Thermo Fisher Scientific Xcalibur 2.0 Creating and Searching Libraries User guide

For Research Use Only

Not for use in Diagnostic Procedures

Xcalibur®

Getting Productive:

Creating and Searching Libraries

XCALI-97102 Revision C June 2006

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Thermo Electron Corporation Xcalibur: Getting Productive with Libraries v

Preface ............................................................................................vii

About This Guide .....................................................................vii

Related Documentation ............................................................vii

Safety and Special Notices........................................................viii

Contacting Us..........................................................................viii

Assistance..............................................................................viii

Changes to the Manual and Online Help................................ix

Chapter 1 Overview of Library Browser............................................................1

Quick Reference Guide...............................................................2

Specifying the Peak Detection Algorithm....................................4

Chapter 2 Managing Libraries ............................................................................7

Creating a Library Entry with

Spectral Data............................................................................8

Opening a Raw Data File (.raw) in Qual Browser ....................8

Viewing a Spectrum in Qual Browser.....................................10

Subtracting Background Spectra ............................................12

Exporting a Spectrum to Library Browser ..............................14

Editing a User Library...............................................................16

Editing Spectrum Information ...............................................16

Adding an Entry to and Naming a Library.............................18

Attaching a Chemical Structure to a Library Entry.................19

Appending Additional Compounds to the User Library.........27

Managing the NIST Libraries ...................................................34

Adding a Library ....................................................................35

Deleting a Library ..................................................................36

Copying a Library ..................................................................36

Converting Libraries to Another Format ...................................37

Contents

vi Xcalibur: Getting Productive with Libraries Thermo Electron Corporation

Chapter 3 Searching Libraries ......................................................................... 41

Setting Up to Search Libraries Automatically ............................42

Specifying Search Parameters in the Qual View......................42

Specifying Report Options for Library Searches .....................46

Specifying Raw Data Files in Sequence Setup.........................52

Reprocessing Raw Files and Printing Reports............................55

Initiating a Library Search from Qual Browser..........................58

Searching a Library by Using Library Browser...........................62

Customizing the Library Browser Layout ..................................68

Appendix A Example Reports............................................................................... 69

Reports from a Library Search Using Sequence Setup ...............70

Report from a Library Search Using Qual Browser....................80

Report from a Library Search Using Library Browser ................81

Index ................................................................................................... 83

Thermo Electron Corporation Xcalibur: Getting Productive with Libraries vii

Preface

About This Guide Welcome to Xcalibur®, the Thermo Electron mass spectrometry data

system. Xcalibur includes all the software needed to create, search, and

edit libraries.

This Xcalibur Getting Productive manual guides you through the following

procedures:

• How to create and edit custom libraries for MS, MS/MS, or MSn

spectra

• How to search multiple libraries

• How to print library search results in custom-designed reports

In addition to this guide, Thermo Electron provides the following

documents for Xcalibur 2.0:

• Administrator’s Guide: Configuring Xcalibur Software for Compliance with

21CFRPart11

• Getting Productive: Processing Setup and the Analysis of Quantitation Data

• Getting Productive: Qualitative Analysis

• Getting Productive: Quantitative Analysis

• Getting Productive: Creating and Searching Libraries

•Getting Productive: Xreports

• Help available from within the software

Preface

viii Xcalibur: Getting Productive with Libraries Thermo Electron Corporation

Safety and Special

Notices

Make sure you follow the precautionary statements presented in this guide.

The safety and other special notices appear in boxes.

Safety and special notices include the following:

Contacting Us There are several ways to contact Thermo Electron.

Assistance For new product updates, technical support, and ordering information,

contact us in one of the following ways:

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www.thermo.com/finnigan

Contact Technical Support

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Fax: 1-561-688-8736

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IMPORTANT Highlights information necessary to avoid damage to

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optimal performance of the system.

Note Highlights information of general interest.

Tip Helpful information that can make a task easier.

Preface

Thermo Electron Corporation Xcalibur: Getting Productive with Libraries ix

Changes to the Manual

and Online Help

To suggest changes to this guide or to the Help, use either of the following

methods:

• 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]

Thermo Electron Corporation Xcalibur: Getting Productive with Libraries 1

Chapter 1 Overview of Library Browser

The Library Browser is part of Xcalibur®, the Thermo Electron mass

spectrometry data system.

This chapter gives you an overview of the library tools in Xcalibur and how

to use them to create and use personally customized libraries. The

introduction describes the basic features of Library Browser and outlines

what is covered in this manual. A Quick Reference Guide summarizes the

steps for creating, editing, and searching custom libraries and printing

reports of the results.

This chapter also provides information about how to choose a peak

detection algorithm for Xcalibur to use when performing library searches.

This chapter contains the following sections:

• Quick Reference Guide

• Specifying the Peak Detection Algorithm

Note Throughout this manual, the term Library Browser is used

synonymously with the term NIST MS Search to refer to the NIST MS

Search desktop.

