “Importing SRM
Information” on page 79.
Deletes the compound SRM information in the table. See
“Deleting SRM Information” on page 82.
Updates the compound SRM information in the
database.
IMPORTANT If you close the Update SRM
Information dialog box without clicking Update, your
changes are not saved.
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Acquiring the Sample Data
This chapter describes how to use the QuickQuan application to set up and run compound
optimization and acquisition.
Contents
• Setting Up for Acquisition
• Reusing Acquisition Settings
• Creating a Generic Instrument Method
• Creating a Generic Processing Method
• Specifying Template Options
• Creating or Importing a Sequence
• Importing Excel and Sequence Templates
• Saving the QuickQuan Assay
• Running an Acquisition
• Stopping an Acquisition
• Exporting the Instrument and Processing Methods
Setting Up for Acquisition
To set up for acquisition, follow one or both of these procedures:
• Reuse the settings from a previous acquisition run. See “Reusing Acquisition Settings” on
page 88.
• Enter or modify the method files and acquisition settings manually. See these sections:
• “Creating a Generic Instrument Method” on page 88
• “Creating a Generic Processing Method” on page 92
• “Specifying Template Options” on page 97
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Reusing Acquisition Settings
Reusing Acquisition Settings
Instead of entering method files and acquisition settings manually, you can reuse the settings
from a previous acquisition file (.aql file) that you created in the QuickQuan application. The
.aql file contains the configuration settings, acquisition settings, compound optimization
information, assay layout, and template information.
Y To reuse the settings in an .aql file
1. In the QuickQuan window, choose File > Open.
2. In the Open dialog box, select the .aql file and click Open. For an example, open this file:
C:\Xcalibur\examples\QuickQuan\SampleSet\acquire template.aql
IMPORTANT If you are using the TSQ Vantage mass spectrometer and you select an
.aql file created by a QuickQuan version that does not support TSQ Vantage, make
sure to update your template tune and instrument method files to work appropriately
for this instrument.
3. In the QuickQuan left pane, click Acquisition. Verify the acquisition settings on the
following pages:
• Click the Templates icon,
, to view the settings on the Acquisition Templates
page. To edit the template settings, see “Specifying Template Options” on page 97.
• Click the Setup icon,
, to view the sequence settings on the Acquisition Setup
page. To edit the sequence settings, see “Creating or Importing a Sequence” on
page 99.
Creating a Generic Instrument Method
You specify certain settings for the mass spectrometer (MS), autosampler, and LC pump in a
generic instrument method (.meth file), which you create in the Xcalibur Instrument Setup
window. To build the complete instrument method for the assay, the QuickQuan application
uses the generic instrument method and the optimized settings that it determines during
compound optimization.
The QuickQuan application alters the masses and mass ranges specified in the scan event of
the generic instrument method based on the information retrieved from the database for each
compound. The application makes the following adjustments to the instrument method file
for the mass spectrometer only:
• Creates the parent-product transition pairs from the information it retrieves from the
database for each compound.
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Creating a Generic Instrument Method
• Uses this information to create and replicate, as necessary, scan events for the internal
standard (ISTD), if specified, and for all compounds used within the drug set for this
sequence.
• Adds all SRM transitions for each compound to the SRM table of the scan event for the
compound.
The QuickQuan application does not alter instrument methods for the autosampler, LC
pump, or other detectors.
If
• a compound is not optimized by your currently configured mass spectrometer model but
is optimized by another model as recorded in the database,
–and–
• you select the Use Optimization Database for Existing Compounds option in the
Configuration Options Dialog Box when you run an acquisition for this compound (see
“Running an Acquisition” on page 115),
the following occur:
• The QuickQuan application uses the SRM table data in the database from the other
model to populate the SRM table in the instrument method, except for the tube lens
or S-Lens value that the application obtains from the tune file that you attach to the
generic instrument method.
• The application also automatically sets the Use Tuned Tube Lens Value or Use Tuned
S-Lens Value check box at the bottom left of the Xcalibur Instrument Setup window
(see Figure 39). Make sure that the tune file in the generic instrument method that
you select on the Acquisition Templates Page or the instrument method that you
select on the Acquisition Setup Page for the compound contains the desired tube lens
or S-Lens value.
Note You can specify different LC methods for different samples within a sequence.
For example, you might use multiple pumps within the same sequence. See “Bypassing
the LC Column and the Dual-Pump, Dual-Column Configuration” on page 134.
Y To create a generic instrument method
1. In the QuickQuan left pane, click Acquisition, and then
click the Templates icon,
.
–or–
Choose Go > Acquisition > Templates.
2. On the Acquisition Templates page, click Inst Setup. The Xcalibur Instrument Setup
window appears (see Figure 39). For more details on the parameters in this window, click
Help.
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3. (Optional) To use a sample file as the basis for a new instrument method, choose
File > Open and select a .meth file. For example:
C:\Xcalibur\QuickQuan\Templates\ColumnA.meth (for the TSQ Quantum and
non-LDTD autosampler)
–or–
C:\Xcalibur\QuickQuan\Templates\ColumnA_Vantage.meth (for the TSQ Vantage and
non-LDTD autosampler)
–or–
C:\Xcalibur\QuickQuan\Templates\LDTD_Acquisition.meth (for the TSQ Quantum
and LDTD autosampler)
–or–
C:\Xcalibur\QuickQuan\Templates\LDTD_Acquisition_Vantage.meth (for the
TSQ Vantage and LDTD autosampler)
These are generic method files provided by the QuickQuan installer.
4. Verify these mass spectrometer settings:
• Segments: 1
• Scan Events: 1
• Scan Type: SRM
The QuickQuan application uses the scan type to determine how the compounds are
scanned. Currently, the application supports only the SRM scan type.
5. Enter these mass spectrometer settings:
• MS acquire time (min)
• Tune method (not optimized)
See this sample tune method:
C:\Xcalibur\QuickQuan\Templates\tune template.TSQTune (for the
TSQ Quantum)
–or–
C:\Xcalibur\QuickQuan\Templates\tune template_Vantage.TSQTune (for the
TSQ Vantage)
Change the tune file as needed to accommodate your run conditions. For example,
you might want to use higher gas flow rates when you have higher LC flow rates.
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Creating a Generic Instrument Method
Note The QuickQuan application automatically selects the Use Tuned Tube
Lens Value or the Use Tuned S-Lens Value check box (at the bottom left of the
Xcalibur Instrument Setup window), depending on whether the currently
configured mass spectrometer model or another model optimized the compound.
For example, if your configured model is the TSQ Vantage, and the compound
was not optimized by the TSQ Vantage but was previously optimized by the TSQ
Quantum, the application would automatically select the Use Tuned Tube Lens
Value check box so that the instrument method uses the optimized tube lens data
from the tune file for the TSQ Quantum.
Figure 39. Xcalibur Instrument Setup window
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6. Click the Divert Valve tab and enter the divert valve settings on the Divert Valve page.
7. Choose File > Save As. Navigate to your desired folder if necessary, type a new file name
(.meth file extension), and click Save.
8. Close the Xcalibur Instrument Setup window.
Creating a Generic Processing Method
A processing method is a defined set of parameters that provides the Xcalibur and QuickQuan
applications with a recipe for automatic quantitation. Use the Xcalibur Processing Setup
window to create a generic processing method (.pmd file) for automated batch analysis. The
generic processing method is used as the basis for creating a processing method for each drug
set in each sequence in the assay.
To create the processing method, the QuickQuan application modifies the generic method
based on the component information and the data acquired:
• The QuickQuan application renames the generic internal standard (ISTD) component, if
specified, using the ISTD compound names you selected, and creates a partial scan filter
to match the instrument method scan filter for each ISTD component. The application
also retrieves the information for each ISTD from the database and inserts it in the
instrument method.
• The QuickQuan application modifies the generic target component in the same manner
as the generic ISTD component. The application sets the mass range to be the product
mass range and sets the scan filter to SRM.
The generic processing method requires the following:
• Components
Note An external standard method must specify only one component, known as
target. A ISTD method must specify two components, known as target and istd.
• Calibration level and quality control (QC) names and amounts
• Calibration curve settings
• Detection settings
If
• a compound is not optimized by your currently configured mass spectrometer model but
is optimized by another model as recorded in the database,
–and–
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Creating a Generic Processing Method
• you select the Use Optimization Database for Existing Compounds option on the
Configuration Options Dialog Box when you run an acquisition for this compound (see
“Running an Acquisition” on page 115),
the QuickQuan application uses the parent mass and product ion masses data for the other
model, stored in the SRM table in the database, to construct the scan filter and mass range for
the processing method.
After the acquisition, the application performs further refining of the processing method.
Y To create a generic processing method
1. In the QuickQuan left pane, click Acquisition, and then
click the Templates icon,
.
–or–
Choose Go > Acquisition > Templates.
2. On the Acquisition Templates page, click Proc Setup. The Xcalibur Processing Setup
window appears (see Figure 40). For more details on the parameters in this window, click
Help.
3. (Optional) To use a sample file as the basis for your processing method, choose
File > Open and select a .pmd file. For example:
C:\Xcalibur\QuickQuan\Templates\Thermo_template_ExtStd.pmd (for external
standards)
–or–
C:\Xcalibur\QuickQuan\Templates\Thermo_template_IntStd.pmd (for internal
standards)
These are generic method files provided by the QuickQuan installer. If you use one of
these files, go to step 6 to edit the data for the file.
4. On the Identification page (see Figure 40), create a component named target as follows:
a. In the Name list, select New.
b. Type target using lowercase letters.
c. Click OK. The target component appears in the Components list.
5. (ISTD only) Create a component named istd as follows:
a. In the Name list, select New.
b. Type istd using lowercase letters.
c. Click OK. The istd component appears in the Components list.
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Figure 40. Identification page of the Quan view in the Xcalibur Processing Setup window
6. On the Levels page (see Figure 41), enter the calibration levels:
a. In the Components list, select target.
b. Enter the calibration and quality control (QC) level names and amounts for your
standards (external or internal) and QCs.
c. Click OK. Figure 41 shows an example.
Figure 41. Levels page of Quan view in the Xcalibur Processing Setup window
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7. (ISTD only) On the Calibration page (see Figure 42), specify that istd is the internal
standard as follows:
a. In the Components list, select istd.
b. In the Component type area, select the ISTD option.
c. Click OK.
8. On the Calibration page, specify that target is the target compound as follows:
a. In the Components list, select target.
b. In the Component type area, select the Target compound option.
c. (ISTD only) In the Target compounds area, in the ISTD list, select istd.
d. Click OK.
9. On the Calibration page, enter the settings for the calibration curve and click OK.
Figure 42 shows an example.
Figure 42. Calibration page of the Quan view in the Xcalibur Processing Setup window
10. On the Detection page (see Figure 43), enter the detection settings. For more details,
click Help.
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Figure 43. Detection page of the Quan view in the Xcalibur Processing Setup window
11. Choose File > Save As. The File Summary Information dialog box appears.
12. Click OK. In the Save As dialog box, navigate to your desired folder if necessary, type a
new file name (.pmd), and click Save.
13. Close the Xcalibur Processing Setup window.
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Specifying Template Options
Specifying Template Options
The template options include the location of the generic instrument and processing methods,
which internal standards (ISTDs) to use, and the output folder. Specify the template options
on the Acquisition Templates page.
Y To open the Acquisition Templates page
In the QuickQuan left pane, click Acquisition, and then
click the Templates icon,
.
–or–
Choose Go > Acquisition > Templates.
The Acquisition Templates page appears.
Figure 44 shows the Acquisition Templates page with the default instrument method for the
TSQ Vantage and the default processing method for external standards.
Figure 44. Acquisition Templates page
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Specifying Template Options
Y To specify template options
1. In the Template Information area, type the file path or click
desired location for each of the following:
and navigate to the
a. In the Generic Instrument Method box, specify the instrument method (.meth file)
that you created in “Creating a Generic Instrument Method” on page 88.
b. In the Generic Processing Method box, specify the processing method (.pmd file)
that you created in “Creating a Generic Processing Method” on page 92.
c. (Optional) Specify a macro to perform custom manipulations of the data acquisition
results. To do this, in the Processing Macro Template box, specify the Excel template
file (.xls) that was designed to invoke that macro automatically.
For more information, see “Using a Macro” on page 137.
d. In the Output Path box, specify the output folder where you want the QuickQuan
application to create a time-and-date stamped folder. Under this time-and-date
stamped folder, the application stores the data and method files for the acquisition
(for example, files with the file extensions .raw, .meth, .pmd, and .sld) within a folder
for each drug set.
