Xcalibur Creating and Searching Libraries

Technical information contained in this publication is for reference purposes only and is subject to change without notice. Every effort has been made to supply complete and accurate information; however, Thermo Electron Corporation assumes no responsibility and will not be liable for any errors, omissions, damage, or loss that might result from any use of this manual or the information contained therein (even if this information is properly followed and problems still arise).

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Printing History: Revision A printed in May 2003.Software Revision: Xcalibur 1.4

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Contents

Read This First ............................................................................................................................ iii

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

Abbreviations .......................................................................................................................................... v

Typographical Conventions ................................................................................................................... ixData Input ............................................................................................................................. ixBoxed Information................................................................................................................. xTopic Headings..................................................................................................................... xi

Reply Cards ........................................................................................................................................... xii

Overview of Library Browser .................................................................................................. 1-1

1.1 Quick Reference Guide.............................................................................................................. 1-2

1.2 Specifying the Peak Detection Algorithm ................................................................................. 1-4

Creating a Custom Library of Spectra ................................................................................... 2-1

2.1 Creating a Library Entry with Your Spectral Data..................................................................... 2-2Opening a Raw Data File (.raw) in Qual Browser .............................................................. 2-2Viewing a Spectrum in Qual Browser ................................................................................. 2-3Subtracting Background Spectra ......................................................................................... 2-6Exporting a Spectrum to Library Browser .......................................................................... 2-9

2.2 Editing a User Library.............................................................................................................. 2-10Editing Spectrum Information........................................................................................... 2-10Adding an Entry to and Naming a Library ........................................................................ 2-12Attaching a Chemical Structure to a Library Entry........................................................... 2-13Appending Additional Compounds to the User Library ................................................... 2-21

Searching Libraries Automatically ......................................................................................... 3-1

3.1 Setting Up to Search Libraries Automatically ........................................................................... 3-2Specifying Search Parameters and Report Options in Processing Setup ............................ 3-2Specifying Raw Data Files in Sequence Setup.................................................................. 3-12

3.2 Reprocessing Raw Files and Printing Reports ......................................................................... 3-15

_______________ Finnigan Xcalibur: Getting Productive with Libraries __________________ i

Contents

Searching Libraries from Qual Browser and Library Browser ........................................... 4-1

4.1 Initiating a Library Search from Qual Browser......................................................................... 4-2

4.2 Searching a Library by Using Library Browser ........................................................................ 4-6

4.3 Customizing the Library Browser Layout ............................................................................... 4-12

Adding and Converting Libraries ........................................................................................... 5-1

5.1 Adding Libraries to and Deleting or Copying Libraries from the NIST Libraries.................... 5-2

5.2 Converting Libraries to Another Format ................................................................................... 5-3

Example Reports ...................................................................................................................... A-1

A.1 Reports from a Library Search Using Sequence Setup .............................................................A-2

A.2 Report from a Library Search Using Qual Browser ................................................................A-13

A.3 Report from a Library Search Using Library Browser............................................................A-15

ii ___________________Finnigan Xcalibur: Getting Productive with Libraries________________

Read This First

Welcome to Xcalibur®, the Thermo Electron Finnigan™ mass spectrometry data system! Xcalibur includes all the software you need 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 your MS, MS/MS, or MSn spectra

• How to search multiple libraries

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

Getting Productive: Creating and Searching Libraries contains the following chapters:

Chapter 1: Overview and Installation of the Library Browser provides a Quick Reference Guide and describes how to include the NIST MS Search software in your Xcalibur data system.

Chapter 2: Creating a Custom Library of Spectra demonstrates how to create and edit a user library.

Chapter 3: Searching Libraries Automatically shows how to find spectra to compare to your qualitative analytical results, and then shows how to print the results.

Chapter 4: Searching Libraries from Qual Browser and Library Browser demonstrates how to search libraries both from the Qual Browser window and from the Library Browser windows.

Chapter 5: Adding and Converting Libraries discusses the Xcalibur data system’s capability to add, delete, or copy libraries from the NIST libraries list and to convert libraries to another format.

Appendix A: Example Reports shows the printed results of the procedures described in this manual.

Perform the procedures in this manual on your Thermo Finnigan instrument. If you need assistance, refer to the online Help, the Getting Started manual for your instrument, or an appropriate Xcalibur Getting Productive manual.

_________________ Finnigan Xcalibur: Getting Productive with Libraries _______________ iii

Read This FirstChanges to the Manual and Online Help

Changes to the Manual and Online HelpTo suggest changes to this manual or the online Help, please send your comments to:

Editor, Technical PublicationsThermo Electron San Jose355 River Oaks ParkwaySan Jose, CA 95134-1991U.S.A.

You are encouraged to report errors or omissions in the text or index. Thank you.

iv __________________Finnigan Xcalibur: Getting Productive with Libraries________________

Read This First_____________________________________________________________ Abbreviations

AbbreviationsThe following abbreviations are used in this and other manuals and in the online Help.

A ampere

ac alternating current

ADC analog-to-digital converter

AP acquisition processor

APCI atmospheric pressure chemical ionization

API atmospheric pressure ionization

ASCII American Standard Code for Information Interchange

b bit

B byte (8 b)

baud rate data transmission speed in events per second

°C degrees Celsius

CD compact disc

CD-ROM compact disc read-only memory

cfm cubic feet per minute

CI chemical ionization

CIP carriage and insurance paid to

cm centimeter

cm3 cubic centimeter

CPU central processing unit (of a computer)

CRC cyclic redundancy check

CRM consecutive reaction monitoring

<Ctrl> control key on the terminal keyboard

d depth

Da dalton

DAC digital-to-analog converter

dc direct current

DDS direct digital synthesizer

DEP direct exposure probe

DS data system

DSP digital signal processor

_________________ Finnigan Xcalibur: Getting Productive with Libraries _______________ v

Read This FirstAbbreviations

EI electron ionization

EMBL European Molecular Biology Laboratory

<Enter> enter key on the terminal keyboard

ESD electrostatic discharge

ESI electrospray ionization

eV electron volt

f femto (10-15)

°F degrees Fahrenheit

.fasta file extension of a SEQUEST search database file

FOB free on board

ft foot

FTP file transfer protocol

g gram

G giga (109)

GC gas chromatograph; gas chromatography

GC/MS gas chromatograph / mass spectrometer

GND electrical ground

GPIB general-purpose interface bus

GUI graphical user interface

h hour

h height

HPLC high-performance liquid chromatograph

HV high voltage

Hz hertz (cycles per second)

ICIS Interactive Chemical Information System

ICL Instrument Control Language

ID inside diameter

IEC International Electrotechnical Commission

IEEE Institute of Electrical and Electronics Engineers

in. inch

I/O input/output

k kilo (103, 1000)

K kilo (210, 1024)

KEGG Kyoto Encyclopedia of Genes and Genomes

kg kilogram

vi __________________Finnigan Xcalibur: Getting Productive with Libraries________________

Read This First_____________________________________________________________ Abbreviations

l length

L liter

LAN local area network

lb pound

LC liquid chromatograph; liquid chromatography

LC/MS liquid chromatograph / mass spectrometer

LED light-emitting diode

µ micro (10-6)

m meter

m milli (10-3)

M mega (106)

M+ molecular ion

MB Megabyte (1048576 bytes)

MH+ protonated molecular ion

min minute

mL milliliter

mm millimeter

MS mass spectrometer; mass spectrometry

MS MSn power: where n = 1

MS/MS MSn power: where n = 2

MSn MSn power: where n = 1 through 10

m/z mass-to-charge ratio

n nano (10-9)

NCBI National Center for Biotechnology Information (USA)

NIST National Institute of Standards and Technology (USA)

OD outside diameter

Ω ohm

p pico (10-12)