1 Overview of Library Browser

Quick Reference Guide

2Xcalibur: Getting Productive with Libraries Thermo Electron Corporation

Quick Reference

Guide

Figure 1 is a Quick Reference Guide that provides a one-page summary of

the steps you perform to create, edit, and search libraries and to print reports

by using Xcalibur.

First, create a custom user library of MS/MS or MSn spectra, one entry at a

time. To include a spectrum in a library entry, display a (qualitative) .raw

file data in Qual Browser. In Qual Browser, you can enhance a spectrum by

averaging several scans and by subtracting background scans. Then export

the enhanced spectrum to Library Browser. See “Creating a Library Entry

with Spectral Data” on page 8 for more information on this process.

Second, when the spectrum is exported to Library Browser, you can edit the

spectrum information. For example, you can change the name of the entry

or specify the molecular weight or the CAS (Chemical Abstract Service)

registry number. You can even attach a chemical structure to the library

entry. You can also select which mass-to-charge ratios to include in the

entry. See “Editing a User Library” on page 16 for more information.

Finally, Xcalibur provides three ways to search libraries and print custom

reports:

• Automatically, by using raw (.raw) or result (.rst) files in Sequence Setup

• Manually, by using a single spectrum in Qual Browser

• Manually, by using a single spectrum exported to Library Browser

Refer to “Setting Up to Search Libraries Automatically” on page 42,

“Initiating a Library Search from Qual Browser” on page 58, and

“Searching a Library by Using Library Browser” on page 62 for more

information on searching.

Use the Qual view options in the Processing Setup window to specify a

processing method to print reports automatically. Then reference this

processing method to specify a sequence of files in Sequence Setup. When

you reprocess a sequence, Xcalibur prints the reports.

If you manually search for search results that match a single spectrum, print

the results by using the command File > Print either in Qual Browser or in

Library Browser.

Note For MS/MS and MSn spectra, however, be careful to delete none

of the masses that Xcalibur detected because the presence of a particular

mass-to-charge ratio, rather than its intensity, is an essential criterion for

identification of a compound.

1 Overview of Library Browser

Quick Reference Guide

Thermo Electron Corporation Xcalibur: Getting Productive with Libraries 3

Figure 1. Quick Reference Guide

Create a Library Spectrum

Create the Library Entry

Search Libraries and Print Reports

Automatically, using .raw or .rst files

Manually, using a single spectrum

Collected Printed Reports

Open a raw

file in Qual

Browser

Display a

spectrum

Export

spectrum to

Library Browser

Specify entry

name, CAS#,

MW, in Library

Browser

Name the

library

Attach a

structure

(optional)

Append other

spectra to

library

Specify search

parameters in

Processing Setup

Specify sequence

in Sequence

Setup

Batch reprocess:

choose to print

reports

Open a .raw file

in Qual Browser,

and display the

spectrum Export spectrum

to Library Browser

Specify library

options; search

Specify library

options; search Print report

Print reports

1 Overview of Library Browser

Specifying the Peak Detection Algorithm

4Xcalibur: Getting Productive with Libraries Thermo Electron Corporation

Specifying the Peak

Detection Algorithm

Specify how Xcalibur finds and processes chromatogram peaks by choosing

one of three algorithms: ICIS, Genesis, or Avalon. The ICIS peak detection

algorithm has been designed for MS data and has superior peak detection

efficiency at low MS signal levels. This is the Xcalibur default peak detection

algorithm. The Genesis peak detection algorithm is the original Xcalibur

peak detection algorithm. This algorithm has been provided for backward

compatibility with Xcalibur 1.0 studies. The Avalon peak detection

algorithm supports detectors other than MS and detects negative

chromatographic peaks and shoulders more accurately than Genesis or

ICIS.

For the examples in this manual, specify the ICIS algorithm:

1. Open Qual Browser from the Roadmap view of Xcalibur Home Page.

2. Open a .raw file and click the pin in the Chromatogram view to select

it.

3. Right-click the Chromatogram view and choose Peak Detection and

then either Set Peak Detection Algorithm and Detect in this Plot or

Set Peak Detection Algorithm and Detect in all Plots (see Figure 2).

Figure 2. Chromatogram view

1 Overview of Library Browser

Specifying the Peak Detection Algorithm

Thermo Electron Corporation Xcalibur: Getting Productive with Libraries 5

4. Select the ICIS peak detection algorithm. Xcalibur automatically

integrates the peak using the ICIS algorithm.

5. Specify mass tolerance and mass precision (see Figure 3).

a. Select Display > Mass Options. The Global Mass Options dialog

box appears.

b. Specify a mass tolerance bandwidth in the Mass Tolerance box to

calculate spectrum averages, to add and subtract spectra, and to

convert profile data to centroid data. Specify the units of mass

tolerance as mmu or ppm.

c. Specify a mass precision number from 0 to 5 in the Decimals box.