Note The sample data files (.raw) are also stored in the QuickQuan database. You can
read the .raw files using any Xcalibur application that supports .raw data files.
2. (Optional) Select the positive and negative internal standards from the QuickQuan
database as follows:
a. Select the Use Internal Standard check box.
b. In the Positive ISTD Default and Negative ISTD Default lists, select the compounds
you want the QuickQuan application to use by default.
c. (Optional) In the Target Compound and ISTD Reference columns, specify any
additional compounds to override the defaults specified in step b. Click the arrow in
the table cell to display the list of compounds for your selection. Each time you
specify a compound in the last row of the table, the QuickQuan application
automatically adds another blank row.
The application includes the default ISTD compounds as separate components in each
new processing method. The positive compounds reference the default positive ISTD,
and the negative compounds reference the default negative ISTD, unless you specify
additional ISTDs in the table. Each ISTD in the table is also included in the processing
method and references the target compound specified in the table.
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Creating or Importing a Sequence
Use the Acquisition Setup page to set up a sequential sequence containing unknown samples,
calibration standard samples, quality control (QC) samples, and blank samples. Each row of
the sequence corresponds to one sample injection. Each injection is defined by the settings in
its sequence row. The number of calibration levels in each calibration set is defined by the
processing method that you created in “Creating a Generic Processing Method” on page 92.
To create a sequence, use one of the following procedures:
• “Creating a Sequence in the Acquisition Setup Page” on page 99
• “Copying Sequences from Excel” on page 104
• “Importing a Sequence” on page 105
• “Importing Excel and Sequence Templates” on page 106
Creating a Sequence in the Acquisition Setup Page
On the Acquisition Setup Page, you can create multiple sequences for an assay.
Y To display the Acquisition Setup page
In the QuickQuan left pane, click Acquisition, and then click the Setup icon,
.
–or–
Choose Go > Acquisition > Setup.
The Acquisition Setup Page appears.
Y To create sequences on the Acquisition Setup page
1. In the Bracket Type list, select the bracket type applicable to the sequences to be run (see
Figure 45). These are your two choices:
• Open Bracket: Specifies that the sequence contains one open bracket. You can place
your samples and calibrants in any order. Calibration samples are processed before
unknown and QC samples.
IMPORTANT To run front and back calibration curves, select the Open Bracket
type.
• Non Bracketed: Specifies that the sequence does not contain brackets.
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Figure 45. Select bracket type
Note You can select the bracket type only at the beginning, or when the table is
cleared or empty. To clear the table, click Clear All. The QuickQuan application does
not accept multiple bracket types for different sequences in the sequence table.
The items that you can select in the Sample Type column vary, depending on the
selected bracket type.
2. In the sequence table, select the New Sequence check box to designate the start of a new
sequence. See Figure 46.
3. Enter the sample information in each row of the sequence. For a description of each
column in the sequence table, see “Acquisition Setup Page” on page 159.
Repeat steps 2 and 3 to add additional sequences.
IMPORTANT Make sure that you name the vial positions with names that are valid
for your autosampler. the QuickQuan application validates the sequence vial position
names based on your autosampler and displays an error message if the names are not
valid.
If you are using the LDTD autosampler, make sure that you enter serial numbers that
exactly match the serial numbers on the Lazwell sample plates used for your sequence.
Enter the serial number with six digits, between 000000 and 999999. If you enter less
than six digits, the leftmost missing digits autofill with zeros.
4. Choose File > Save to save the sequences to an assay (.aql file).
For a description of the various ways to edit the sequence table, see “Editing a Sequence on
the Acquisition Setup Page” on page 102.
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Figure 46. Sequences for Drugset1 and Drugset2 on the Acquisition Setup page
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Editing a Sequence on the Acquisition Setup Page
You can edit the sequence on the Acquisition Setup page. For a description of each column in
the sequence table, see “Acquisition Setup Page” on page 159.
Y To fill down the entries from one row to a contiguous range of rows
1. Click to highlight the row that you want to copy. Then right-click and choose Fill Down
from the shortcut menu.
2. In the Fill Down Dialog Box, select the columns to be duplicated, select the destination
rows, and click OK.
Y To insert a row or multiple rows in the sequence table
1. To insert a row, click the row below the target location.
Or, to insert multiple rows, hold down the SHIFT key as you click the rows below the
target location.
2. Right-click and choose Insert Rows from the shortcut menu.
Y To clear a row or multiple rows in the sequence table
1. Click the row number to highlight the entire row that you want to clear.
Or, to clear multiple rows, hold down the SHIFT key as you click the rows.
2. Right-click and choose Delete Rows from the shortcut menu.
Fill Down Dialog Box
Use the Fill Down dialog box to fill selected rows with duplicate entries or appropriately
sequenced number entries. Use the row text boxes to specify the first and last row numbers
that contains the duplicate entries, and the row whose entries you want to duplicate.
Y To open this dialog box
1. In the QuickQuan left pane, click Acquisition, and then click the Setup icon,
Or, choose Go > Acquisition > Setup.
.
2. On the Acquisition Setup Page, right-click the sequence table and choose Fill Down from
the shortcut menu.
–or–
1. In the QuickQuan left pane, click Acquisition, and then click the Aria icon,
Or, choose Go > Acquisition > Aria.
.
2. On the Acquisition Aria Configuration Page, right-click the Batch Overrides table and
choose Fill Down Grid from the shortcut menu.
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Y To fill down the entries from one row to a contiguous range of rows
1. In the table, click the row that you want to copy.
2. Right-click the table and choose Fill Down or Fill Down Grid from the shortcut menu.
The Fill Down dialog box appears.
Figure 47. Fill Down dialog box
3. In the Fill Down dialog box, select the columns to be duplicated, select the destination
rows, and click OK.
The available columns vary depending on which table you are filling down:
• For a description of the sequence table columns, see the “Acquisition Setup Page” on
page 159.
• For a description of the batch overrides columns, see the “Acquisition Aria Configuration
Page” on page 165.
The Fill Down dialog box contains these parameters.
Table 6. Fill Down dialog box parameters (Sheet 1 of 2)
Parameter
Description
Row Controls
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Fill From Row
Specifies the first row to receive new data.
To Row
Specifies the last row to receive new data.
Using Row
Specifies which row the initial data comes from.
Create Samples in Selected
Empty Rows During Fill Down
When selected, specifies that a new sample be created in
an empty row during a fill down that includes that row
in its fill down range. When not selected, specifies that
the empty row is ignored during a fill down that
includes that row in its fill down range.
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Table 6. Fill Down dialog box parameters (Sheet 2 of 2)
Parameter
Description
Buttons
Selects all the check boxes in the Select Columns area.
Clears all the check boxes in the Select Columns area.
Copying Sequences from Excel
You can copy sequences or portions of a sequence from a Microsoft Excel file to the
Acquisition Setup page. You can also copy sequences from the Acquisition Setup page to an
Excel file. The copied sequence can contain all the columns that appear in the Acquisition
Setup page.
Y To display the Acquisition Setup page
In the QuickQuan left pane, click Acquisition, and then click the Setup icon,
.
–or–
Choose Go > Acquisition > Setup.
The Acquisition Setup Page appears.
Y To copy sequences or portions of sequences from an Excel file
1. In the QuickQuan application, verify that the correct bracket type has been selected to
match the bracket type of the sequences in the Excel file.
IMPORTANT You cannot change the bracket type after you copy the sequence data
onto the Acquisition Setup page, unless you clear the sequence table by clicking Clear
All.
2. In the Excel file, verify that the column headings and column order match the columns
on the Acquisition Setup page. Format all cells in the columns and rows that you want to
copy from as text format.
3. In the Excel file, select the columns and rows of the sequence, or portions of the sequence,
and press CTRL+C.
4. On the Acquisition Setup page, position the pointer in the appropriate location in the
sequence table and press CTRL+V.
5. Verify that the correct values appear.
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Y To copy sequences or portions of sequences from the Acquisition Setup page to an
Excel file
1. On the Acquisition Setup page, select the columns and rows that you want to copy and
press CTRL+C.
2. In the Excel file, format all cells in the columns and rows that you want to paste into as
text format.
3. Position the pointer in the appropriate location in the Excel table and press CTRL+V.
Importing a Sequence
You can import a sequence (.sld or .csv file) that you created previously in the Xcalibur
Sequence Setup window. See “Sequence Template File” on page 113 for a description of the
main sequence columns. You can import the information for all the columns in the
QuickQuan sequence table, except the New Sequence column.
Tip Instead of importing a sequence, you can copy the sequence from a Microsoft Excel
file to the Acquisition Setup page. See “Copying Sequences from Excel” on page 104.
If you are using the LDTD autosampler, you can enter the serial number of the LazWell
plate in the sequence for import, by entering this number in the column you redefined for
Heading 3 of the Xcalibur User Label. You can also enter the drug set name in the column
you redefined for Heading 5 of the Xcalibur User Label. For details, refer to the Xcalibur
User Guide, in the section for the Change menu of the Home Page window.
Y To display the Acquisition Setup page
In the QuickQuan left pane, click Acquisition, and then click the Setup icon,
.
–or–
Choose Go > Acquisition > Setup.
The Acquisition Setup Page appears.
Y To import a sequence
1. On the Acquisition Setup page, click Import.
2. In the Open dialog box, select a sequence file (.sld or .csv file) to import and click Open.
The QuickQuan application displays the imported sequence in the table on the
Acquisition Setup page.
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Note You can import open bracket or non-bracketed sequences. The imported
sequence data overwrites any data previously entered or selected on the Acquisition
Setup page, including the bracket type.
If the imported sequence is of a bracket type other than open bracket or
non-bracketed, a warning message informs you that the QuickQuan application will
convert the imported sequence to the non-bracketed type by default.
3. (Optional) Edit the sequence to specify a drug set for each sample.
Figure 46 shows two sequences: one for Drugset1 and one for Drugset2.
Importing Excel and Sequence Templates
Another way to import a sequence is to import an Excel template (.xls) and a corresponding
sequence template (.sld) using these procedures:
1. “Creating an Excel Template for the Assay” on page 106
2. “Creating a Sequence Template” on page 109
3. “Importing the Excel and Sequence Templates” on page 111
Creating an Excel Template for the Assay
The Excel template file describes the assay to be run, including the drug sets to use for each
sequence in the assay, vial positions, instrument method, processing method, number of
samples per sequence, and injection order (specified by row order). You can use multiple
plates in a single sequence and specify more than one plate by indicating different vial
positions.
In the Excel worksheet, you can specify the vial position for each sample. If the autosampler
supports vial validation, the QuickQuan application automatically validates each vial position
specified in the Excel worksheet at run time.
Y To create the Excel template for the assay
1. In columns 2 through 6, enter the following:
• Drug set name
• Vial position
IMPORTANT Make sure that you name the vial positions with names that are
valid for your autosampler.
• Sample name
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• Generic instrument method
• Generic processing method
Each row corresponds to an injection. Figure 48 shows an example of an Excel template.
2. To indicate the start of a new sequence, type an x in column 1.
3. To indicate the end of the assay, type an x in column 1 in the row after the last injection.
See Figure 49.
4. Save the Excel template as an .xls file.
Figure 48. Excel template for an assay
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Figure 49. The start of a new sequence and the end of the assay in the Excel template
Start of new sequence
End of assay
IMPORTANT All sequences in the Excel template must have the same number of samples,
and the number of samples in each sequence of the Excel template (.xls file) must match
the number of samples in the corresponding sequence template (.sld file).
This restriction does not apply if you use the sequence table to define your sequence
instead of importing from the Excel and sequence templates. When you use the sequence
table, you can enter your sequences with different numbers of samples.
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Creating a Sequence Template
The sequence template (.sld file) is a generic sequence to be run for the entire assay. The
sequence template must correspond to the Excel template. You create the sequence template
in the Xcalibur Home Page window – Sequence Setup page. See Xcalibur Help for details on
how to create the sequence on the Sequence Setup page.
The sequence template specifies the following:
• Sample injection types and arrangement (standards, QCs, blanks, and unknowns)
• Injection volume used for each sample (if you are using the Thermo PAL autosampler)
• Generic processing method
• Calibration or QC level
• Serial number for the LDTD LazWell plate in the column you redefined for Heading 3 of
the Xcalibur User Label (if you are using the LDTD autosampler)
• Drug set name in the column you redefined for Heading 5 of the Xcalibur User Label
At run time, the QuickQuan application replaces the drug set name, vial position, instrument
method, processing method, and sample name with the information specified in the Excel
template for each sequence in the assay.
IMPORTANT The number of samples in the sequence template (.sld file) must match the
number of samples in each sequence of the corresponding Excel assay layout template (.xls
file).