Pa pascal

PCB printed circuit board

PID proportional / integral / differential

P/N part number

P/P peak-to-peak voltage

_________________ Finnigan Xcalibur: Getting Productive with Libraries ______________ vii

Read This FirstAbbreviations

ppm parts per million

psig pounds per square inch, gauge

RAM random access memory

RF radio frequency

RMS root mean square

ROM read-only memory

RS-232 industry standard for serial communications

s second

SIM selected ion monitoring

solids probe direct insertion probe

SRM selected reaction monitoring

SSQ single stage quadrupole

TCP/IP transmission control protocol / Internet protocol

TIC total ion current

Torr torr

TSQ triple stage quadrupole

u atomic mass unit

URL uniform resource locator

V volt

V ac volts alternating current

V dc volts direct current

vol volume

w width

W watt

WWW World Wide Web

Note. Exponents are written as superscripts. In the corresponding online Help, exponents are sometimes written with a caret (^) or with e notation because of design constraints in the online Help. For example:

MSn (in this manual) MS^n (in the online Help)

105 (in this manual) 10^5 (in the online Help)

viii _________________Finnigan Xcalibur: Getting Productive with Libraries________________

Read This First___________________________________________________Typographical Conventions

Typographical ConventionsTypographical conventions have been established for Thermo Electron San Jose manuals for the following:

• Data input

• Boxed information

• Topic headings

Data Input

Throughout this manual, the following conventions indicate data input and output via the computer:

• Messages displayed on the screen are represented by capitalizing the initial letter of each word and by italicizing each word.

• Input that you enter by keyboard is represented in bold face letters. (Titles of topics, chapters, and manuals also appear in bold face letters.)

• For brevity, expressions such as “choose File > Directories” are used rather than “pull down the File menu and choose Directories.”

• Any command enclosed in angle brackets < > represents a single keystroke. For example, “press <F1>” means press the key labeled F1.

• Any command that requires pressing two or more keys simultaneously is shown with a plus sign connecting the keys. For example, “press <Shift> + <F1>” means press and hold the <Shift> key and then press the <F1> key.

• Any button that you click on the screen is represented in bold face letters and a different font. For example, “click on Close”.

_________________ Finnigan Xcalibur: Getting Productive with Libraries ______________ ix

Read This FirstTypographical Conventions

Boxed Information

Information that is important, but not part of the main flow of text, is displayed in a box such as the one below.

Boxed information can be of the following types:

• Note – information that can affect the quality of your data. In addition, notes often contain information that you might need if you are having trouble.

• Tip – helpful information that can make a task easier.

• Important – critical information that can affect the quality of your data.

• Caution – information necessary to protect your instrument from damage.

• CAUTION – hazards to human beings. Each CAUTION is accompanied by a CAUTION symbol. Each hardware manual has a blue CAUTION sheet that lists the CAUTION symbols and their meanings.

• DANGER – laser-related hazards to human beings. It includes information specific to the class of laser involved. Each DANGER is accompanied by the international laser radiation symbol.

Note. Boxes such as this are used to display information.

x___________________Finnigan Xcalibur: Getting Productive with Libraries________________

Read This First___________________________________________________Typographical Conventions

Topic Headings

The following headings are used to show the organization of topics within a chapter:

Chapter 1Chapter Name

1.2 Second Level Topics

Third Level Topics

Fourth Level Topics

Fifth Level Topics

_________________ Finnigan Xcalibur: Getting Productive with Libraries ______________ xi

Read This FirstReply Cards

Reply CardsThermo Electron San Jose manuals contain one or two reply cards. All manuals contain a Customer Registration / Reader Survey card and some contain a Change of Location card. These cards are located at the front of each manual.

The Customer Registration / Reader Survey card has two functions. First, when you return the card, you are placed on the Thermo Electron San Jose mailing list. As a member of this list, you receive application reports and technical reports in your area of interest, and you are notified of events of interest, such as user meetings. Second, it allows you to tell us what you like and do not like about the manual.

The Change of Location card allows us to track the whereabouts of the instrument. Fill out and return the card if you move the instrument to another site within your company or if you sell the instrument. Occasionally, we need to notify owners of our products about safety or other issues.

xii__________________Finnigan Xcalibur: Getting Productive with Libraries________________

Chapter 1Overview of Library Browser

The Library Browser is part of Xcalibur®, the Finnigan™ mass spectrometry data system.

This chapter gives you an overview of how to use the library tools in Xcalibur to create and use your own custom libraries. A Quick Reference Guide summarizes the steps for creating, editing, and searching custom libraries and printing reports of your results.

Additionally, this chapter gives you information about how to choose the peak detection algorithm that you want Xcalibur to use when you perform library searches.

This chapter contains the following topics:

• 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.

_______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 1-1

Overview of Library BrowserQuick Reference Guide

1.1 Quick Reference GuideFigure 1-1 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, you create a custom user-library of MS/MS or MSn spectra, one entry at a time. To include a spectrum in a library entry, you display your (qualitative) .raw file data in Qual Browser. In Qual Browser, you can enhance a spectrum by averaging several scans and by subtracting background scans. You then export the enhanced spectrum to Library Browser.

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 you can specify the molecular weight or the CAS (Chemical Abstract Service) registry number. You can even attach a chemical structure to the library entry. Additionally, you can select which mass-to-charge ratios you want to include in the entry. (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, not its intensity, is an essential criterion for identification of a compound.)

Finally, Xcalibur provides three ways to search libraries and print custom reports, as follows:

• 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

You can specify in a Processing Method to print reports automatically by using the Qual view options in the Processing Setup window. You then reference the Processing Method when you specify a sequence of files in Sequence Setup. When you reprocess a sequence, Xcalibur prints your reports.

Alternatively, if you manually search for hits that match a single spectrum, then you can print results by using the command File > Print either in Qual Browser or in Library Browser.

1-2 ________________Finnigan Xcalibur: Getting Productive with Libraries________________

Overview of Library Browser______________________________________________________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

Figure 1-1. Quick Reference Guide for creating, editing, and searching custom libraries and for printing 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 thelibrary

Attach a structure (optional)

Append otherspectra to library

Specify search parameters in Processing Setup

Specify sequence in Sequence Setup

Batch reprocess: choose to print reports

Open a .raw filein Qual Browser, and display the spectrum

Export spectrum to Library Browser

Specify libraryoptions; search

Specify libraryoptions; search Print report

Print reports


Overview of Library BrowserSpecifying the Peak Detection Algorithm

1.2 Specifying the Peak Detection Algorithm

You can specify how Xcalibur finds and processes your 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, as follows:

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

2. Open a raw file and click on the pin in the chromatogram view to select it.

3. Right-click on the chromatogram view and choose Select 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 1-2.

4. Select the ICIS peak detection algorithm. The peak will automatically be integrated using the ICIS algorithm.

5. Specify mass tolerance and mass precision as follows. See Figure 1-3.

a. Select Display > Mass Options. The Global Mass Options dialog box is displayed.

b. Specify a mass tolerance bandwidth in the Mass Tolerance text 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 text box. Xcalibur applies a number of decimal places to mass intensity values for data processing calculations.

Note: For new Processing Methods only, you can choose either the ICIS, the Genesis, or the 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.


Overview of Library Browser________________________________________ Specifying the Peak Detection Algorithm

6. Specify the relative scale as follows. See Figure 1-4.

a. Select the chromatogram view, right click on the view, and choose Display Options.

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

c. Under the Y axis Units group box, select the Relative option button. (Xcalibur uses the Relative scale to calculate mass spectral data and the Absolute scale to calculate UV/PDA/other data.)

Figure 1-2. Xcalibur - Qual Browser display of the Chrom view shortcut menu. Specify which algorithm Xcalibur uses to find and measure peaks.


Overview of Library BrowserSpecifying the Peak Detection Algorithm

Figure 1-3. Global Mass Options dialog box

Figure 1-4. Display Options dialog box - Chromatogram Axis page


Chapter 2Creating a Custom Library of Spectra

You can create a custom library of MS/MS spectra by using the Xcalibur data system. 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.