Xcalibur applies a number of decimal places to mass intensity values

for data processing calculations. Click OK.

Note For new processing methods only, you can choose either the ICIS,

Genesis, or Avalon Xcalibur peak detection algorithm as the default

setting for each type of detector. From the Roadmap view of the Home

Page, choose Tools > Configuration and select the appropriate default

option on the Peak Detection page.

Figure 3. Global Mass Options dialog box

1 Overview of Library Browser

Specifying the Peak Detection Algorithm

6Xcalibur: Getting Productive with Libraries Thermo Electron Corporation

6. Specify the relative scale (see Figure 4).

a. Select the chromatogram view, right-click the view, and choose

Display Options.

b. Click the Axis tab to display the Axis page.

c. Under the Y-axis Units area, select the Relative option. (Xcalibur

uses the Relative scale to calculate mass spectral data and the

Absolute scale to calculate UV/PDA/other data.) Click OK.

Figure 4. Display Options dialog box - Chromatogram Axis page

Thermo Electron Corporation Xcalibur: Getting Productive with Libraries 7

Chapter 2 Managing Libraries

Use the Xcalibur data system to create a custom library of MS/MS spectra.

The Xcalibur data system includes a subset of the NIST mass spectral library

called nistdemo. The NIST/EPA/NIH Main Library contains more than

100,000 compounds whose MS-type spectra were obtained primarily in

electron ionization (EI) scan mode. You might want to create a custom

library that includes MS/MS spectra or spectra of MSn analyses.

This chapter contains the following sections:

•Creating a Library Entry with Spectral Data

•Editing a User Library

•Managing the NIST Libraries

•Converting Libraries to Another Format

Note Refer to the online Help for more information: Choose Help on

the menu bar in any Xcalibur window. For assistance with Library

Browser specifically, choose Help > Help Topics on the Library Browser

menu bar.

2 Managing Libraries

Creating a Library Entry with Spectral Data

8Xcalibur: Getting Productive with Libraries Thermo Electron Corporation

Creating a Library

Entry with

Spectral Data

To create a library entry with MS or MS/MS (or MSn) spectral data, use the

Qual Browser window. creating a library entry with your spectral data

The procedure in this section uses steroid data. The raw data files are

included with the Xcalibur data system in the C:\Xcalibur\examples\data

directory.

To create a library entry, complete the following tasks detailed in this

section:

•Opening a Raw Data File (.raw) in Qual Browser

•Viewing a Spectrum in Qual Browser

•Subtracting Background Spectra

•Exporting a Spectrum to Library Browser

Opening a Raw Data File

(.raw) in Qual Browser

To view MS/MS raw data, use the Qual Browser window. Open a data file

to expand the Qual Browser menu bar.

To display the raw data of a steroids data file

1. Display the Xcalibur Home Page from the Microsoft®Windows®

Desktop in either of the following ways:

• Click Start > Programs > Xcalibur > Xcalibur.

• Double-click the Xcalibur shortcut on the desktop.

2. Click the Qual Browser button on the Xcalibur Home Page to display

the Qual Browser window.

3. Choose File > Open or click the Open button in the toolbar to display

the Open Raw File dialog box.

2 Managing Libraries

Creating a Library Entry with Spectral Data

Thermo Electron Corporation Xcalibur: Getting Productive with Libraries 9

4. Browse to the Xcalibur\examples\data\steroids14.raw file (see Figure 5).

5. Select the Add: Window option button and click Open to display the

data for the steroids (see Figure 5).

Leave the Qual Browser window open, and go on to the next section,

“Viewing a Spectrum in Qual Browser” .

Figure 5. Open Raw File dialog box, showing the selection of

steroids14.raw

2 Managing Libraries

Creating a Library Entry with Spectral Data

10 Xcalibur: Getting Productive with Libraries Thermo Electron Corporation

Viewing a Spectrum in

Qual Browser

To view a mass spectrum, use the interactive cells of the Qual Browser

window. This procedure continues from the previous section, “Opening a

Raw Data File (.raw) in Qual Browser” on page 8.

To display a mass spectrum of the raw data in a window containing four

cells

1. Confirm that Xcalibur displays the Chromatogram view as shown in

Figure 6. If it does not, do the following:

a. Choose View > Info Bar to hide the Information bar.

b. Click the Maximize button in the upper right corner of the window

to enlarge the window display area.

c. Choose Grid > Delete > All Cells to display a single cell.

d. Choose View > Chromatogram to display only the chromatogram

in the cell.

Figure 6. Qual Browser window, showing the Chromatogram view of steroids14.raw

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Thermo Fisher Scientific Xcalibur 2.0 Creating and Searching Libraries User guide

Thermo Fisher Scientific Xcalibur 2.0 Creating and Searching Libraries User guide

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