In addition, the calibration or QC levels in the sequence template must match the levels
defined in the processing method template (.pmd file). See “Creating a Generic Processing
Method” on page 92.
For example, when you are using the Thermo PAL autosampler, the sequence template (.sld
file) shown in Figure 50 corresponds to the Excel template shown in Figure 48. In this
example, 27 samples must be defined in the sequence template, because the Excel template
has 27 samples per drug set. The sequence in the .sld file is specified only once, and the
QuickQuan application refers back to it multiple times.
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Figure 50. Sequence template corresponding to the Excel template
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Importing the Excel and Sequence Templates
Y To import an Excel template and a sequence template
1. Choose File > Import Acquisition Sequence > From Templates to open the Import
Sequence Templates Dialog Box (see Figure 51).
2. Select the Excel template and the corresponding sequence template.
3. Click OK to close the dialog box and execute the import. The QuickQuan application
displays the imported sequence in the table on the Acquisition Setup page.
Note You can import open bracket or non-bracketed sequences. The imported
sequence data overwrites any data previously entered or selected on the Acquisition
Setup page, including the bracket type.
If the imported sequence is of a bracket type other than open bracket or
non-bracketed, a warning message informs you that the QuickQuan application will
convert the imported sequence to the non-bracketed type by default.
Import Sequence Templates Dialog Box
You can create a sequence in the QuickQuan application by importing an Excel template and
a sequence template.
For details on how to create a sequence by importing templates, see “Importing Excel and
Sequence Templates” on page 106.
Y To open this dialog box
Choose File > Import Acquisition Sequence > From Templates. The Import Sequence
Templates dialog box appears.
Figure 51. Import Sequence Templates dialog box
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The Import Sequence Templates dialog box contains these parameters.
Parameter
Description
Excel Template
Specifies the Excel Template File (.xls) that describes
the assay to be run.
Sequence Template
Specifies the Sequence Template File (.sld) that is a
generic sequence to be run for the entire assay. The
sequence template must correspond to the Excel
template.
Excel Template File
The Excel template must contain these column headings in the order shown.
Table 7. Excel template columns (Sheet 1 of 2)
Column
Information
1—New
Sequence
Type an x in column 1 in the first row to indicate the start of a new
sequence.
Type an x in column 1 in the row after the last injection to indicate the
end of the assay.
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2—Drug
Type the name of the drug set associated with the QuickQuan sequence.
The QuickQuan application creates a new folder for each drug set based
on the drug set name specified.
3—Vial
Position
Type the vial position in the autosampler tray to use for the given sample.
4—Sample
Name
Type the name of the sample in this row.
QuickQuan 2.4 User Guide
Make sure the nomenclature for the vial positions is valid for the
autosampler that you plan to use for the acquisition. If the autosampler
supports vial validation, the QuickQuan application automatically
validates each vial position specified in the Excel worksheet at run time.
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Table 7. Excel template columns (Sheet 2 of 2)
Column
Information
5—Instrument Provide the file path of the generic instrument method file (.meth) that
Method
defines the LC conditions for the sample. (See “Creating a Generic
Instrument Method” on page 88.)
You can set different instrument methods within the Excel file for each
sample in a sequence, for example, to perform column equilibration and
sample elution in tandem.
6—Processing
Method
Provide the file path of the generic processing method file (.pmd) that
contains the peak detection settings. (See “Creating a Generic Processing
Method” on page 92.)
You can use multiple processing methods within a single sequence,
specifically for sequences containing multiple drug sets. For each drug set,
the QuickQuan application creates a separate processing method in a drug
set folder under the acquisition output folder.
Sequence Template File
The QuickQuan application can use an Xcalibur sequence template to specify a generic
sequence to run for the entire assay. The sample types and injection volume used for each
sample are specified within this generic sequence. The arrangement of sample types
(standards, QCs, blanks, and unknowns) in the sequence template is preserved in the Excel
template. The QuickQuan application determines the data file name, injection vial,
instrument method, processing method, and sample name information at run time with the
information specified in the Excel template for each sequence in the assay. The number of
samples in the selected sequence template must match the number of samples in each
sequence of the selected Excel template file.
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On the Xcalibur Sequence Setup page, create a sequence template for the assay with the
following information (one sample per row).
Parameter
Description
Sample Type
The sample type defines how the QuickQuan application
processes the sample data. Each sample must be classified as one of
the following sample types:
• Unknown
• Blank
• Quality Control (QC)
• Standard clear
• Standard update
• Standard bracket
Injection Volume
(Not needed if using the LDTD autosampler) The volume in
microliters of the sample to be injected.
Processing Method
The generic processing method. See “Creating a Generic
Processing Method” on page 92.
Level
The calibration or QC level in the generic processing method.
Serial Number
(If you are using the LDTD autosampler) You can enter the serial
number for the LDTD LazWell plate in the sequence as follows:
1. In the Xcalibur application, choose Change > User Labels. In
the Heading 3 box, rename the column to Serial Number.
Click OK.
2. Choose Change > Column Arrangement. Make sure that the
Serial Number column name shows under the Displayed
Columns area. Click OK.
3. On the Sequence Setup page, in the Serial Number column,
enter the 6-digit serial number of the LDTD LazWell plate.
Drug Set
You can enter the drug set name in the sequence as follows:
1. In the Xcalibur application, choose Change > User Labels. In
the Heading 5 box, rename the column to Drug Set. Click
OK.
2. Choose Change > Column Arrangement. Make sure that the
Drug Set column name shows under the Displayed Columns
area. Click OK.
3. On the Sequence Setup page, in the Drug Set column, enter
the name of the drug set.
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Saving the QuickQuan Assay
Saving the QuickQuan Assay
Save the QuickQuan assay in an .aql file.
Y To save the QuickQuan assay
1. Choose File > Save As to open the Save As dialog box.
2. If necessary, navigate to your desired folder.
3. In the File Name box, enter a name for the assay.
4. Click Save.
Running an Acquisition
If you are using the Aria OS system, refer to the QuickQuan and Aria OS Quick Start and the
Acquisition Aria Configuration Page for details on how to configure the QuickQuan
application for use with this system.
Before running an assay, you can specify whether the QuickQuan application optimizes all the
compounds in the assay, or only the unoptimized compounds that are not in the optimization
database.
Y To prepare to run an acquisition
1. Open the Xcalibur application to the Real Time Plot view.
2. In the Xcalibur application, verify that devices are ready, and make sure the initial system
parameters are within the acceptable ranges.
3. Verify that the vessel holding the compounds for tuning is ready and in position. Verify
the same for assay plates.
Y To display the Configuration Options dialog box
In the QuickQuan left pane, click Acquisition, and then click the Run icon,
.
–or–
Choose Go > Run.
The Configuration Options Dialog Box appears.
Y To set up and run the acquisition
1. To run an analytical experiment with real-time compound optimization, in the
Configuration Options Dialog Box, select the Compound Optimization and
Acquisition option. See Figure 52, Figure 53, or Figure 54.
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2. (If not using the LDTD autosampler) (Optional) If you want to use the Aria OS system,
select the Aria check box.
Note The Aria check box is available only if you have the Aria OS system installed.
Figure 52. Configuration Options dialog box with the Aria OS system installed
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Figure 53. Configuration Options dialog box with Thermo PAL configured and without the
Aria OS system
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Figure 54. Configuration Options dialog box with LDTD configured and supporting
optimization
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Figure 55. Configuration Options dialog box with LDTD configured but not supporting
optimization
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3. (Optional) To use optimization information that is already in the database, select the
Use Optimization Database for Existing Compounds check box. The QuickQuan
application optimizes only the compounds in the tune plate that are required for
acquisition but are considered not tuned.
If you clear this check box, the application optimizes all compounds that are in the
tune plate and updates the database with new information for these compounds.
4. In the Instrument Settings area, verify the following:
a. The Instrument column lists only the required instruments.
• If you are using the Aria OS system, then the Instrument column should list only
the mass spectrometer.
• If you are not using the Aria OS system, then the Instrument column should list
the mass spectrometer, LC pump, and autosampler (if you are using a
non-LDTD autosampler); or the mass spectrometer and autosampler (if you are
using an LDTD autosampler).
If the required instruments do not appear, see “Configuring Instruments without the
Aria OS System” on page 133, or if you are running with the Aria OS system, see
“Configuring Instruments with the Aria OS System” on page 134. You must
configure the instruments before doing the next steps.
b. For each required instrument, click the corresponding cell in the In Use column to
turn on the Yes value.
c. (If not using the Aria OS system) For the start instrument selected to initiate the run,
click the corresponding cell in the Start Instrument column to turn on the Yes value,
and to turn off the Yes value for the other instruments.
Note Typically, you select the autosampler to be the start instrument because it
controls when a run starts. In this case, the In Use column displays Yes for all
instruments to be used for the sequence submission, including the autosampler.
This means the instruments are awaiting a contact closure event to start
operation. When all instruments used in the run report that they are waiting for
contact closure, the start instrument initiates the run.
5. In the Number of Quan Masses box, type the number of masses to use for postacquisition
processing. The valid range is 1 to 3.
6. In the Threshold % box, type a percentage. All masses for postprocessing indicated in the
Num Quan Masses box must meet the specified percentage threshold of the highest
intensity ion.
7. In the Mass Window Width box, type the width value used to set the mass range for the
processing method.
8. (Optional) To set the devices to standby after the acquisition has finished, select the
Put Instrument into Standby After Batch check box.
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9. (Optional) To start postprocessing after each sequence has been acquired, select the
Do Post Processing after Acquisition check box.
You can also select these options:
• To produce a summary report for the acquisition data after postprocessing has
completed, select the Generate Excel Summary check box.
• To execute a custom Excel macro after data acquisition and postprocessing have
finished, select the Run User Defined Macro check box. (For details, see “Using a
Macro” on page 137.)
10. Click OK to start the acquisition. The QuickQuan application displays the Acquisition
Status page. See Figure 56.
Tip You can view the status of the run from the Xcalibur Real Time Plot view, the
QuickQuan Acquisition Status page, or both.
If you are running an acquisition with the Aria OS system, then the QuickQuan
application launches the Aria application automatically if it is not running already.
After initialization, the QuickQuan application submits the sequences (batches) directly
to the Aria OS system. For more information on the Aria windows, refer to the
QuickQuan and Aria OS Quick Start and the Aria OS User Guide.
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Figure 56. Acquisition Status page
When you run the acquisition, the QuickQuan application creates a time-and-date stamped
folder under the folder you specified as the output folder (see “Specifying Template Options”
on page 97). Under the time-and-date stamped folder, the application creates a folder for each
drug set (for example, 01_Drugset2 and 02_Drugset1) and then puts the raw and processed
data in these drug set folders (see Figure 57).
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Figure 57. Time-and-date stamped folder location of raw files, result files, and Excel acquisition file
Note After you start the acquisition run, you can launch other instances of the
QuickQuan application if you want to submit other sequences for optimization or
acquisition. Each new instance places the optimization or acquisition sequence into the
queue to be processed in the order of submission. Each QuickQuan instance continues
processing until the sequence analysis from that instance is complete or you cancel the
run.
Stopping an Acquisition
Y To stop an acquisition before the run is finished
On the QuickQuan toolbar, click
.
Stopping the run before it is completed might cause loss of data and incomplete results.
Confirm that you really want to proceed with this action.
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Exporting the Instrument and Processing Methods
Exporting the Instrument and Processing Methods
You can export the generic instrument method (.meth) and processing method (.pmd) from
the Acquisition Templates page for use with other applications.
Y To export the methods
1. On the Acquisition Templates page, specify the template information. See “Specifying
Template Options” on page 97.
2. Choose File > Export Methods. The Export Methods Dialog Box appears.
Note The File > Export Methods menu is available only when you’re in the
Acquisition Templates page.
3. In the Output Path box, specify the file path for the exported files.
4. In the Base Filename box, type the name that becomes part of the exported folders and
method files.
5. To create a single instrument method and processing method for all the selected drug sets,
select the Combine Drug Sets into single method check box.
If you want to create a separate instrument method and processing method for each
selected drug set, clear this check box.
6. In the Database Drug Sets list, select the drug sets and compounds for the exported
methods. To select multiple drug sets, hold down the CTRL key before making your
selections.
7. Click Export. The QuickQuan application creates a time-and-date stamped folder at the
specified output path and stores the instrument method and processing method for the
selected drug sets in that folder.
Export Methods Dialog Box
Use this dialog box to export methods from the Acquisition Templates page for use with other
applications. You can export the instrument method (.meth) and processing method (.pmd)
for any drug sets in the QuickQuan database. See “Exporting the Instrument and Processing
Methods” on page 124.