• Creating a Library Entry with Your Spectral Data

• Editing a User Library

Note. Refer to the online Help for more information, as follows: Choose Help on the menu bar in any Xcalibur window. If you need assistance specifically for Library Browser, choose Help > Help Topics on the Library Browser menu bar.

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.


Creating a Custom Library of SpectraCreating a Library Entry with Your Spectral Data

2.1 Creating a Library Entry with Your Spectral Data

You can create a library entry with your MS or MS/MS (or MSn) spectral data

from the Qual Browser window.

The procedure in this topic uses steroid data. The raw data files are included with your Xcalibur data system in the directory C:\Xcalibur\examples\data.

This topic contains the following topics:

• 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

You can view your MS/MS raw data in the Qual Browser window. You need to open a data file to expand the Qual Browser menu bar.

Display the raw data of a steroids data file, as follows:

1. Display the Xcalibur Home Page from your Microsoft® Windows® Desktop in either of the following ways:

• Click on Start > Programs > Xcalibur > Xcalibur.

• Double-click on the Xcalibur icon.

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

3. Choose File > Open, or click on the Open button in the toolbar to display the Open Raw File dialog box.

4. Browse to the file Xcalibur\examples\data\steroids14.raw. See Figure 2-1.


Creating a Custom Library of Spectra__________________________________ Creating a Library Entry with Your Spectral Data

5. Select the Add: Window option button, and then click on Open to display the data for the steroids. (Figure 2-1)

Leave the Qual Browser window open, and go on to the next topic: Viewing a Spectrum in Qual Browser.

Viewing a Spectrum in Qual Browser

You can view a mass spectrum in the interactive cells of the Qual Browser window. This procedure is a continuation of the procedure in the previous topic: Opening a Raw Data File (.raw) in Qual Browser.

Set up to display a mass spectrum of the raw data in a window containing four cells, as follows:

1. Ensure that Xcalibur displays the Chromatogram view as shown in Figure 2-2. If it does not, do the following:

Figure 2-1. Open Raw File dialog box, showing the selection of steroids 14.raw



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

b. Click on the Maximize button in the upper right corner of your 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.

2. Specify that the raw data is displayed in a grid of four cells (as shown in Figure 2-3), as follows:

a. Choose Grid > Insert Cells > Left to display two cells in the window.

b. Choose Grid > Insert Cells > Below to display four cells in the window.

3. Click on the lower left cell, and then choose View > Scan Filters to display the scan filter data. The cell lists the filters contained in the total ion current (TIC) chromatogram over a specified time range.

Figure 2-2. Qual Browser window, showing the Chromatogram view of steroids14.raw



4. Display a mass range chromatogram in the upper left cell, as follows:

a. Click on the pin in the upper right corner of the cell to make it active.

b. The last entry in the scan filter list is for a mass range chromatogram of all ions between m/z 150 and 375. Click and hold on the last entry in the list. Xcalibur surrounds the entry with a box and displays a page cursor.

c. Drag the page cursor to the upper left cell, and release the mouse button. The filter is automatically applied, and Xcalibur displays the mass range chromatogram.

5. Display an averaged mass spectrum in the upper right cell, as follows:

a. Click on the pin in the upper right corner of the cell to make it active.

b. Choose View > Spectrum to set up to display a mass spectrum.

c. Click and hold in the upper left cell at a position just to the left of the chromatogram peak.

d. Drag the cursor horizontally across the peak, and release the mouse button. Xcalibur displays a mass spectrum in the upper right cell. This spectrum is the average of the scans in the retention time range that you selected. For example, see the upper right cell in Figure 2-3.

Leave the Qual Browser window open, and go to the next topic: Subtracting Background Spectra.



Subtracting Background Spectra

You can subtract background spectra in the Chromatogram view to eliminate background peaks from either one range (either side of the chromatogram peak of interest) or two ranges (both sides of the chromatogram peak of interest). This procedure is a continuation of the procedure in the previous topic: Viewing a Spectrum in Qual Browser.

Select two scan ranges for background subtraction, as follows:

1. Click on the pin button in the spectrum to select it.

2. Choose Actions > Subtract Spectra > 2 Ranges to display the crosshair cursor labeled -1.

3. Click and hold on a baseline region in the upper left cell that is close to the chromatographic peak of interest.

Figure 2-3. Qual Browser window, showing the following views (clockwise from lower left): Scan Filter view, (filtered) Chromatogram view, (averaged) Spectrum view, and (unfiltered) Chromatogram view



4. Drag the cursor across a few scans that are representative of the first scan range you want to subtract.

5. Release the mouse button to define the first range. The label on the cursor changes to -2.

6. Click and hold on a baseline region on the other side of the peak of interest.

7. Drag the cursor across a few scans that are representative of the second scan range you want to subtract. See Figure 2-4.

8. Release the mouse button to define the second range.

When you release the mouse button, Xcalibur subtracts an average of the selected scans and redraws the Spectrum view. The Spectrum view header shows the number of subtracted scans. For example, SB: 12 0.52-0.56, 0.92-0.99 indicates the following:

• Qual Browser has applied background subtraction to the spectrum by using a 12-scan average.

• Retention time ranges used in the subtraction are 0.52 to 0.56 min and 0.92 to 0.99 min.

Leave the Qual Browser window open, and go on to the next topic: Exporting a Spectrum to Library Browser.



Figure 2-4. Qual Browser window, showing background subtracted scans in the Spectrum view (upper right)



Exporting a Spectrum to Library Browser

You can export a spectrum from the Spectrum view of Qual Browser to the Library Browser to create a library entry for a custom library. This topic is a continuation of the previous topic: Subtracting Background Spectra.

Export the enhanced spectrum to Library Browser, as follows:

1. Right click on the Spectrum view (upper right cell) and choose Library > Export to Library Browser to export the MS/MS spectrum of the steroid to the Library Browser. Xcalibur displays the Library Browser windows. See Figure 2-5.

Xcalibur converts the mass and intensity data of the spectrum to a text file and copies the file to the Spec List pane. The Qual Browser window stays open.

Leave the Library Browser windows open, and go on to the next topic: Editing a User Library.

Figure 2-5. Library Search window of Library Browser


Creating a Custom Library of SpectraEditing a User Library

2.2 Editing a User LibraryYou can edit a user library entry that contains the MS/MS spectrum you exported from Qual Browser.


• Editing Spectrum Information

• Adding an Entry to and Naming a Library

• Attaching a Chemical Structure to a Library Entry

• Appending Additional Compounds to the User Library

Editing Spectrum Information

Edit your MS/MS spectrum information in Library Browser, as follows. This procedure is a continuation of the procedure in the previous topic: Exporting a Spectrum to Library Browser.

1. Choose Windows > Librarian to display the Librarian window. Because the information for the MS/MS spectrum is stored as a text file, the source of the data is listed as Text File in the Plot/Text pane. See Figure 2-6.

Figure 2-6. Librarian window, showing the spectrum information as a text file

2-10 _______________Finnigan Xcalibur: Getting Productive with Libraries________________

Creating a Custom Library of Spectra_______________________________________________________ Editing a User Library

2. Click on the Edit Spectrum button to display the Spectrum Information dialog box. See Figure 2-7. The dialog box displays information specific to the spectrum.

3. Change the name of the spectrum reference, as follows:

a. Click and drag your cursor in the Name text box to highlight the entire text string.

b. Rename the spectrum to give it a more useful name than the default text string. For this example, type hydrocortisoneMS2.

Leave the Spectrum Information dialog box open, and go to the next topic: Adding an Entry to and Naming a Library

Figure 2-7. Spectrum information dialog box showing raw spectrum information

_______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 2-11


Adding an Entry to and Naming a Library

In Library Browser, you can add a library entry to a library, and you can name the library. This procedure is a continuation of the previous topic: Editing Spectrum Information.