Y To open this dialog box
1. In the QuickQuan left pane, click Acquisition, and then
click the Templates icon,
.
–or–
Choose Go > Acquisition > Templates.
2. Choose File > Export Methods.
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5 Acquiring the Sample Data
Exporting the Instrument and Processing Methods
Figure 58. Export Methods dialog box
The Export Methods dialog box contains these parameters.
Parameter
Definition
Output Path
Specifies the folder path for the exported method files.
Base File Name
Specifies the file name. The QuickQuan application appends a
time-and-date stamp suffix to this base file name when it generates
the export method file.
Combine drug sets
into single methods
Specifies whether to create a single instrument method and
processing method for all the selected drug sets, or create an
instrument method and processing method for each selected
drug set.
Database Drug Sets
Specifies which drug sets and compounds from the QuickQuan
database to include with the exported methods.
Creates a time-and-date stamped folder at the specified output
path, and creates the instrument method and processing method
for the selected drug sets.
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6
Reviewing the Quantitation Results
This chapter describes how to display the QuickQuan quantitation results.
Contents
• Reviewing the Results
• Generating an Acquisition Summary Report
• How the QuickQuan Application Performs Postprocessing
Reviewing the Results
Use the Acquisition Results Summary page to display and review the quantitation results.
Y To display the Acquisition Results Summary page
In the QuickQuan left pane, click Acquisition, and then click
the Results Summary icon,
.
–or–
Choose Go > Acquisition > Results Summary.
The Acquisition Results Summary page appears.
Y To display and review the quantitation results
1. In the Root Directory box, type or browse to the time-and-date stamped folder that the
QuickQuan application created after the acquisition run, for example:
your_output_folder\timestamp_folder_for_selected_acquisition
This time-and-date stamped folder should be under the output folder that you selected in
“Specifying Template Options” on page 97.
See Figure 59.
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Reviewing the Results
Figure 59. Acquisition Results Summary page
2. Select a sequence in the Sequence Name column and click Quan Browser. Xcalibur
Quan Browser starts and displays the data in the Quan Browser window. See Figure 60.
3. On the right side of the Quan Browser window, select a component to display the results.
For example, select reserpine to view the results for this compound.
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6 Reviewing the Quantitation Results
Generating an Acquisition Summary Report
Figure 60. Results for reserpine in the Quan Browser window
Generating an Acquisition Summary Report
The QuickQuan application compiles the individual sample acquisition reports into an
acquisition summary report (.xls) that you can open using Excel.
The Acquisition Summary Report contains all or some of the following data, depending on
whether you have specified a short or long summary report for the processing method:
•
•
•
•
•
•
•
•
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Raw file name
Sample type, name, and ID
Expected and calculated amount
Units
%Diff
Level
%RSD (relative standard deviation)
Peak status
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Reviewing the Quantitation Results
Generating an Acquisition Summary Report
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
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Response
Equation
Area
Height
ISTD area and height
Retention time (RT), Rel RT, Del RT
Signal-to-noise ratio (S/N)
Start and end time
Start and end height
Integ code
Search window
Threshold
Smoothing
Acquisition date
Duration
Exp method
Processing method
Vial
Injection volume
Sample weight and volume
ISTD base amount and calculated amount
Dilution factor
Figure 61 shows a sample acquisition summary report.
Figure 61. Excel acquisition summary report
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6 Reviewing the Quantitation Results
How the QuickQuan Application Performs Postprocessing
If you make changes while in Quan Browser, you can then export the modified data to the
individual sample acquisition reports. The changes are then added to this acquisition
summary report for your review.
Each time the acquisition summary report is run, the QuickQuan application adds the new
data to the data already existing in the report. This might result in duplicate entries that have
the same component name, file name, and sample ID. In this case, the application prevents
duplicate data in the acquisition summary report by retaining only the most recent data for a
particular component/file name/sample ID set.
Y To generate an acquisition summary report
1. In the QuickQuan window, choose Reports > Acquisition Summary Report. The
Browse for Folder dialog box appears.
2. Select the folder that contains your acquisition data and individual sample report files
(.xls). For example, select the time-and-date stamped folder that the QuickQuan
application created after the acquisition completed:
your_output_folder\timestamp_folder_for_selected_acquisition
This time-and-date stamped folder should be under the output folder that you specified
in “Specifying Template Options” on page 97.
3. Click OK.
The QuickQuan application creates a Microsoft Excel file (.xls) that combines multiple
Xcalibur acquisition reports for each sequence of the assay into a single acquisition
summary report. It stores the report in the same folder that you selected.
How the QuickQuan Application Performs Postprocessing
To obtain postprocessed data, you must specify the configuration settings for postprocessing
in the Configuration Options Dialog Box before running the acquisition (see “Running an
Acquisition” on page 115).
After you have configured the postprocessing options, the QuickQuan application does the
following:
1. Submits the acquired sequence to the Xcalibur data system.
2. Monitors the acquisition files being generated for each sequence that is submitted, and
performs the back-end processing that communicates with the Xcalibur data system. At
the completion of each sequence, the application attempts to postprocess the sequence,
using the information about each compound assigned to the drug sets for each sequence.
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Reviewing the Quantitation Results
How the QuickQuan Application Performs Postprocessing
3. Determines the required expected retention time (RT) for each component in the
processing method. The application determines this value by extracting the filtered mass
chromatogram specified for each component, using the most concentrated calibrant level
as specified in the processing method (.meth file). The application uses the most intense
data point as the expected RT and enters it in the processing method for that component.
4. Selects from one to three masses when the component specifications in the processing
method are created. The application uses only the one to three product ions with the
greatest intensity in the quantification of the component by selecting these masses from
the scan corresponding to the expected RT determined above. The top ions are selected
only from those whose intensities are greater than the user-defined threshold of the
intensity of the base peak for the scan.
5. Instructs the Xcalibur data system to reprocess the sequence with the new processing
modifications when the component modification process is complete.
If
• a compound is not optimized by your currently configured mass spectrometer model but
is optimized by another model as recorded in the database,
–and–
• you select the Use Optimization Database for Existing Compounds option on the
Configuration Options Dialog Box when you run acquisition for this compound (see
“Running an Acquisition” on page 115),
the QuickQuan application uses the parent mass and product ion masses data for the other
model, stored in the SRM table in the database, to construct the scan filter and mass range for
acquisition postprocessing.
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A
Configuration Procedures
This appendix includes configuration procedures that you might need to use periodically.
Contents
• Configuring Instruments without the Aria OS System
• Configuring Instruments with the Aria OS System
• Bypassing the LC Column and the Dual-Pump, Dual-Column Configuration
Configuring Instruments without the Aria OS System
Y To configure the instruments
1. Close the QuickQuan and Xcalibur applications (if currently open).
2. From the Windows taskbar, choose Start > All Programs > Thermo Foundation 1.0 >
Instrument Configuration to open the Thermo Foundation Instrument Configuration
window.
3. In the Instrument Configuration window, configure these instruments:
• LC pump (only if you are using a non-LDTD autosampler)
• autosampler (Thermo PAL, LDTD, or other)
• mass spectrometer (TSQ Quantum or TSQ Vantage)
4. Click Done.
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A
Configuration Procedures
Configuring Instruments with the Aria OS System
Configuring Instruments with the Aria OS System
If you plan to use the Aria OS system, you can use the next procedure to configure the mass
spectrometer for optimization. For more information on running the QuickQuan application
with the Aria OS system, refer to the QuickQuan and Aria OS Quick Start.
Y To configure the mass spectrometer for the Aria workflow
1. Close the QuickQuan, Aria, and Xcalibur applications (if currently open).
2. From the Windows taskbar, choose Start > All Programs > Thermo Foundation 1.0 >
Instrument Configuration to open the Thermo Foundation Instrument Configuration
window.
3. In the Instrument Configuration window, configure only the mass spectrometer. Remove
all other devices from the configuration.
4. Click Done.
Bypassing the LC Column and the Dual-Pump, Dual-Column
Configuration
You can bypass the chromatography column during optimization and have the samples
infused directly into the ion source. This option requires a Thermo PAL autosampler with
multiple injection ports, multiple valves, and a stream selector.
To increase throughput for a gradient analysis, you can set up your liquid
chromatography/mass spectrometry (LC/MS) system in a dual-pump, dual-column
configuration and equilibrate one column while performing sample elution with the other
column. Figure 62 shows the required configuration.
To alternate columns between consecutive injections, you must use two instrument methods.
In the first method, pump 1 produces a gradient for sample elution on the first column, and
pump 2 produces a gradient that re-equilibrates the second column. In the second method,
pump 1 produces a gradient for sample elution on the second column, and pump 2 produces
a gradient that re-equilibrates the first column.
Using these alternating instrument methods (along with valve switching) allows for each
injection to run through a separate column and removes the wait time for column
equilibration.
The QuickQuan application also enables you to use different instrument methods for
acquisition and optimization.
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A Configuration Procedures
Bypassing the LC Column and the Dual-Pump, Dual-Column Configuration
Figure 62. Injection valve configuration
Infusion inlet
1
6
Infusion tee
2
5
Injection inlet
Open port
3
1
To waste
6
2
Sample loop
3
5
4
4
Pump 1
Pump 2
Column 1
10 1
2
9
3
Column 2
4
8
7
To waste
8
6
1
To waste
5
To waste
2
7
3
6
5
4
To detector
1
6
2
5
To waste
3
4
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B
Using a Macro
This appendix describes how the QuickQuan application uses a macro to perform custom
calculations.
The application includes a Microsoft Excel template file for data reduction
(Data_Reduction.xls). You can customize this template to perform the calculations and
display the assay results that you require. The file is located in the following folder:
C:\Xcalibur\QuickQuan\Templates
The Data Reduction template file contains two sheets:
• Sheet 1 in the template is a blank report.
• Sheet 2 is the Calculations page. Figure 63 shows an example.
Figure 63. Example of the Calculations page
The processing macro Excel file must implement a macro named “RunUserMacro,” which the
QuickQuan application invokes during the data reduction. At a minimum, this macro must
recalculate the Calculations page. Setting up the data reduction in this way allows the
application to provide your custom results in real time.
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B
Using a Macro
To use the macro for postprocessing calculations, you must do both of the following:
• Select the Run User Defined Macros check box when you specify the configuration
settings. See “Running an Acquisition” on page 115.
• Select the processing macro template when you select the template files. See “Specifying
Template Options” on page 97.
The QuickQuan application saves the data reduction results in the acquisition output folder.
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C
QuickQuan Page Reference
This appendix describes the main pages that you can display in the QuickQuan window.
Contents
• Compounds Browse Page
• Optimization Setup Page
• Optimization Tune Report Page
• Acquisition Templates Page
• Acquisition Setup Page
• Acquisition Aria Configuration Page
• Acquisition Results Summary Page
Compounds Browse Page
Use the Compounds Browse page for the following procedures:
• “Defining the Compounds in the Database” on page 11
• “Defining the Drug Sets in the Database” on page 21
• “Viewing Compound and Drug Set Data” on page 29
• “Updating SRM Information” on page 79
In the Compounds Browse page, you can search the compound, drug set, SRM, and source
type tables in the currently opened QuickQuan database.
Y To display the Compounds Browse page
In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
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Compounds Browse Page
The Compounds Browse page contains these parameters.
Table 8. Compounds Browse page parameters (Sheet 1 of 2)
Parameter
Description
Compound Browser
Displays the table you select in the Table list.
The tables are not editable on this page. To edit a table, see one of
these procedures:
• “Defining the Compounds in the Database” on page 11
• “Defining the Drug Sets in the Database” on page 21
• “Updating SRM Information” on page 79
Table
Specifies one of the following table types for display in the
Compound Browser:
• “Compounds Table” on page 141
• “Drug Set Names Table” on page 142
• “Source Type Table” on page 143
• “SRM Table” on page 144
Compound
Specifies SQL query commands for filtering the data.
To filter the data shown in the current table, type an SQL
statement in the Compounds box and click Query.
Buttons
Use the arrow buttons when the table contains many rows and you
want to move up or down in the table without having to scroll row
by row.
Displays the first screen of rows in the displayed table.
Displays the previous screen of rows in the displayed table.
Displays the next screen of rows in the displayed table.
Displays the last screen of rows in the displayed table.
Filters the data in the currently displayed table using the SQL
statement in the Compound box.
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Compounds Browse Page
Table 8. Compounds Browse page parameters (Sheet 2 of 2)
Parameter
Description
Opens the Add Compounds Dialog Box, which you use to add
and edit compound information in the database or delete
compounds from the database.
For details, see “Defining the Compounds in the Database” on
page 11.