Add a spectrum entry to and name the library, as follows:

1. In the Spectrum Information dialog box, click on Add to Library. This displays the Choose Library To Save To dialog box. See Figure 2-8.

2. Type the name of a library in the combo box. For example, type ms2test.

3. Click on OK to name the library, copy the spectrum to the library, and return to the Librarian window.

4. Click on the Lib. Search tab to return to the Library Search window.

Leave the Library Browser windows open, and go on to the next topic: Attaching a Chemical Structure to a Library Entry.

Figure 2-8. Choose Library To Save To dialog box, showing the user-library ms2test



Attaching a Chemical Structure to a Library Entry

You can attach a chemical structure from the nistdemo list of structures to an entry in your custom library. Alternatively, you can attach a structure from a program such as ChemDraw™. ChemDraw saves drawings of chemical structures in the file format .mol.

You cannot attach a structure to a text file. Consequently, you need to set the search parameters in Library Browser so that the name of the compound source changes to a name other than Text File in the Librarian window. This procedure is a continuation of the procedure in the previous topic: Adding an Entry to and Naming a Library.

Attach a structure to the entry hydrocortisoneMS2, and change the source of the entry from Text File to user-library ms2test, as follows:

1. In the Library Search window, select and then delete the steroids entry in the Spec List.

2. Display Qual Browser to export the raw spectrum of hydrocortisone. You export the spectrum to search the library ms2test for a hit, as follows:

a. Click on the Qual Browser button in the task bar at the bottom of your monitor screen to redisplay the Qual Browser window.

b. In the Spectrum view, right click the mouse button, and choose Library > Export to Library Browser. The Library Browser windows display.

3. Specify to search the library ms2test, as follows:

a. Choose Tools > Search Options to open the Library Search Property dialog box. See Figure 2-9.

b. Click on the Libraries tab to display the Available Libs and the Included Libs list of libraries.

c. Ensure that ms2test is listed in the Included Libs list box. See Figure 2-10. If ms2test is not in the Included Libs list box, then highlight ms2test in the Available Libs list box, and click on Add.

d. Click on OK to return to the Library Search window.



Figure 2-9. Library Search Property dialog box

Figure 2-10. Libraries page of the Library Search Property dialog box, showing the library ms2test added to the Included Libs list box



4. Select steroids14 in the Spec List pane. Right click on this entry and select Library Search. Library Browser finds the entry hydrocortisoneMS2 and copies it to the Hit List pane. See Figure 2-11.

5. Copy the hit to the Spec List pane, as follows:

a. Select the Hit List entry hydrocortisoneMS2. Right click on this entry and select Copy from the shortcut menu.

b. Move the cursor to the Spec List pane, and then left click the mouse button to make the Spec List pane active.

c. Right click to display the shortcut menu and select Paste to paste the entry hydrocortisoneMS2 to the Spec List window.

6. Choose the Librarian tab to open the Librarian window. See Figure 2-12.

Figure 2-11. Library Search window, showing the results of searching the library ms2test



7. Save the structure of hydrocortisone from the library nistdemo to the ms2test entry hydrocortisoneMS2, as follows:

a. Click on the Edit Spectrum button in the toolbar to display the Spectrum Information dialog box. See Figure 2-13.

b. Click on the Attach Struct button to display the Open dialog box. This allows searching for chemical structure files from other sources. See Figure 2-14.

c. If you do not have other structure files, click on Cancel to display the Attach Structure To User Spectrum dialog box. See Figure 2-15.

d. Click on nistdemo in the Get Structure From group box. Then, click on Open Library.

Figure 2-12. Librarian window, showing the ms2test library entry hydrocortisoneMS2



Figure 2-13. Spectrum Information dialog box, showing the name of entry edited to hydrocortisoneMS2

Figure 2-14. Open dialog box



e. Type hydrocortisone in the Substring Search text box. Then, click on Substring Search. Library Browser scans the nistdemo library and finds the MS data and the structure of hydrocortisone.

f. Click on Accept to accept the structure, and return to the Spectrum Information dialog box. See Figure 2-16.

Figure 2-15. Attach Structure To User Spectrum dialog box



g. Click on Add to Library to display the Choose Library To Save To dialog box. See Figure 2-17.

Figure 2-16. Spectrum Information dialog box, showing the structure of hydrocortisone from the nistdemo library to be included in the user-library entry



h. Click on OK to close the Choose Library To Save To dialog box and return to the Librarian window. The source of the entry hydrocortisoneMS2 displays as ms2test.

8. Highlight the entry in the Spec List that causes the Text File designation to appear in the Plot pane. Click on the Delete From Library button in the toolbar to delete the entry. The warning shown in Figure 2-18 is displayed.

9. Click on the Lib. Search tab to return to Library Browser’s Library Search window.

10. Double click on the entry hydrocortisoneMS2 in the Spec List.

The chemical structure of hydrocortisone is attached to the ms2test library entry hydrocortisoneMS2.

Leave the Library Browser windows open, and go on to the next topic: Appending Additional Compounds to the User Library.

Figure 2-17. Choose Library To Save To dialog box

Figure 2-18. Warning bar that appears after you delete an entry from the Spec List



Appending Additional Compounds to the User Library

You can append to your user library ms2test the three remaining steroids in the file steroids14.raw. The compounds are as follows:

• Deoxycorticosterone

• Methyltestosterone

• Progesterone

This procedure describes exporting spectra to Library Browser using unenhanced spectra. When you create your custom library of spectra, you might want to include the steps that were omitted here for brevity. Refer to the related topics Subtracting Background Spectra and Attaching a Chemical Structure to a Library Entry for more information. This procedure is a continuation of the previous topic: Attaching a Chemical Structure to a Library Entry.

Append three library entries of MS/MS steroid data to the user library ms2test, as follows:

1. Click on the Qual Browser button in the task bar at the bottom of your monitor screen to redisplay the Qual Browser window.

2. Display the MS/MS spectrum of the second steroid peak, as follows:

a. Ensure that the pin in the Spectrum view (upper right cell) in Qual Browser is active.

b. Move your cursor to the Chromatogram view in the lower right cell. Then, click and hold just to the left of the second chromatographic peak.

c. Drag the cursor horizontally across the peak to average the scans you select. Xcalibur displays the spectrum in the Spectrum view.

3. Right click on the mass spectrum to display a shortcut menu. Then, choose Library > Export to Library Browser to export the spectrum. Xcalibur displays a message box, as shown in Figure 2-19.

4. Click on Prepend to add the entry to the Clipboard window.

Figure 2-19. Message box, asking whether to overwrite or to append the spectrum to be exported to Library Browse



5. Edit the spectrum information, as follows:

a. Choose Window > Librarian in Library Browser to display the Librarian window.

b. Select the unedited entry in Spec List pane as shown in Figure 2-20.

c. Click on the Edit Spectrum button to display the Spectrum Information dialog box.

d. Select all of the text in the Name text box, and then type the name you want for the entry. For the second steroid, type deoxycorticosteroneMS2.

e. Click on Add to Library to display the Choose Library To Save To dialog box. Click on OK to copy your next spectrum entry to the library ms2test. (The entry Text File in the Librarian window does not change.)

Figure 2-20. Librarian window, showing a steroid spectrum in the list of ms2test library entries



6. Copy and paste the library entry deoxycorticosteroneMS2 from the Hit List pane to the Spec List pane. See Figure 2-21.

a. Choose Window > Lib. Search in Library Browser to display the Library Search window.

b. Select steroids14 in the Spec List pane. Right click on this entry and select Library Search. Library Browser finds the entry deoxycorticosteroneMS2 and copies it to the Hit List pane.

c. Select the Hit List entry deoxycorticosteroneMS2. Right click on this entry and select Copy from the shortcut menu.

d. Move the cursor to the Spec List pane, and then left click the mouse button to make the Spec List pane active.

e. Right click to display the shortcut menu and select Paste to paste the entry deoxycorticosteroneMS2 to the Spec List window.

Figure 2-21. Library Browser panes, showing the results of a search from the Spec List pane



7. Choose Window > Librarian to display the Librarian window. See Figure 2-22.

8. Highlight the entry from the source Text File, and then click on the Delete From Library button in the toolbar to delete the entry. See Figure 2-23.

Figure 2-22. Librarian window, showing the entry from the source Text File highlighted



9. Click on the Qual Browser button in the task bar at the bottom of your monitor screen to redisplay the Qual Browser window.

10. Repeat Steps 2 through 7 (above) to append the third steroid entry methyltestosteroneMS2 to the Library Manager list.

11. Repeat Steps 2 through 6 (above) to append the fourth steroid entry progesteroneMS2 to the Library Manager list.

The Library Search window of the Library Browser should appear similar to Figure 2-24.

Figure 2-23. Librarian window, showing the entries from the source ms2test only



12. Close the windows, and return to the Xcalibur Home Page, as follows:

a. Choose File > Exit to close Library Browser and return to Qual Browser.

b. Choose File > Exit again to close the Qual Browser window and return to the Xcalibur Home Page.

In this chapter, you did the following:

• Created a user library containing four MS/MS spectra

• Edited a library entry to include compound structure

Go to the next chapter: Searching Libraries Automatically.

Figure 2-24. Library Search window, showing the Compare Result pane containing the MS/MS spectra of four steroids


Chapter 3Searching Libraries Automatically

After you create your custom library of spectra, you can search it and/or other libraries automatically. You need to set up method files in Xcalibur windows to search libraries automatically:

• Use the Xcalibur Processing Setup window to create a Processing Method file (.pmd).

• Use the Sequence Setup window to reprocess data files in a sequence list (.sld) with the Processing Method that you created.


• Setting Up to Search Libraries Automatically

• Reprocessing Raw Files and Printing Reports

Note. If you need more information about setting up methods, refer to online Help.


Searching Libraries AutomaticallySetting Up to Search Libraries Automatically

3.1 Setting Up to Search Libraries Automatically

You can set up Xcalibur to search libraries automatically.


• Specifying Search Parameters and Report Options in Processing Setup

• Specifying Raw Data Files in Sequence Setup

Specifying Search Parameters and Report Options in Processing Setup

You need to specify in Processing Setup your search parameters and report options.


• Setting Up the Qual View to Search a Library

• Specifying Report Options for Library Searches

Setting Up the Qual View to Search a Library

You need to set up the Qual view in the Processing Setup window to search libraries automatically. For this example, use steroids data.

Specify parameters for a qualitative library search in the Qual view, as follows:

1. From the Xcalibur Home Page, click on the Processing Setup button. The Processing Setup window is displayed.

2. Open a raw data file in the Qual view, as follows:

a. Choose File > New to display the Identification page of the Quan view.

b. Click on the Qual button to display the Qual view.

c. Choose File > Open Raw File to display the Open Raw File dialog box.

d. Select the file C:\Xcalibur\examples\data\steroids14.raw, and then click on Open to display the raw data. See Figure 3-1.

Note. To use the Library Search Constraints page, you need to have specific knowledge about the target compounds in your chromatogram. This is not always possible in automated processing


Searching Libraries Automatically_____________________________________ Setting Up to Search Libraries Automatically

3. Ensure that the MS option is selected in the Type list box of the Detector group box and that ICIS is selected in the Peak Detect list box.

4. Specify a scan filter on the Identification page, as follows:

a. Click on the down arrow of the Filter combo box to display the scan filters in steroids14.raw.

b. Click on one of the filters to select it.

5. Click on OK to accept changes to Identification page.

6. Click on the Advanced button to display the ICIS Advanced Parameters dialog box. See Figure 3-2.

a. Ensure that the INCOS Noise option button is selected in the Noise Method group box.

Figure 3-1. Processing Setup window, showing the Qual view

Note. For more information about the algorithms that Xcalibur uses to perform library searches, refer to the online Help.



b. Click on OK to close the dialog box, and return to the Processing Setup window.

7. Click on OK to apply your changes to the Identification page.

8. Specify the name of the library you want to search, as follows:

a. Click on the Library Search Options tab to display search type options.

b. Click on Search List to display the Search List dialog box. See Figure 3-3.

Figure 3-2. ICIS Advanced Parameters dialog box, showing the option INCOS Noise

Note. Xcalibur generates the Available Libraries list dynamically. Each time you open the Search List dialog box, Xcalibur lists the libraries available on your system at that time.

Libraries listed in the Selected Libraries list, on the other hand, might not exist on your system. They might have been selected on another system or deleted or renamed since the Processing Method was created.



c. Highlight MS2test in the Available Libraries list box, and then click on Add to move the library name to the Selected Libraries list box.

d. Click on OK to select MS2test, and return to the Qual view of Processing Setup.

Leave the Qual view open, and go to the next topic: Specifying Report Options for Library Searches.

Figure 3-3. Search List dialog box, showing the selected library MS2test



Specifying Report Options for Library Searches

You need to specify report options to produce and print reports automatically. This procedure is a continuation of the procedure in the previous topic: Setting Up the Qual View to Search a Library.

Specify that you want to display the data in steroids14.raw in the format of a custom report template, as follows:

1. Click on the Reports button on the View bar in the Processing Setup window, or choose View > Reports to display the Reports view. See Figure 3-4.

Note. Refer to the manual: Xcalibur Getting Productive: Merlin, the Custom Report Wizard for more information about how to create custom report templates by using Microsoft Word.

Note. If the Apply Changes? dialog box displays, read the message , and then click on Yes.



2. Click on the Enable cell in the Sample Reports group box to display a check box . Then, select the check box to enable Row 1. See Figure 3-5.

Figure 3-4. Processing Setup window, showing the Reports view



3. Specify the sample brackets in Row 1, as follows:

a. Click on Yes in the Std column, and then clear the check box to exclude the bracket for standards from your report.

b. Click on Yes in the QC column, and then clear the check box to exclude the bracket for quality control samples.

c. Click on Yes in the Other column, and then clear the check box.

4. Specify the name of a Report Template (.doc), as follows:

a. Double-click on the Report Template Name cell to display the Browse For Sample Report Template dialog box.

b. Scroll to select the file C:\Xcalibur\Templates\CustLibrSearRept2.doc. See Figure 3-6.

Figure 3-5. Processing Setup window, showing the Reports view with Row 1 enable



c. Click on Open to select the report template, and display the filename in the Report Template Name cell.

5. Click on OK to apply your changes to the Reports view. See Figure 3-7.

Figure 3-6. Browse For Sample Report Template dialog box



6. Save the Processing Method, as follows:

a. Choose File > Save As to display the File Summary Information dialog box. See Figure 3-8.

Figure 3-7. Processing Setup window, showing the Reports view and a specified Report Template Name



b. Type in the Description text box, and then click on OK to display the Save As dialog box.

c. Name the Processing Method, as follows: C:\Xcalibur\examples\methods\steroidsMS2.pmd. See Figure 3-9. (Ensure that you save the Processing Method to the specified directory because you will need to retrieve it later.)

d. Click on Save to save the method, and return to the Reports view.

7. Choose File > Exit to close the Processing Setup window, and return to the Xcalibur Home Page.

Go to the next topic: Specifying Raw Data Files in Sequence Setup.

Figure 3-8. File Summary Information dialog box



Specifying Raw Data Files in Sequence Setup

You need to specify the raw files for which you want to process data so you can search libraries and print reports automatically. This procedure is a continuation of the procedure in the previous topic: Specifying Report Options for Library Searches.

Display the Sequence Setup window, and open the sequence list C:\Xcalibur\examples\methods\steroid.sld, as follows:

1. Click on the Sequence Setup button on the Xcalibur Home Page to display the Sequence Setup window.

Figure 3-9. Save As dialog box, showing the Processing Method file steroidsMS2.pmd



2. Open a sequence list file into the Sequence Setup window, as follows:

a. Choose File > Open to display the Open dialog box.

b. Scroll to select the Sequence file C:\Xcalibur\examples\methods\steroid.sld, and then double-click to display the list of samples. See Figure 3-10.