Opens the Add Drug Sets Dialog Box, which you use to add and
edit drug set information in the database or delete drug sets from
the database.
For details, see “Defining the Drug Sets in the Database” on
page 21.
Opens the Update SRM Information Dialog Box, which you use
to update SRM information in the database.
For details, see “Updating SRM Information” on page 79.
Compounds Table
Y To view the contents of the Compounds table
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
The Compounds Browse Page appears.
2. In the Table list, for the TSQ Quantum mass spectrometer, select [COMPOUNDS], or
for the TSQ Vantage mass spectrometer, select [COMPOUNDS_VANTAGE].
The Compounds table contains information used to tune each compound in the QuickQuan
database. To modify the information in the Compounds table, use the Add Compounds
Dialog Box. For details, see “Defining the Compounds in the Database” on page 11.
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Compounds Browse Page
The Compounds table contains the following information for each compound in the
database.
Parameter
Description
Compound
Name of a compound in the database. To add or delete a
compound name, use the Add Compounds Dialog Box.
Parent Mass
Monoisotopic mass for the compound. To specify the parent mass
for a compound, use the Add Compounds Dialog Box.
Polarity
Resulting polarity stored in the database after tuning: positive,
negative, or both. If the compound has not been tuned, then this
value shows as <NULL>.
Charge State
Charge state for the compound: 1 to 10. To select the charge state
for a compound, use the Add Compounds Dialog Box.
Num Products
Number of product ions to be acquired for the compound:
1 to 10. To select the number of product ions for a compound,
use the Add Compounds Dialog Box.
Source Type
Ion source type for tuning the compound, where
• 0 = untuned
• 1 = ESI
• 2 = APCI
• 3 = APPI
• 4 = H-ESI
To specify the ion source type for tuning a compound, use the
Configuration Options Dialog Box.
Drug Set Names Table
Y To view the contents of the Drug Set Names table
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
The Compounds Browse Page appears.
2. In the Table list, select [DRUGSETNAME].
The Drug Set Names table contains the drug sets that you can combine for a given sequence
or tune vial. You can group multiple compounds by selecting the compounds under a
common drug set name. You can associate up to 10 compounds with a single drug set.
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Compounds Browse Page
To modify the information in the Drug Set Names table, see “Defining the Drug Sets in the
Database” on page 21.
The Drug Set Names table contains the following information for each drug set in the
database.
Parameter
Description
Drug Set
Name of the drug set in the database. To add a drug
set or to delete it from the database, use the Add
Drug Sets Dialog Box.
Compound1 to Compound10
Compounds associated with the selected drug set. To
add a compound to a drug set, use the Add Drug Sets
Dialog Box.
Source Type Table
Y To view the contents of the Source Type table
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
The Compounds Browse Page appears.
2. In the Table list, for the TSQ Quantum mass spectrometer, select
[SOURCETYPETABLE], or for the TSQ Vantage mass spectrometer, select
[SOURCETYPETABLE_VANTAGE].
The Source Type table contains the information about the compound after it has been
optimized. The QuickQuan application optimizes for a specific source type: ESI, APPI,
APCI, or H-ESI. The compound’s polarity, tune file name, and the source type used during
optimization are saved to this table.
You cannot modify the information in the Source Type table. The application updates the
Source Type table whenever an optimization run has finished.
The Source Type table contains the following information for each tuned compound in the
database.
Table 9. Source Type table parameters (Sheet 1 of 2)
Thermo Scientific
Parameter
Description
Compound
Name of a compound in the database.
Polarity
The true polarity detected after optimization.
Tune File
The template tune file (.TSQtune) used for optimization.
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Compounds Browse Page
Table 9. Source Type table parameters (Sheet 2 of 2)
Parameter
Description
Raw File
The data collected during real-time tuning.
PDF File
A report stored as a PDF file showing the content of the tune file
generated after optimization.
Source Type
The ion source type used for this compound during optimization,
where
• 0 = untuned
• 1 = ESI
• 2 = APCI
• 3 = APPI
• 4 = H-ESI
SRM Table
Y To view the contents of the SRM table
1. In the QuickQuan left pane, click Compounds.
–or–
Choose Go > Browse Compounds.
The Compounds Browse Page appears.
2. In the Table list, for the TSQ Quantum mass spectrometer, select [SRMTABLE], or for
the TSQ Vantage mass spectrometer, select [SRMTABLE_VANTAGE].
The SRM table contains information about the SRM transitions detected for a given
compound during optimization. The table can hold more than one entry for a given
compound, depending on the number of transitions selected.
The QuickQuan application updates the SRM table whenever an optimization run has
finished. To modify the information in the SRM table, see “Updating SRM Information” on
page 79.
The SRM table contains the following information for each compound in the database.
Table 10. SRM table parameters (Sheet 1 of 2)
144
Parameter
Description
Compound
Name of the compound.
Parent Mass
Detected mass of the parent compound.
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Optimization Setup Page
Table 10. SRM table parameters (Sheet 2 of 2)
Parameter
Description
Product Mass
Detected product ion mass of the parent compound.
Col Energy
Optimal collision energy of the product ion.
Q1
Peak width setting used during optimization. Q1 is set to 0.2 for
H-SRM; for other modes, Q1 is set to 0.7.
The Q1 setting is used to set the peak width for ions passed by the
Q1 mass analyzer. The lower the peak width setting, the higher
the resolution.
Q3
Peak width setting used during optimization. Q3 is always set
to 0.7.
The Q3 setting is used to set the peak width for ions passed by the
Q3 mass analyzer. The lower the peak width setting, the higher
the resolution.
Tube Lens or SLens
Optimal tube lens offset (if you are using the TSQ Quantum) or
S-Lens offset (if you are using the TSQ Vantage).
Width
Scan width used during optimization.
Max Intensity
Maximum intensity of the product ion.
Optimization Setup Page
IMPORTANT If you do not have Aria OS system installed, before you can access the
settings on the Optimization Setup page, you must first configure an autosampler. To
configure an autosampler, see “Configuring Instruments without the Aria OS System” on
page 133.
Even if you configure an LDTD autosampler, you must have the correct TSQ and LDTD
driver versions before the Optimization Setup page is available.
Use the Optimization Setup page to set up compound optimization. For details, see
“Understanding the Compound Optimization Process” on page 33.
On the Optimization Setup page, the QuickQuan application uses the information specified
in a tune plate to optimize all the compounds within the plate. The application monitors the
status of each compound during optimization, and adds the data returned from optimization
to the central database. The optimization data for each compound stored in the QuickQuan
database includes the polarity, tube lens or S-Lens offset, parent ion mass, product ion mass or
masses, collision energy, max intensity, source type, tune status report file (.pdf ), and tune
data file (.raw).
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Optimization Setup Page
Tip If your system includes a Thermo PAL autosampler with multiple injection ports,
multiple valves, and a stream selector, you can speed up the optimization process. For
details, see “Bypassing the LC Column and the Dual-Pump, Dual-Column
Configuration” on page 134.
Y To display the Optimization Setup page
In the QuickQuan left pane, click Optimization, and then click the Setup icon,
.
–or–
Choose Go > Optimization > Setup.
The Optimization Setup page contains these parameters.
Table 11. Optimization Setup page parameters (Sheet 1 of 8)
Parameter
Description
Tune and Method Files
Tune File
Specifies the generic tune file (.TSQTune) to use for the tune
plate, for example:
C:\Xcalibur\QuickQuan\Templates\
tune template.TSQTune (for the TSQ Quantum)
–or–
C:\Xcalibur\QuickQuan\Templates\
tune template_Vantage.TSQTune (for the TSQ Vantage)
If you are only acquiring data and not optimizing, a tune file
is not necessary.
Instrument Method
Specifies the base method file (.meth) that contains the
instrument settings for tune optimization, for example:
C:\Xcalibur\QuickQuan\Templates\Tune_LC_Pos.meth
(for the TSQ Quantum)
–or–
C:\Xcalibur\QuickQuan\Templates\
Tune_LC_Pos_Vantage.meth (for the TSQ Vantage)
Note This base instrument method used for optimization is
different from the instrument method used for acquisition.
The QuickQuan application uses this base method file to
create a new method for optimization, then deletes the
created method after optimization completion.
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Optimization Setup Page
Table 11. Optimization Setup page parameters (Sheet 2 of 8)
Parameter
Description
Aria AS Method
(Available only if the Aria OS system is installed) Specifies the
method file (.tmt) that contains the autosampler (AS) settings
for tune optimization.
The QuickQuan application installs the following template
file:
C:\Xcalibur\QuickQuan\Templates\Optimization.tmt
The Aria application installs the following template file:
C:\Aria Data\AS Methods\QuickQuan Opt
Template.tmt
Tip Start with a template and update the AS method as
appropriate for your system. For details on how to update
AS methods, refer to the Aria OS User Guide. Use a different
name to save the updated method file.
Aria LC Method
(Available only if the Aria OS system is installed) Specifies the
method file (.htc) that contains the LC settings for tune
optimization.
The QuickQuan application installs the following template
file:
C:\Xcalibur\QuickQuan\Templates\Optimization.htc
The Aria application installs the following template file:
C:\Aria Data\LC Methods\QuickQuan Opt
Template.htc
Tip Start with a template and update the LC method as
appropriate for your system. For details on how to update
LC methods, refer to the Aria OS User Guide. Use a
different name to save the updated method file.
PDF/RAW Files Output
Path
Thermo Scientific
Specifies the output folder where the tune status report file
(.pdf ) and tune sample data file (.raw) are stored.
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Optimization Setup Page
Table 11. Optimization Setup page parameters (Sheet 3 of 8)
Parameter
Description
Optimization Settings
Ion Source
(Not selectable if using an LDTD autosampler) Specifies the
type of ion source you are using: ESI, APCI, APPI, or H-ESI.
Note For the LDTD autosampler, the only available ion
source is ESI.
Intensity Threshold
Specifies the minimum intensity threshold for the product
ions. If a compound fails the threshold, the system skips that
compound’s optimization and proceeds to the next
compound in the list.
Range: 500 to 1000000
H-SRM
(When using an LDTD autosampler: selectable only prior to
any drug set assignment or when the tune plate data is not
from an import file) Activates tuning for H-SRM (precursor
ion peak width = 0.2 amu). The H-SRM mode is either
turned on or turned off for the entire tune plate. Compounds
tuned in H-SRM keep their H-SRM parameters during data
acquisition.
Note The mass spectrometer adjusts the user-specified
parent mass to the detected mass. This adjustment might
result in the storing of a different parent mass in the
QuickQuan database than the one you originally specified
for the compound.
Clear this check box to specify tuning for unit resolution
(precursor ion peak width = 0.7 amu).
Polarity
(Available only when the tune plate data is not from an
import file; selectable only prior to any drug set assignment)
Specifies the polarity used for optimization: Positive,
Negative, or Both. If you select Both, TSQ determines the
best polarity (positive or negative) during optimization.
Note This setting applies to the entire tune plate when you
enter the polarity manually. Once you start to apply a drug
set to the tune plate, you must clear the plate if you want to
change this setting.
If the polarity settings are imported from the tune plate data
file, then those settings apply individually to each drug set
and override the polarity specified here.
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Optimization Setup Page
Table 11. Optimization Setup page parameters (Sheet 4 of 8)
Parameter
Description
Injection Volume (ul)
(Available only if using a non-LDTD autosampler) Specifies
the sample amount to inject for each compound being
optimized. The flow rate for the infusion with the injection
volume determines how long the infusion sample is present
during the tuning session.
Range: 0 to 500 ul
Use Autosampler Infusion
During Optimization
(Available only if the autosampler supports both infusion- and
injection-based optimization) Specifies whether optimization
is based on infusion or injection.
IMPORTANT To match this infusion or injection option
selection, make sure that the file you selected for the
Instrument Method contains the correct infusion or
injection settings for the autosampler. If necessary, use the
Thermo Xcalibur Instrument Setup window to modify your
instrument method.
Plate Setup
Plate Type
(Available only if using a non-LDTD autosampler) Specifies
either the 96-well or 384-well plate type.
Autosampler Tray Name
(Available only if using a non-LDTD autosampler) Specifies
the autosampler tray that contains the compounds to be
optimized.
Desorptions Per Well
(Available only if using an LDTD autosampler; selectable
only prior to any drug set assignment or when the tune plate
data is not from an import file) Specifies the number of times
that sample desorption can occur with adequate intensity
within each well.
Default: 1
Range: 1 to 10
Note This setting applies to the entire tune plate. Once you
start to apply a drug set to the tune plate, you must clear the
plate if you want to change this setting.
If the desorptions number is imported from the tune plate
data file, then that setting overrides the number specified
here.