3. Specify to include only two samples in the list, as follows:

a. Highlight Rows 1 through 10, and then choose Edit > Delete Row to leave three samples remaining in the sequence. Xcalibur displays a message box to confirm the Delete Row command. Click on Yes.

b. Highlight Row 3, and then choose Edit > Delete Row to leave two samples remaining in the sequence. Xcalibur displays a message box to confirm the Delete Row command. Click on Yes. See Figure 3-11.

4. If necessary, click on the left side of the horizontal scroll bar at the bottom of the workspace to display the Sample Type column. Double-click on the Row 1 cell in the Sample Type column to display a drop-down list box. Then, scroll up to select Unknown.

5. If necessary, expand the width of the Path column to ensure that the directory is the one in which your raw files are stored. For example, raw files containing steroids data are found in C:\Xcalibur\examples\data.

Figure 3-10. Sequence Setup window, showing a list of two files contained in steroid.sld

Note. Sequence Setup allows you to create a sequential list containing a variety of sample types or brackets. However, for qualitative analysis the type is usually unknown.



6. Double-click on the Row 1 cell in the Processing Method column to display the Select Processing Method dialog box. Browse to select the Processing Method C:\Xcalibur\examples\methods\steroidsMS2.pmd. See Figure 3-12.

7. Repeat Steps 4 and 5 for the second row of the sequence. Step 6 is repeated automatically for subsequent rows.

8. Save the sequence list file, as follows:

a. Choose File > Save As to display the File Summary Information dialog box. Type practice in the Description text box, and then click on OK.

b. Type steroidPractice in the File Name text box to name your sequence.

c. Click on Save to save your sequence list, and return to the Sequence Setup window.

You are now ready to reprocess your Xcalibur Sequence and print custom reports automatically. Go on to the next topic: Reprocessing Raw Files and Printing Reports.

Figure 3-11. Sequence Setup window, showing a list of two files contained in steroid.sld

Figure 3-12. Sequence Setup window, showing the edited list of two files contained in steroid.sld


Searching Libraries Automatically____________________________________ Reprocessing Raw Files and Printing Reports

3.2 Reprocessing Raw Files and Printing Reports

You can reprocess your raw data and print reports automatically by using Sequence Setup. This procedure is a continuation of the procedure in the previous topic: Specifying Raw Data Files in Sequence Setup.

Reprocess a list of raw files, and print library search reports, as follows:

1. In Sequence Setup, click and hold on the row number in Row 1, and then drag your cursor to Row 2 to select the rows in the current sequence that you want to reprocess. Xcalibur highlights the selected rows.

2. Choose Actions > Batch Reprocess, or click on the Batch Reprocess toolbar button to display the Batch Reprocess Setup dialog box.

3. Ensure that the Process Rows text box reads 1-2. If it does not, double-click on the text box, and then type 1-2.

4. Select only the following check boxes:

• Qual

• Peak Detection & Integration

• Library Search

• Reports

• Print Sample Reports

• Replace Sample Info

The dialog box should look like Figure 3-13.

5. Click on OK to initiate batch reprocessing of the selected samples. If Xcalibur displays a message box, as shown in Figure 3-14, click on Yes.

6. Click on the button in the Task bar to display the Processing Status window. See Figure 3-15.

Two beeps signal the end of the batch reprocessing.


Searching Libraries AutomaticallyReprocessing Raw Files and Printing Reports

Figure 3-13. Batch Reprocess Setup dialog box, showing selected options

Figure 3-14. Message box, asking if you want to save changes to the sequence list


Searching Libraries Automatically____________________________________ Reprocessing Raw Files and Printing Reports

7. Go to your printer to get your printed reports (one for each sample). See that they resemble those shown in Appendix A: Example Reports.

8. Choose View > Roadmap View to close Sequence Setup and display the Roadmap View.


• Set up a Processing Method in Processing Setup to search libraries automatically

• Reprocessed a sequence of data files in Sequence Setup

• Printed library search results of raw data automatically

Go to the next chapter: Searching Libraries from Qual Browser and Library Browser.

Figure 3-15. Processing Status window, showing two samples in the queue


Chapter 4Searching Libraries from Qual Browser

and Library Browser

You can search libraries from the Qual Browser window or by using the Library Browser windows. You can search for hits on one spectrum at a time, and then print the search results on the single spectrum. Appendix A: Example Reports contains examples of reports you can print by following the procedures in this chapter.


• Initiating a Library Search from Qual Browser

• Searching a Library by Using Library Browser

• Customizing the Library Browser Layout


Searching Libraries from Qual Browser and Library BrowserInitiating a Library Search from Qual Browser

4.1 Initiating a Library Search from Qual Browser

You can initiate a library search from the Qual Browser window.

Perform a library search from the Qual Browser window, as follows:

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

2. Open a raw file that contains steroids data, as follows:

a. Choose File > Open, or click on the Open button in the toolbar to display the Open Raw File dialog box.

b. Browse to the file Xcalibur\examples\data\steroids14.raw, and then click on Open.

3. Refer to the topic Viewing a Spectrum in Qual Browser in Chapter 2, and follow the procedure. See Figure 4-1.

Figure 4-1. Qual Browser window, showing the following views (clockwise from lower left): Scan Filter view, (filtered) Chromatogram view, (averaged) Spectrum view, (unfiltered) Chromatogram view


Searching Libraries from Qual Browser and Library Browser____________________________________ Initiating a Library Search from Qual Browser

4. Select one or more libraries to search, as follows:

a. Right-click on the Spectrum view (upper right) to display the shortcut menu.

b. Choose Library > Options from the shortcut menu to display the Search Properties dialog box. See Figure 4-2.

c. Ensure that the MS2test and nistdemo libraries are listed in the Selected Libraries list box.

d. Click on OK to save the settings, close the dialog box, and return to the Qual Browser window.

5. Initiate the library search, as follows:

a. Right-click on the Spectrum view (upper right) to display a shortcut menu.

b. Choose Library > Search from the shortcut menu to submit the spectrum to a library search. Library spectra that match your spectrum (hits) are displayed in a four-pane Library Search Results view. See Figure 4-3.

Figure 4-2. Search Properties dialog box, showing selected libraries MS2test and nistdemo


Searching Libraries from Qual Browser and Library BrowserInitiating a Library Search from Qual Browser

The interactive cells of the Library Search Results view show the following library search results, displayed clockwise from the upper left quadrant, as follows.

• Hits list

• Molecular structure, including formula, molecular weight, name, and library index number

• Difference spectrum (Raw Data minus Library Entry)

• Peaks above the X-axis are relatively more intense in your spectrum than in the library entry.

• Peaks below the X-axis are relatively more intense in the library entry than in your sample spectrum.

• Comparison of your sample spectrum and the library entry

6. Print the results of the search, as follows:

a. Choose File > Print Preview to display the Print dialog box. See Figure 4-4.

Figure 4-3. Qual Browser window, showing the Library Search Results view cascaded with the Raw Data view. Refer to the text above for a description of the contents of each cell.


Searching Libraries from Qual Browser and Library Browser____________________________________ Initiating a Library Search from Qual Browser

b. Ensure that the following two option buttons are selected:

• Cells In The Selected Window

• One Page

c. Click on OK to close the dialog box, and preview your results.

d. Click on Print to display the Print dialog box again, and then click on OK.

e. Click on OK in the second Print dialog box to print your results. Refer to Appendix A for an example of library search results initiated from Qual Browser.

7. Close the Library Search Results view, and reveal the Qual Browser window.

Leave the Qual Browser window open, and go to the next topic: Searching a Library by Using Library Browser.