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Optimization Setup Page
Table 11. Optimization Setup page parameters (Sheet 5 of 8)
Parameter
Description
Wells Per Drug Set
(Available only if using an LDTD autosampler and the tune
plate data is not from an import file; selectable only prior to
any drug set assignment) Specifies the number of wells that
you plan to set up in the tune plate for each drug set.
Default: 1
Range: 1 to 96
Note This setting applies to the entire tune plate when you
specify it manually. Once you start to apply a drug set to the
tune plate, you must clear the plate if you want to change
this setting.
If the well positions are imported from the tune plate data
file, then the number of wells applies individually to each
drug set and overrides the number specified here.
Plate Serial Number
(Available only if using an LDTD autosampler) Specifies the
exact 6-digit serial number for the LazWell plate used for this
optimization run.
If you enter less than six digits for the serial number, the
leftmost missing digits autofill with zeros.
Default: 000000
Range: 000000 to 999999
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Optimization Setup Page
Table 11. Optimization Setup page parameters (Sheet 6 of 8)
Parameter
Description
Order By
(Selectable only prior to any drug set assignment or when the
tune plate data is not from an import file) Specifies whether
the QuickQuan application automatically advances the
highlights for the wells in the tune plate horizontally by row
order or vertically by column order.
Default: Order by row
Note This setting applies to the entire tune plate. Once you
start to apply a drug set to the tune plate, you must clear the
plate if you want to change this setting.
If the order setting is imported from the tune plate data file,
then that setting overrides the setting specified here.
Clears all wells in the plate of their drug set assignments.
If the H-SRM, Polarity, Desorptions Per Well, Wells Per Drug
Set, Order By, Losses/Adducts, Max. Desorptions Needed, or
Apply items were previously hidden or disabled, then clicking
Clear Plate shows and enables these fields.
(Selectable only when the well is already assigned to a drug
set) Clears the selected well of its drug set assignment.
If you are using an LDTD autosampler, then when you click
Clear Well, the QuickQuan application asks whether you
want to also clear all related wells in the same group. If you
click Yes, the application clears all wells in the group
associated with the same drug set as the selected well. If you
click No, the application cancels your clear well action.
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Optimization Setup Page
Table 11. Optimization Setup page parameters (Sheet 7 of 8)
Parameter
Description
Tune Plate graphic
Specifies the layout of the tune plate.
Click any well position in this graphic and use the Drug Set
List to assign a drug set to a well or group of wells.
The assigned well positions in the tune plate graphic
correspond to these color-coded highlights:
•
Red: At least one compound in the well (drug set) is
not optimized.
•
Orange: At least one compound in the drug set is
not optimized by the currently configured mass
spectrometer model but is optimized by another model,
and at least one compound is not optimized by the
currently selected ion source but is optimized by another
ion source.
•
Yellow: All compounds in the drug set are optimized
by the currently configured mass spectrometer model,
and at least one compound is not optimized by the
currently selected ion source but is optimized by another
ion source.
•
Dark Green: All compounds in the drug set are
optimized by the currently selected ion source, and at
least one compound is not optimized by the currently
configured mass spectrometer model but is optimized by
another model.
•
Light Green: All compounds in the drug set are
optimized by the currently configured mass spectrometer
model and the currently selected ion source.
For wells with orange or dark green highlight colors that
contain at least one compound optimized by a mass
spectrometer model other than the currently configured
model, the letter for the other model also appears.
For example, when you use the TSQ Vantage, a “Q”,
,
appears in the wells containing at least one compound not
optimized by the TSQ Vantage but optimized by the
TSQ Quantum. Conversely, when you use the TSQ
Quantum, a “V”,
, appears in the wells containing at least
one compound not optimized by the TSQ Quantum but
optimized by the TSQ Vantage.
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Optimization Setup Page
Table 11. Optimization Setup page parameters (Sheet 8 of 8)
Parameter
Description
Displays the Open dialog box that you use to import
individual text files (.txt) containing compound, drug set, or
tune plate information. For details, see “Importing
Compounds Using a Text File” on page 13, “Importing Drug
Sets Using a Text File” on page 24, or “Importing Tune Plate
Information Using a Text File” on page 54.
You can also import the compound, drug set, and tune plate
information combined in one text file. For details, see
“Importing Compound, Drug Set, and Tune Plate
Information Using a Text File” on page 57.
(When using an LDTD autosampler: selectable only prior to
any drug set assignment or when the tune plate data is not
from an import file) Opens the Losses/Adducts Dialog Box
that you use to specify these QuickQuan functions:
• Disallow product ion losses that are not very specific. The
choices are H2O, NH3, CH3, and two user-definable
losses.
• Select adducts. The choices are: M+H, M+Na, M+NH4,
and three user-definable adducts for positive ions; M-H,
M-COO, and three user-definable adducts for negative
ions.
Drug Set Selector
Current Well:
[Compound: Mass]
Displays the position of the selected or highlighted well in the
tune plate graphic. If this well is already assigned to a drug set,
then the drug set name appears. If that drug set contains only
one compound, then the compound name and mass also
appear.
(Selectable only if the tune plate data is not from an import
file) Assigns the selected drug set to the selected well.
Thermo Scientific
Max. Desorptions Needed
(Available only if using an LDTD autosampler and the tune
plate data is not from an import file) Displays the calculated
maximum number of times sample desorption is needed to
optimize the selected drug set.
Drug Set List
Displays all drug sets that you added or imported into the
database.
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Optimization Tune Report Page
Optimization Tune Report Page
You can use the Optimization Tune Report page to do the following:
• View a tune results report (.pdf file). For details, see “Viewing the Optimization Results”
on page 72.
• Open Xcalibur Qual Browser to see the raw data results for the selected compound.
The QuickQuan application generates a tune report for optimizations that fail as well as those
that succeed, as long as the optimization creates a raw file. The application automatically
displays the latest tune report for the compound, even if the compound was optimized by a
mass spectrometer model other than your currently configured model.
The tune report includes the averaged spectra, tube lens or S-Lens offset curves, breakdown
curves, and tune status information.
Y To display the Optimization Tune Report page
In the QuickQuan left pane, click Optimization, and then
click the Tune Report icon,
.
–or–
Choose Go > Optimization > Tune Report.
The Optimization Tune Report page contains these parameters.
Table 12. Optimization Tune Report page parameters (Sheet 1 of 2)
Parameter
Description
Compound List
Specifies the compound whose tune results you want to view.
If the optimization failed but the compound raw file is
available, or if the maximum intensity is below the threshold
you specified in the Configuration Options Dialog Box, a red
crossmark, , shows next to the compound name in the list.
In this case, the tune report might be missing some
information because the optimization run did not complete
successfully.
If the compound was optimized by a mass spectrometer
model other than your currently configured model, a dark
green checkmark, , shows next to the compound name in
the list.
If the compound was optimized by your currently configured
mass spectrometer model, a light green checkmark, , shows
next to the compound name in the list.
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Acquisition Templates Page
Table 12. Optimization Tune Report page parameters (Sheet 2 of 2)
Parameter
Description
Tune Report pane
(Read-only) Displays the QuickQuan optimization report
(.pdf file) for the selected compound.
Use the toolbar at the top of the pane to view, save, and print
this report.
The report file (.pdf ) is stored in the output folder that you
selected in the “Optimization Setup Page” on page 145.
Note If the selected compound was optimized by the TSQ
Quantum mass spectrometer, the tune report shows the tube
lens information. If the compound was optimized by the
TSQ Vantage mass spectrometer, both pages of this report
show the S-Lens information instead of the tube lens
information.
Refreshes the Tune Report pane.
The QuickQuan application automatically updates the
display.
Starts Xcalibur Qual Browser and loads the sample data (.raw
file) collected for the selected compound after optimization.
The .raw data file is stored in the output folder that you
selected in the “Optimization Setup Page” on page 145.
Acquisition Templates Page
Use the Acquisition Templates page to select the template files that the QuickQuan
application uses to establish the starting conditions for an assay and, if applicable, to specify
internal standards.
For details, see “Specifying Template Options” on page 97.
Y To display the Acquisition Templates page
In the QuickQuan left pane, click Acquisition, and then
click the Templates icon,
.
–or–
Choose Go > Acquisition > Templates.
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Acquisition Templates Page
The Acquisition Templates page contains these parameters.
Table 13. Acquisition Templates page parameters (Sheet 1 of 3)
Parameter
Description
Template Information
Generic Instrument Method
Specifies the file path of the instrument method (.meth file)
for automated analysis, for example:
C:\Xcalibur\QuickQuan\Templates\ColumnA.meth
(for the TSQ Quantum and non-LDTD autosampler)
–or–
C:\Xcalibur\QuickQuan\Templates\
ColumnA_Vantage.meth (for the TSQ Vantage and
non-LDTD autosampler)
–or–
C:\Xcalibur\QuickQuan\Templates\
LDTD_Acquisition.meth (for the TSQ Quantum and
LDTD autosampler)
–or–
C:\Xcalibur\QuickQuan\Templates\
LDTD_Acquisition_Vantage.meth (for the
TSQ Vantage and LDTD autosampler)
The QuickQuan application uses the generic instrument
method, along with optimized settings from the
optimization, to build the complete instrument method for
the assay.
Generic Processing Method
Specifies the file path of the processing method (.pmd file)
for automated batch analysis, for example:
C:\Xcalibur\QuickQuan\Templates\
Thermo_template_ExtStd.pmd
(for external standards)
–or–
C:\Xcalibur\QuickQuan\Templates\
Thermo_template_IntStd.pmd
(for internal standards)
The generic processing method contains a defined set of
parameters that provide the QuickQuan application with a
recipe for automatic quantitation.
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Acquisition Templates Page
Table 13. Acquisition Templates page parameters (Sheet 2 of 3)
Parameter
Description
Processing Macro Template
Specifies the Microsoft Excel template (.xls file) that was
designed to invoke a macro automatically. You can use
macros to perform custom manipulations of the data
acquisition results.
For details, see “Using a Macro” on page 137.
Note In addition to selecting the processing macro
template, you must select the Run User Defined Macros
check box in the Configuration Options Dialog Box to
perform the data reduction.
Output Path
Specifies the folder where the QuickQuan application
creates a time-and-date stamped folder to store the data and
template files for an acquisition (for example, .raw, .meth,
.pmd, and .sld files). The application downloads files for
processing to the Xcalibur data system.
Opens the Xcalibur Instrument Setup window that you use
to create a new generic instrument method.
For details, see “Creating a Generic Instrument Method”
on page 88.
Opens the Xcalibur Processing Setup window that you use
to create a new generic processing method.
For details, see “Creating a Generic Processing Method” on
page 92.
Internal Standard
Use Internal Standard
Activates the internal standard (ISTD) selections. If you
select this check box, you must specify a compound for at
least one of the following:
• Positive ISTD default
• Negative ISTD default
The ISTD lists contain all the compounds in the
QuickQuan database.
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Acquisition Templates Page
Table 13. Acquisition Templates page parameters (Sheet 3 of 3)
Parameter
Description
Positive ISTD Default
Specifies the compound to be used as the positive internal
standard.
When the QuickQuan application creates the instrument
and processing methods, it uses the positive ISTD
compound as a reference for drug sets that contain positive
compounds.
Negative ISTD Default
Specifies the compound to be used as the negative internal
standard.
When the QuickQuan application creates the instrument
and processing methods, it uses the negative ISTD
compound as a reference for drug sets that contain negative
compounds.
Additional Internal Standards Specifies any target compound and its ISTD reference.
and Reference Selections
• Target Compound: Specifies the compound that you
want to use an ISTD reference for. This target
compound must be different from the negative and
positive defaults.
• ISTD Reference: Specifies the ISTD compound to be
used as a reference for the corresponding target
compound.
To specify a compound or ISTD, click the arrow in the
table cell to display the list of compounds for your
selection. Each time you specify a compound in the last row
in the table, the QuickQuan application automatically adds
another blank row.
When the application creates the instrument and
processing methods, it uses each additional ISTD
compound as a reference for the corresponding target
compound specified in the table.
If a positive ISTD default is specified and the negative
ISTD default is not specified, or vice versa, the application
uses the first available ISTD from the Additional Internal
Standards and Reference Selections table as the default for
the one not specified.
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Acquisition Setup Page
Acquisition Setup Page
Use the Acquisition Setup page to create an acquisition sequence containing unknown
samples, calibration standard samples, quality control (QC) samples, and blank samples.
For details, see these procedures:
• “Creating a Sequence in the Acquisition Setup Page” on page 99
• “Importing a Sequence” on page 105
Y To display the Acquisition Setup page
In the QuickQuan left pane, click Acquisition, and then click the Setup icon,
.
–or–
Choose Go > Acquisition > Setup.
One row of the sequence corresponds to one sample. Each sample is defined by the settings in
the corresponding row.
For quantitative analysis, you can generate a sequence semi-automatically based on a
processing method. The QuickQuan application supports both open bracket or
non-bracketed sequences.
The Acquisition Setup page contains these parameters.
Table 14. Acquisition Setup page parameters (Sheet 1 of 7)
Parameter
Description
Toolbar
Displays the Open dialog box that you use to import a
sequence (.sld or .csv file) previously created in Xcalibur
Sequence Setup.
For details, see “Importing a Sequence” on page 105.
Moves highlight for selection up one row.
Row
Shows the number of the currently selected row.
Moves highlight for selection down one row.
Removes all samples from the sequence table.
Moves rows up to fill in empty rows from a prior deletion,
or changes the displayed number of rows (see Maximum
Rows parameter below).
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Acquisition Setup Page
Table 14. Acquisition Setup page parameters (Sheet 2 of 7)
Parameter
Description
Maximum Rows
Changes the displayed number of rows on the Acquisition
Setup page.
You enter the maximum number of rows in the
Maximum Rows box and click Compress.
Bracket Type
Specifies the bracket type applicable to the sequence to be
run. There are two choices:
• Open Bracket: Specifies that the sequence contains
one open bracket.
• Non Bracketed: Specifies that the sequence does not
contain brackets.
You can select only one of these bracket types for the
entire sequence table.
Automatically resizes each column in the sequence table
to a width that fully shows the content of the column.
Sequence Table
New Sequence
Specifies the start of a new acquisition sequence.
To indicate a new sequence, select this check box.
Drug Set
Specifies which drug set is associated with the acquisition
sequence.
If you want to change the drug set, type the new drug set
name; or click the cell, click the small arrow to the right
of the cell, and then select the desired drug set in the
Drug Set Selection dialog box.
Sample Name
Displays the name that you assign to your sample.
To change a sample name, click the cell and type the new
name.
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Acquisition Setup Page
Table 14. Acquisition Setup page parameters (Sheet 3 of 7)
Parameter
Description
Sample Type
Displays the type of sample described by the sequence
row. Different sets of sample types are presented for
different bracket types. The sample type defines how the
Xcalibur data system processes the sample data. Each
sample must be classified as one of the following Xcalibur
sample types:
• Unknown
• Blank
• Quality Control (QC)
• Standard clear
• Standard update
• Standard bracket
To change the sample type, click the cell and select a
sample type from the list.
Level
Displays the name of the level (for calibration or quality
control (QC) samples only). The level values come from
the selected processing method. If you select a new
processing method, the level values automatically update
once you click in this cell.
To change a level, click the cell and select the new level
from the list.
Sample ID
Specifies a unique identification (ID) number for each
sample.
To change the current ID number, click the cell and type
the new ID number.
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Acquisition Setup Page
Table 14. Acquisition Setup page parameters (Sheet 4 of 7)
Parameter
Description
Instrument Method
Specifies the file path and file name of the instrument
method (.meth file extension) that defines the
acquisition.
The QuickQuan application automatically populates this
parameter with the instrument method that you selected
in “Specifying Template Options” on page 97.
If you want to select a different method, click the cell and
click the small arrow to the right of the cell. In the
Select Instrument Method dialog box, select the .meth
file and click Open.
To create a method, see “Creating a Generic Instrument
Method” on page 88.
Vial Position
Specifies the vial position in the autosampler.
To change the position, click the cell and type the new
position.
IMPORTANT Make sure that you name the vial
positions with names that are valid for your
autosampler.
Injection Volume
(Not available if using the LDTD autosampler) Specifies
the injection volume in microliters of sample to be
injected.
To change the volume, click the cell and type the new
volume.
If you are using an autosampler, you can set the default
injection volume in the Autosampler dialog box in the
Xcalibur Instrument Setup window. The minimum and
maximum injection volumes that you can use depend on
the autosampler you select. The usable range depends on
the injection mode and can be smaller than the range
displayed in the status bar. For more details, consult your
autosampler manual.
Comment
Displays any comments that you have entered about the
sample.
To change the comment, click the cell and type the new
comment.
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Acquisition Setup Page
Table 14. Acquisition Setup page parameters (Sheet 5 of 7)
Parameter
Description
Dilution Factor
Displays the dilution factor that was used to prepare the
sample.
To change the dilution factor, click the cell and type the
new factor.
Valid range: 0.001 to 1000.000 (one thousand)
If you have specified a processing method for the current
sequence, the Xcalibur data system automatically enters
the Dilution Factor value from the processing method
settings.
ISTD Correction Amount
Specifies the correction amount for the internal standard.
If the value is not 0.000, the value is used in an algorithm
to correct for the case where the ISTD amounts in the
active processing method are correct, but the ISTD
amount in one or more samples is different from the
specified amount.
This correction eliminates the need to remake the samples
to the internal standard concentrations or amounts
specified in the processing method, and then rerun the
samples.
For each component defined as an ISTD, a bulk
adjustment factor can be applied to the base response of
each ISTD defined in the processing method.
• If no correction is required, confirm that a value of
0.000 is entered in the ISTD Corr Amt cell.
• If a correction is required, enter the sum of all ISTD
amounts or concentrations actually in the sample
into the ISTD Corr Amt cell for the sample requiring
adjustment. The value entered should use the same
units as specified in the processing method. Do not
type the units; for example, type 20, not 20 ng.
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Table 14. Acquisition Setup page parameters (Sheet 6 of 7)
Parameter
Description
Sample Volume
Displays the volume of a component that has been placed
in the sample. The unit for this volume is specified in the
Processing Setup window and is only included in
Xcalibur reports. The Xcalibur data system does not
convert units.
To change the sample volume, click the cell and type the
new sample volume.
If you have specified a processing method for your
sequence, the Xcalibur data system automatically enters
the units for the sample volume of the calibration and
quality control (QC) samples from the processing
method settings.
Sample Weight
Displays the amount of a component that has been placed
in the sample. The unit for this volume is specified in the
Processing Setup window and is only included in
Xcalibur reports. The Xcalibur data system does not
convert units.
To change the sample weight, click the cell and type the
new sample weight.
If you have specified a processing method for your
sequence, the Xcalibur data system automatically enters
the sample weights of the calibration and quality control
(QC) samples from the processing method settings.
Processing Method
Specifies the file path and file name of the processing
method (.pmd), that shows the QuickQuan application
how to process the raw data.
The application automatically populates this parameter
with the processing method that you selected in
“Specifying Template Options” on page 97.
If you want to select a different method, click the cell and
click the small arrow to the right of the cell. In the
Select Processing Method dialog box, select the .pmd file
and click Open.
To create a method, see “Creating a Generic Processing
Method” on page 92.
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Acquisition Aria Configuration Page
Table 14. Acquisition Setup page parameters (Sheet 7 of 7)
Parameter
Description
Calibration File
Specifies an existing calibration curve file (.xcal), rather
than have the QuickQuan application create one.
To specify a calibration file, click the cell and click the
small arrow to the right of the cell. In the
Select Calibration File dialog box, select the .xcal file and
click Open.
File Name
The QuickQuan application automatically creates the file
names for the raw and result files of the acquired sample
data. The file name is a combination of the drug set name
for the sequence, followed by an underscore and a suffix
number.
• When you select the New Sequence check box to
create a sequence, the suffix number starts at that
time at 01.
• The suffix number increments by 1 for each sample
in the sequence. For example: 01, 02, and so on.
Serial Number
(Available only if using the LDTD autosampler) Specifies
the 6-digit serial number of the LDTD LazWell plate.
If you enter less than six digits for the serial number, the
leftmost missing digits autofill with zeros.
Default: 000000
Range: 000000 to 999999
Acquisition Aria Configuration Page
IMPORTANT The Aria Configuration page is available only if you have the Aria OS
system installed on your computer.
You can use the QuickQuan application with the Aria OS system to increase the throughput
of the acquisition. For an overview, refer to the QuickQuan and Aria OS Quick Start.
Use the Aria Configuration page to specify the default AS methods and LC methods for the
Aria system. You can also specify method and LC system overrides for the individual
sequences.
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Acquisition Aria Configuration Page
Y To display the Aria Configuration page
In the QuickQuan left pane, click Acquisition, and then click the Aria icon,
.
–or–
Choose Go > Acquisition > Aria.
The Aria Configuration page contains these parameters.
Table 15. Aria Configuration page parameters (Sheet 1 of 2)
Parameter
Description
Methods
Default AS Method
Specifies the AS method (.tmt file) for the Aria OS system
to use if no AS method has been set.
To specify the AS method, click
. In the Open dialog
box, select the .tmt file and click Open.
The Aria application installs the following default file:
C:\Aria Data\AS Methods\Default.tmt
The QuickQuan application provides the following
template file:
C:\Xcalibur\QuickQuan\Templates\Acquisition.tmt
Tip Start with a template and update the AS method as
appropriate for your system. For details on how to
update AS methods, refer to the Aria OS User Guide.
Use a different name to save the updated method file.
Default LC Method
Specifies the LC method (.htc file) for the Aria OS system
to use if no LC method has been set.
To specify the LC method, click
. In the Open dialog
box, select the .htc file and click Open.
The Aria application installs the following default file:
C:\Aria Data\LC Methods\Default.htc
The QuickQuan application provides the following
template file:
C:\Xcalibur\QuickQuan\Templates\Acquisition.htc
Tip Start with a template and update the LC method as
appropriate for your system. For details on how to
update LC methods, refer to the Aria OS User Guide.
Use a different name to save the updated method file.
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Acquisition Aria Configuration Page
Table 15. Aria Configuration page parameters (Sheet 2 of 2)
Parameter
Description
Available LC Systems
LC System 1 to LC System 4
Displays the status of the LC Systems. If a system is
unavailable, its label appears grayed.
To change the availability of an LC System, refer to the
Aria OS User Guide.
Batch Overrides Option and Table
Use Batch Overrides
Activates the Batch Overrides table. If activated, the
QuickQuan application uses the specified overrides for
the methods and LC systems. If not activated, it uses the
defaults.
Drug Set
Displays the drug set name for each sequence, in the
Batch Overrides table. The sequence row number from
the “Acquisition Setup Page” on page 159 also appears.
AS Method
Specifies a method to override the default AS method for
the sequence.
To specify an override method, click the small arrow to
the right of the cell. In the Open dialog box, select the
.tmt file and click Open.
LC Method
Specifies a method to override the default LC method for
the sequence.
To specify an override method, click the small arrow to
the right of the cell. In the Open dialog box, select the
.htc file and click Open.
LC1 to LC4
Specifies the LC systems for each sequence.
To change the LC systems for a sequence, select or clear
the LC check boxes in the corresponding row.
Tip You can copy (CTRL+C) and paste (CTRL+V) the information in the Batch
Overrides table, except for the Drug Set name. For multiple instances of the QuickQuan
application, you can copy from the table of one instance and paste into the table of
another instance. Or, you can copy and paste information within the same table.
Pick any area of the table to copy from, small or large, as long as the destination area to
paste to contains the same exact number of rows and columns. Select just the first column
to select the entire row. If the area you are copying contains more rows or columns than
the destination area, you lose the information in the overflow rows and columns.
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C
QuickQuan Page Reference
Acquisition Results Summary Page
Acquisition Results Summary Page
Use the Acquisition Results Summary page to display and review the quantitation results.
For details, see “Reviewing the Results” on page 127.
Y To display the Acquisition Results Summary page
In the QuickQuan left pane, click Acquisition, and then click
the Results Summary icon,
.
–or–
Choose Go > Acquisition > Results Summary.
The Acquisition Results Summary page contains these parameters.
Parameter
Description
Results
Root Directory
Specifies the folder that contains the results, for example:
your_output_folder\timestamp_folder_for_selected_acquisition
Combined
Sequence
Specifies the created acquisition sequence file (.sld) that combines all
sequences (drug sets) in the assay.
Click View to open the Xcalibur Quan Browser window and show the
contents of the combined sequence.
Refreshes the Results table.
Starts Xcalibur Qual Browser and loads the raw data collected in the
acquisition.
Starts Xcalibur Quan Browser and loads the raw data collected in the
acquisition.
Results Table
168
Sequence Name
Lists the individual acquisition sequence files (.sld files) that make up
the combined sequence.
Date
Lists the date when the QuickQuan application ran the sequences.
Raw Files
Lists the number of generated raw data files.
Results
Lists the number of generated result data files.