Figure 4-4. Print dialog box


Searching Libraries from Qual Browser and Library BrowserSearching a Library by Using Library Browser

4.2 Searching a Library by Using Library Browser

You can search a library by using the Library Browser window. This procedure is a continuation of the procedure in the previous topic: Initiating a Library Search from Qual Browser.

Perform a library search on a spectrum you export from Qual Browser, as follows:

1. Ensure that the pin in the Spectrum view (upper right) in the Qual Browser window is active.

2. Right-click on the Spectrum view to display the shortcut menu.

3. Choose Library > Export to Library Browser to open automatically the Library Browser windows.

When you export a spectrum to Library Browser, Xcalibur automatically does the following:

• Copies information about the exported spectrum into the directory C:\Xcalibur\Libspecs. The file is given an extension of .msd, and the filename is truncated to the first eight characters of the original filename.

• Creates an index file containing details about the exported spectrum

When Library Browser opens, Xcalibur automatically does the following:

• Picks up the index file

• Locates the exported .msd spectrum files, and then lists them in the Spec List pane.

4. Define your search parameters in Library Browser, as follows:

a. Choose Tools > Library Search Options to display the Library Search Property dialog box. See Figure 4-5.

Note. You can display data files in Library Browser only by exporting them from Qual Browser. You can export a spectrum into Library Browser from Qual Browser after you open a raw file (.raw) or a result file (.rst) in Qual Browser.


Searching Libraries from Qual Browser and Library Browser____________________________________ Searching a Library by Using Library Browser

b. Click on the Libraries tab to display the Available Libs: and the Included Libs. libraries. See Figure 4-6. This dialog box allows you to specify the libraries you want to search and in what order you want to search them.

• If you want to add a library to the search list, click on its name in the Available Libs: list box, and then click on Add.

• If you want to exclude a library from the search list, click on its name in the Included Libs: list box, and then click on Exclude.

In this example include both MS2test and nistdemo. Click on OK to save the settings, close the dialog box, and return to a Library Browser window.

Figure 4-5. Library Search Property dialog box



c. Observe the Automation / No Automation check box in the Other Options group box of the search page of the Library Search Property dialog box (Figure 4-5).

• If the check box is checked for Automation, go to Step 4e.

• If the check box is not checked go to Step 4d.

d. Click on the Automation tab to display the Automation dialog box. See Figure 4-7. Select the Automatic Search On check box.

e. Click on OK to save the parameters, close the dialog box, and return to the Library Browser windows. (The option to search automatically is active for the next time you open the Library Browser windows.)

Figure 4-6. Libraries Search Property dialog box, showing the included libraries MS2test and nistdemo



5. Double-click on the entry in the Spec List pane to begin a library search. The interactive panes of Library Browser change to display the results of the search, as follows. See Figure 4-8.

• Hit List History drop-down list shows the results of the search.

• Hit List pane contains a list of spectral results.

• Structure panes (tab) display the chemical structure of the compound associated with the highlighted entry.

• Text panes display compound names, a mass/intensity list, scan filter of the highlighted entry. (Refer to the online Help in Library Browser for more information.)

• Plot panes display a single mass spectrum of a selected entry.

• Compare pane displays the difference between two spectra and presents them in various ways.

Figure 4-7. Automation dialog box, showing option to search libraries automatically when exporting spectra to Library Browser



6. Right-click on HydrocortisoneMS2 in the Hit List pane to copy it to the first position in the Spec List pane. See Figure 4-9.

7. Click on Print in the button bar to print the search results. Refer to Appendix A: Example Reports for an example of library search results initiated from Library Browser.

Leave the windows open, and go on to the next topic: Customizing the Library Browser Layout.

Figure 4-8. Library Browser default window, showing the library search results on the raw spectrum that you exported from Qual Browser



Figure 4-9. Library Browser default window, showing file copying from Hit List to Spec List panes


Searching Libraries from Qual Browser and Library BrowserCustomizing the Library Browser Layout

4.3 Customizing the Library Browser Layout

You can customize the layout of the Library Browser windows. You can also customize the appearance of each of the windows. Refer to the online Help in Library Browser for more information.


• Used Qual Browser and Library Browser to search libraries

• Printed library search results


Chapter 5Adding and Converting Libraries

Library Manager allows you to add libraries to a NIST library file and to convert libraries from one format to another. You can open the Xcalibur Library Manager dialog box from the Tools menu of the Xcalibur HomePage – Roadmap view.


• Adding Libraries to and Deleting or Copying Libraries from the NIST Libraries

• Converting Libraries to Another Format


Adding and Converting LibrariesAdding Libraries to and Deleting or Copying Libraries from the NIST Libraries

5.1 Adding Libraries to and Deleting or Copying Libraries from the NIST Libraries

To add a library to or delete a library from the NIST libraries list you use the Xcalibur Library Manager dialog box – Manage Libraries page. See Figure 5-1. This page also allows you to copy a library to another location.

The Add button allows you to add a library to the NIST Libraries list. You can either copy the library file to your local computer or link to the library at a remote location without copying files.

The Delete button allows you to delete a library in the NIST Libraries list.

The Archive button allows you to copy a selected library to another directory on your computer or network.

Note. Because libraries can be large, you might save time using the Link option rather than the Copy option.

Figure 5-1. Xcalibur Library Manager dialog box - Manage Libraries page


Adding and Converting Libraries_________________________________________ Converting Libraries to Another Format

5.2 Converting Libraries to Another Format

To convert one type of source library to another type of library you use the Xcalibur Library Manager dialog box – Convert Libraries page. See Figure 5-2. This page also allows you to copy a library to another location

The Convert Libraries page contains the Source Library Details group box, the Target Libraries Details group box, the Options group box, and the Convert button.

The Source Library Details group box allows you to specify the type of library you want to convert, to specify the library you want to convert, and to select entries in the library that you want to convert.

The Target Library Details group box allows you to specify the type of library to which you want to convert (the target), to select the path and folder for the target library, and to specify the path and folder for the target.

The Options group box allows you to specify whether the converted library is to create a new library, to replace an existing library, or to append (add) the new (converted) entries to a previously created target library.

The Convert button allows you to initiate the library conversion you have specified using the Convert Libraries page. When you click on the Convert button, Xcalibur opens the Library Conversion Status dialog box in which you can follow the progress of the conversion.


Adding and Converting LibrariesConverting Libraries to Another Format

Figure 5-2. Xcalibur Library Manager dialog box - Convert Libraries page


Appendix AExample Reports

This appendix contains examples of results you can obtain by using Xcalibur Library Browser software.

_______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ A-1

Example ReportsReports from a Library Search Using Sequence Setup

A.1 Reports from a Library Search Using Sequence Setup

This topic includes examples of library search reports that Xcalibur prints automatically from Sequence Setup

A-2 ________________Finnigan Xcalibur: Getting Productive with Libraries________________

Example Reports_________________________________Report from a Library Search Using Qual Browser

A.2 Report from a Library Search Using Qual Browser

This topic includes an example report of a library search that you can print from Qual Browser.

_______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ A-13

Example Reports_______________________________ Report from a Library Search Using Library Browser

A.3 Report from a Library Search Using Library Browser

This topic includes an example report of a library search that you can print from Library Browser.

_______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ A-15

Index

________________________________________________________________________

Index

Aadding an entry to a library, procedure, 2-12adding libraries to the NIST libraries list, 5-2adding plots to a view, 2-4algorithms (note), 3-3appending additional compounds to the user library, procedure, 2-21appending spectra, Message box (figure), 2-21Attach Structure To User Spectrum dialog box (figure), 2-18attaching a chemical structure to a library entry, procedure, 2-13Automation dialog box (figure), 4-9Avalon peak detection algorithm, 1-4

Bbackground, subtracting, procedure, 2-6brackets (note), 3-13Browse For Sample Report Template dialog box, (figure), 3-9

CChoose Library To Save To dialog box

figure, 2-12, 2-20Chromatogram view (figure), 2-4Configuration dialog box, Xcalibur (figure), 1-5converting libraries to another format, 5-3copying libraries from the NIST libraries list, 5-2creating a custom library of spectra, procedure, 2-1creating a library entry with your spectral data, 2-2custom reports, example, 3-8

Ddeleting libraries from the NIST libraries list, 5-2detecting peaks

ICIS algorithm (note), 3-3specifying ICIS algorithm (figure), 1-5

Eexporting a spectrum to Library Browser, procedure, 2-9

Ffigures

Attach Structure To User Spectrum dialog box, 2-18Automation dialog box, 4-9Batch Reprocess Setup dialog box, 3-16Browse For Sample Report Template dialog box, 3-9Choose Library To Save To dialog box, 2-12, 2-20Chromatogram view, 2-4File Summary Information dialog box, 3-11ICIS Advanced Parameters dialog box, 3-4

Librarian window, 2-10, 2-16, 2-22, 2-24, 2-25Libraries To Search And The Search Order dialog box,

4-8Library Browser windows, 2-9Library Search Property dialog box, 2-14Library Search Results view, 4-4Library Search window, 2-15, 2-23, 2-26Message box

Saving Sequence List, 3-16Spec List, 2-21

Open dialog box, 2-17Open Raw File dialog box, 2-3Peak Detection page, 1-5Print dialog box, 4-5Processing Setup window, Qual view, 3-3Processing Status window, 3-17Qual Browser window, 2-4, 2-6, 2-8, 4-2Reports view

enabling row 1, 3-8specifying report template, 3-10

Save As dialog box, 3-12Search List dialog box, 3-5Search Properties dialog box, 4-3Sequence Setup window, 3-13, 3-14Spectrum Information dialog box, 2-11, 2-17, 2-19User Search Options dialog box, 4-7Xcalibur Configuration dialog box, 1-5

File Summary Information dialog box (figure), 3-11

GGenesis peak detection algorithm, 1-4

IICIS

peak detection algorithm, 1-4specifying (figure), 1-5

ICIS Advanced Parameters dialog box (figure), 3-4INCOS Noise option button (figure), 3-4

Llayouts, customizing in Library Browser, 4-12Librarian window (figure), 2-10, 2-16, 2-22, 2-24, 2-25libraries

adding entries to, 2-12adding to the NIST libraries list, 5-2appending compounds to, 2-21appending entries to (figure), 2-22attaching structures to

figure, 2-18, 2-19procedure, 2-13

converting to another format, 5-3copying from the NIST libraries list, 5-2creating entries in, 2-2deleting from the NIST libraries list, 5-2managing (figure), 2-10

_______________ Finnigan Xcalibur: Getting Productive with Libraries __________________ I

Index

________________________________________________________________________

naming, 2-12searching

from Library Browser, 4-6from Qual Browser, 4-2

specifying which to search, 2-14specifying, in Processing Setup (figure), 3-5specifying, to search in Qual Browser (figure), 4-3

Libraries To Search And The Search Order dialog box (figure), 4-8Library Browser

contents, 4-9customizing layouts, 4-12definition, 1-1exporting a spectrum to, 2-9figure, 2-9

library searchProcessing Method search list (note), 3-4

Library Search Property dialog box (figure), 2-14Library Search Results view (figure), 4-4Library Search window (figure), 2-15, 2-23, 2-26

Mmass defect, 4-9mass-to-charge ratios list (figure), 2-11Message box

appending spectra (figure), 2-21Saving Sequence list (figure), 3-16

Nnaming libraries

figure, 2-12procedure, 2-12

NIST MS Search (note), 1-1notes

algorithm, 3-3custom report templates, 3-6displaying files in Library Browser, 4-6Library Browser definition, 1-1Merlin, 3-6online Help access, 2-1Sequence Setup window, 3-13target compounds

using Library Search Constraints page, 3-2user libraries, 3-4

Oonline Help access (note), 2-1Open dialog box (figure), 2-17Open Raw File dialog box (figure), 2-3opening a raw data file in Qual Browser, procedure, 2-2overview of Library Browser, 1-1

PPeak Detection page (figure), 1-5peak detection, specifying ICIS algorithm (figure), 1-5plots, adding to a view, 2-4Print dialog box (figure), 4-5

printing reportsin Library Browser, 4-10in Qual Browser, 4-4in Sequence Setup, 3-15

proceduresaccessing online Help (note), 2-1adding an entry to a library, 2-12adding libraries to the NIST libraries list, 5-2appending additional compounds to the user library,

2-21attaching a chemical structure to a library entry, 2-13converting libraries to another format, 5-3copying libraries from the NIST libraries list, 5-2creating a custom library of spectra, 2-1creating a library entry with your spectral data, 2-2customizing Library Browser layout, 4-12deleting libraries from the NIST libraries list, 5-2exporting a spectrum to Library Browser, 2-9naming a library, 2-12opening a raw data file in Qual Browser, 2-2overview of Library Browser, 1-1printing reports in Sequence Setup, 3-15reprocessing raw files in Sequence Setup, 3-15searching libraries from Library Browser, 4-6searching libraries from Qual Browser, 4-2setting up Qual view to search a library, 3-2specifying ICIS for peak detection, 1-4specifying raw data files in Sequence Setup, 3-12specifying report options for library searches, 3-6specifying report options in Processing Setup, 3-2specifying search parameters in Processing Setup, 3-2subtracting background spectra, 2-6viewing a spectrum in Qual Browser, 2-3

Processing Setup windowQual view (figure), 3-3Reports view, 3-6

Processing Status window (figure), 3-17

QQual Browser

exporting a spectrum to Library Browser, 2-9figure, 2-4, 2-6, 2-8

Qual Browser window (figure), 4-2Qual view

in Processing Setup (figure), 3-3setting up, to search a library, 3-2

qualitative analysis, reprocessing data, 3-15Quick Reference Guide, 1-2

Rreports

designing custom (note), 3-6example of custom, 3-8, A-2printing

in Library Browser, 4-10in Qual Browser, 4-4in Sequence Setup, 3-15

template name, specifying (figure), 3-10

II___________________Finnigan Xcalibur: Getting Productive with Libraries________________

Index

________________________________________________________________________

Reports viewenabling row 1 (figure), 3-8specifying report template (figure), 3-10

reprocessing in Sequence Setup, 3-15

SSave As dialog box, (figure), 3-12Scan Filter view (figure), 2-6, 2-8, 4-2search libraries

Automation dialog box, 4-9Spectral Import Options dialog box, 4-8

Search List dialog box (figure), 3-5Search Properties dialog box (figure), 4-3search results in Library Browser, 2-15searching libraries

from Spec List (figure), 2-23in Library Browser, 2-14

Sequence Setup windowfigure, 3-13, 3-14note, 3-13

Sequence Setup, specifying files, 3-12Spec List, searching from (figure), 2-23specifying peak detection with the ICIS algorithm, 1-4Spectral Import Options dialog box, 4-8

spectrumas text file (figure), 2-10background subtracting (figure), 2-8imported from Qual Browser (figure), 2-9

Spectrum Information dialog boxfigure, 2-11, 2-17, 2-19

Spectrum view (figure), 2-6, 2-8, 4-2status, processing (figure), 3-17structures, attaching to library entry

figure, 2-18, 2-19procedure, 2-13

subtracting background spectra, procedure, 2-6

UUser Search Options dialog box (figure), 4-7

Vviewing a spectrum in Qual Browser, procedure, 2-3views

Chromatogram, 2-6, 2-8, 4-2cursor actions in, 2-3Library Search Results in Qual Browser, 4-4Scan Filter, 2-6, 2-8, 4-2Spectrum, 2-6, 2-8, 4-2using interactively, 2-3

WWarning box (figure), 2-20

XXcalibur Configuration dialog box (figure), 1-5

_______________ Finnigan Xcalibur: Getting Productive with Libraries _________________ III

Documents

Xcalibur Creating and Searching Libraries