Path
Lists the path for the folder where the QuickQuan application stores
the data and template files for the acquisition (for example, .raw,
.meth, .pmd, .sld, and .xls files).
QuickQuan 2.4 User Guide
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D
QuickQuan Menu and Toolbar Reference
This appendix provides a reference to the QuickQuan menus, toolbar, and status bar.
Contents
• File Menu
• Go Menu
• Reports Menu
• View Menu
• Help Menu
File Menu
The File menu contains these commands.
Table 16. File menu commands (Sheet 1 of 2)
Keyboard
Shortcut
Command
Description
New
Populates the QuickQuan pages with the
default settings. Used to create a new
QuickQuan assay file (.aql).
Open
Displays the Open dialog box. Used to open CTRL+O or
a saved QuickQuan assay file (.aql).
ALT+F+O
Save
Saves any changes to the current (open)
QuickQuan assay file (.aql).
Save As
Opens the Save As dialog box to save a new ALT+F+A
or changed QuickQuan assay file (.aql) with
a new file name.
Open Database
Opens the Select Data Source Dialog Box to ALT+F+D
create or choose file data sources and
machine data sources.
CTRL+N or
ALT+F+N
CTRL+S or
ALT+F+S
See “Selecting a File Data Source” on page 5.
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QuickQuan Menu and Toolbar Reference
File Menu
Table 16. File menu commands (Sheet 2 of 2)
Command
Description
Import Acquisition
Sequence—From File
Displays the Open dialog box to import an
acquisition sequence as a sequence file (.sld)
or an Excel file (.csv).
Keyboard
Shortcut
ALT+F+I+F
See “Importing a Sequence” on page 105.
Import Acquisition
Opens the Import Sequence Templates
Sequence—From Template Dialog Box to import an acquisition
sequence as an Excel template (.xls) plus a
sequence template (.sld).
ALT+F+I+T
See “Importing Excel and Sequence
Templates” on page 106.
Export Methods
Opens the Export Methods Dialog Box to
export methods for use with other
applications. You can export the generic
instrument method (.meth file) and
processing method (.pmd file) for any drug
sets in the QuickQuan database.
ALT+F+E
See “Exporting the Instrument and
Processing Methods” on page 124.
Note This command is active only when
you are in the Acquisition Templates Page.
Print
Opens the Print dialog box to print the
content of the QuickQuan status page.
CTRL+P or
ALT+F+P
Print Preview
Opens the print preview showing the first
page of the QuickQuan status page.
ALT+F+V
Print Setup
Opens the Print Setup dialog box to specify
printing parameters for the content in the
QuickQuan window.
ALT+F+R
Recently Accessed Files List
Opens the selected file.
Choose the file name of the recently accessed
QuickQuan file that you want to open.
Exit
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QuickQuan 2.4 User Guide
Closes the QuickQuan application.
ALT+F+X
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D
QuickQuan Menu and Toolbar Reference
Go Menu
Go Menu
The Go menu contains these commands.
Keyboard
Shortcut
Command
Description
Browse Compounds
Opens the Compounds Browse Page where you ALT+G+B
manage your compounds, drug sets, and SRM
information.
Optimization—Setup
Opens the Optimization Setup Page where you
set up optimization data.
Optimization—Status
Opens the Optimization Status page where you ALT+G+O+T
view status messages during the optimization
run.
Optimization—Tune
Report
Opens the Optimization Tune Report Page
where you review tune reports containing
optimization results.
ALT+G+O+S
ALT+G+O+R
Acquisition—Templates Opens the Acquisition Templates Page where
you select the acquisition template files and
specify internal standards.
ALT+G+A+M
Acquisition—Setup
Opens the Acquisition Setup Page where you
create an acquisition sequence.
ALT+G+A+S
Acquisition—Aria
(Available only if you have the Aria OS system ALT+G+A+A
installed) Opens the Acquisition Aria
Configuration Page where you specify the
default methods and batch overrides for the Aria
OS system.
Acquisition—Status
Opens the Acquisition Status page where you
ALT+G+A+T
view status messages during the acquisition run.
Acquisition—Results
Summary
Opens the Acquisition Results Summary Page
where you review the quantitation results.
ALT+G+A+R
Run
Opens the Configuration Options Dialog Box
where you start an optimization or acquisition
run.
ALT+G+R
See “Running an Optimization” on page 61 or
“Running an Acquisition” on page 115.
Stop
Thermo Scientific
Stops the current optimization or acquisition
run.
ALT+G+S
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QuickQuan Menu and Toolbar Reference
Reports Menu
Reports Menu
The Reports menu contains these commands.
Command
Description
Acquisition
Summary Report
Opens the Browse for Folder dialog box to specify a
location for the acquisition summary report.
Keyboard
Shortcut
ALT+R+A
For example:
your_output_folder\timestamp_folder_for_selected_
acquisition
The QuickQuan application generates the report
automatically in a Microsoft Excel file (.xls). The
report concatenates every acquisition report for each
sequence of the assay into a single acquisition
summary report.
Each time the acquisition summary report is run, the
QuickQuan application adds the new data to the data
already existing in the report. This might result in
duplicate entries that have the same component name,
file name, and sample ID. In this case, the application
prevents duplicate data in the acquisition summary
report by retaining only the most recent data for a
particular component/file name/sample ID set.
See “Generating an Acquisition Summary Report” on
page 129.
Optimization
Summary Report
The QuickQuan application generates the report
automatically in a Microsoft Excel file (.xls). The
report shows the compound information that the
application collected during optimization using the
current tune plate.
ALT+R+O
See “Generating an Optimization Summary Report”
on page 78.
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QuickQuan Menu and Toolbar Reference
View Menu
View Menu
The View menu contains these commands.
Keyboard
Shortcut
Command
Description
Toolbar
Displays or hides the QuickQuan toolbar
(see “Toolbar and Status Bar” on page 173).
ALT+V+T
Status Bar
Displays or hides the QuickQuan status bar
(see “Toolbar and Status Bar” on page 173).
ALT+V+S
Toolbar and Status Bar
The QuickQuan window contains a toolbar at the top of the window below the menus, and a
status bar at the bottom of the window.
Y To show or hide the toolbar
Choose View > Toolbar.
The toolbar contains these shortcut icons for frequently used menu commands.
Icon
Description
New
Populates the QuickQuan pages with the default settings to
create a new QuickQuan assay file (.aql).
Open
Displays the Open dialog box to open a saved QuickQuan assay
file (.aql).
Save
Saves any changes to the current (open) QuickQuan assay file
(.aql).
Run
Displays the Configuration Options Dialog Box to run the
selected optimization or acquisition.
See “Running an Optimization” on page 61 or “Running an
Acquisition” on page 115.
Stop
Stops the current optimization or acquisition run.
Y To show or hide the status bar
Choose View > Status Bar.
At the bottom left side of the QuickQuan window, the status bar displays a text description of
the menu command or toolbar icon that the cursor arrow is pointing to. If the cursor arrow is
pointing to something other than a command or icon (for example, the menu label “File”),
the Status Bar displays the text “For Help, press F1.”
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QuickQuan Menu and Toolbar Reference
Help Menu
Help Menu
The Help menu contains these commands.
174
Keyboard
Shortcut
Command
Description
QuickQuan Help
Displays the Help topics for the QuickQuan
application.
ALT+H+H
Glossary
Displays the Glossary.
ALT+H+G
How to Use Help
Displays information for using the Help.
ALT+H+U
About QuickQuan
Displays the QuickQuan version information, the
release and copyright date, and the user license
agreement.
ALT+H+A
QuickQuan 2.4 User Guide
Thermo Scientific
I
Index
Symbols
C
.aql file, saving 115
calibration curves
Quan Browser, figure 129
settings 95
calibration levels, creating 94
calibration parameters 41
charge state, selecting 12
column order, setting 45
combined information text file 59, 60
compounds
Add Compounds dialog box 19
adding manually 11
compounds table 30, 141
deleting 17
importing 13, 17
optimization settings 33
viewing 29
Compounds Browse page 29, 30, 139
Configuration Options dialog box
description 67
for acquisition 116, 117, 118, 119
for optimization 62, 63, 64
A
acquiring data 87, 115
Acquisition Aria Configuration page 165
acquisition results summary 127
Acquisition Results Summary page 168
acquisition sequences
creating 99
example, figure 101
Excel template, figure 107
importing 99
importing Excel template 106
importing sequence template 106
reuse settings 88
running 115
stopping 123
Acquisition Setup page 159
acquisition status, displaying 122
acquisition summary report 129
Acquisition Templates page 97, 155
adducts, selecting 46
Aria OS system
for configuration 134
for optimization 36, 41, 62, 65
autosampler tray, selecting 44
autosampler, Thermo PAL 34
B
backup for database 4
bracket type 100, 104, 106, 111, 160
Thermo Scientific
D
data source, selecting 5, 6, 7, 8
databases
about 3
backup 4
limit 3
permissions 4
selecting 9
selecting data source 5, 6, 7, 8
devices standby, setting 120
documentation vii
drug set selector 49
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Index: E
drug sets
Add Drug Sets dialog box 27
adding manually 21
described 21
drug set selector 49
drug set table 31, 142
drug set text file 24
importing 24
selecting 49
tune plate 49
viewing 29
internal standards, specifying 92, 93, 95, 97
ion source, selecting 42
L
LazWell plate 45, 100, 105, 109, 114
LC methods 41
LDTD autosampler 44, 49, 51, 100
levels, creating calibration 94
Login dialog box 8
losses, selecting 46
Losses/Adducts dialog box 46
E
Excel
acquisition summary report 129
optimization summary report 78
sequence template 106, 112
template, figure 107
tune report 78
Export Methods dialog box 124
exporting instrument and processing methods 124
F
File menu 169
Fill Down dialog box 102
M
macros, selecting 98
manuals vii
mass window width, setting 120
maximum desorptions needed 42, 49, 51, 52
methods
generic instrument method 88
generic processing method 92
generic, selecting 98
LC 41
minimum intensity threshold, setting 42
N
G
generic tune files, selecting 41
Go menu 171
number of masses, setting 120
number of products ions, selecting 12
O
H
Help menu 174
highlight colors, tune plate 50
H-SRM, selecting 42
I
Import Sequence Templates dialog box 111
importing
acquisition sequence 105
compounds 13
drug sets 24
Excel and sequence templates 111
SRM information 79
infusion-based optimization 43, 149
injection-based optimization 43, 149
instrument methods
creating 88
generic, selecting 98
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optimization
about 33
Optimization Setup page 37, 38, 39, 40, 145
Optimization Tune Report page 154
optimized settings 33
reuse settings 35
reviewing results 72
running 61
Optimization Setup page 37, 38, 39, 40, 145
Optimization Tune Report page 154
output folder 98, 123
P
PDF files
acquisition output folder, figure 122
output folder 42, 98, 123
peak detection, settings 96
plate serial number, setting 45, 100
plate type, selecting 43
Thermo Scientific
Index: R
polarity, selecting 42
postprocessing after acquisition 131
processing methods
creating 92
generic, selecting 98
product ions, selecting number 12
R
raw data files
acquisition 87
acquisition output folder, figure 122
output folder 41, 42, 123
output folder, acquisition 98
reports
acquisition summary 127, 129
optimization summary 78
Reports menu 172
results
acquisition, displaying 127
summary 127
row order, setting 45
S
sample desorption, setting 44
sample types 113, 161
Select Data Source dialog box 7
Select Database dialog box 9
selected reaction monitoring (SRM) 79
sequence table 100, 102
sequences
copying from Excel 104
creating 99
creating Excel template 106
creating sequence template 109
example, figure 101
Excel template 106, 112
Excel template, figure 107
importing 99
importing Excel template 106
importing sequence template 106
sequence template 113
sequence template, figure 110
source type table 143
SRM information
deleting 82
importing 79
updating 79
SRM table 144
Thermo Scientific
T
text files
combined information 59, 60
compounds 13, 15
drug sets 24
SRM information 80
tune plate information 56
Thermo Foundation Instrument Configuration window 133,
134
Thermo PAL autosampler 34
threshold percent, setting 120
toolbar and status bar 173
tune parameters, described 41
tune plate
graphic 48
highlight colors 50
information text file 56
inspecting 66
selecting drug sets 49
setting up 45
tune report
Excel summary 78
figure 75
viewing 72
U
Update SRM Information dialog box 82
user guides vii
V
View menu 173
W
wells for drug set, setting 44
X
Xcalibur data system
Instrument Setup window
for acquisition 88, 89, 91, 157
for optimization 34, 43, 149
Processing Setup window 92, 93, 157
Qual Browser 73, 74, 154, 155, 168
Quan Browser 128
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