Sie sind auf Seite 1von 102

'JOOJHBO¥™

9DBMJCVS
(FUUJOH1SPEVDUJWF
$SFBUJOHBOE4FBSDIJOH
-JCSBSJFT

3FWJTJPO"
9$"-*
Finnigan™ is a trademark of and Xcalibur® is a registered trademark of Thermo Electron Corporation. Microsoft® and Windows® are registered
trademarks of Microsoft Corporation. ChemDraw™ is a trademark of CambridgeSoft Corporation.

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).
This publication is not part of the Agreement of Sale between Thermo Electron Corporation and the purchaser
of a GC/MS or LC/MS system. In the event of any conflict between the provisions of this document and those
contained in Thermo Electron Corporation’s Terms and Conditions, the provisions of the Terms and Conditions
shall govern.
System Configurations and Specifications supersede all previous information and are subject to change
without notice.

Printing History: Revision A printed in May 2003.


Software Revision: Xcalibur 1.4

The products of Thermo Electron San Jose are produced under ISO 9001 accredited quality management systems.

Published by Technical Publications, Thermo Electron Corporation, San Jose, California.


Copyright© 2003 Thermo Electron Corporation. All rights reserved. Printed in the United States of America.
Customer Registration... Register now and receive all the privileges associated with being a Thermo
Electron, Finnigan product user, including application reports and technical reports.
Name _______________________________________________________________________________________
Title ________________________________________________________________________________________
Company ___________________________________________________________________________________
Address _____________________________________________________________________________________
City/State/Postal Code _________________________________________________________________________
Country _____________________________________________________________________________________
Telephone _____________________________________________________ Ext. _________________________
System Type _______________________ Serial # _____________________ Date Purchased_________________

Tell us more... Let us know more about how you use this product:
My Organization Is: (Check one only) My Primary Application Is: (Check one only)
‰ Commercial (for profit) lab ‰ Analytical
‰ Government lab ‰ Biomedical
‰ Hospital / Clinic ‰ Clinical / Toxicology
‰ Research Institute ‰ Energy
‰ University / College ‰ Food / Agriculture
‰ Veterinary ‰ Forensic / Toxicology
‰ Other ___________________________ ‰ Pharmaceutical
‰ Research / Education
‰ Other ___________________________
Job Function: (Check one only)
‰ Administration
‰ Lab Management
‰ Operator
‰ Other ___________________________

Reader Survey... Help us to improve the quality of our documentation by answering a few questions:
Finnigan Xcalibur Getting Productive: Revision A
Creating and Searching Libraries XCALI-97062
Strongly Strongly
Agree Agree Disagree Disagree
The manual is well organized. 1 2 3 4
The manual is clearly written. 1 2 3 4
The manual contains all of the information I need. 1 2 3 4
The instructions are easy to follow. 1 2 3 4
The instructions are complete. 1 2 3 4
The technical information is easy to understand. 1 2 3 4
The figures are helpful. 1 2 3 4
I was able to operate the system by using this manual. 1 2 3 4
(If not, please comment below.)

Additional Comments: (Attach additional sheets if necessary.)


___________________________________________________________________________________
___________________________________________________________________________________
___________________________________________________________________________________
___________________________________________________________________________________
___________________________________________________________________________________
___________________________________________________________________________________
___________________________________________________________________________________
Tear this sheet from the manual, fold it closed, stamp it, and drop it in the mail.
fold
From _______________________________ Place
____________________________________ Stamp
Here
____________________________________

EDITOR, TECHNICAL PUBLICATIONS


THERMO ELECTRON SAN JOSE
355 RIVER OAKS PARKWAY
SAN JOSE, CA 95134-1991
UNITED STATES OF AMERICA

fold
Contents
'JOOJHBO9DBMJCVS ________________________________________________________________________

Contents

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


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

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

Typographical Conventions ................................................................................................................... ix


Data Input ............................................................................................................................. ix
Boxed Information................................................................................................................. x
Topic 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..................................................................... 2-2
Opening a Raw Data File (.raw) in Qual Browser .............................................................. 2-2
Viewing a Spectrum in Qual Browser ................................................................................. 2-3
Subtracting Background Spectra ......................................................................................... 2-6
Exporting a Spectrum to Library Browser .......................................................................... 2-9

2.2 Editing a User Library.............................................................................................................. 2-10


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

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


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

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

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries __________________ i
Contents
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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________________ 5IFSNP


&-&$530/$03103"5*0/
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.

5IFSNP
&-&$530/$03103"5*0/ _________________ Finnigan Xcalibur: Getting Productive with Libraries _______________ iii
Read This First
Changes to the Manual and Online Help @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

Changes to the Manual and Online Help


To suggest changes to this manual or the online Help, please send your
comments to:
Editor, Technical Publications
Thermo Electron San Jose
355 River Oaks Parkway
San Jose, CA 95134-1991
U.S.A.
You are encouraged to report errors or omissions in the text or index.
Thank you.

iv __________________Finnigan Xcalibur: Getting Productive with Libraries________________5IFSNP


&-&$530/$03103"5*0/
Read This First
'JOOJHBO9DBMJCVS _____________________________________________________________ Abbreviations

Abbreviations
The 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

5IFSNP
&-&$530/$03103"5*0/ _________________ Finnigan Xcalibur: Getting Productive with Libraries _______________ v
Read This First
Abbreviations@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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________________5IFSNP


&-&$530/$03103"5*0/
Read This First
'JOOJHBO9DBMJCVS _____________________________________________________________ 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

5IFSNP
&-&$530/$03103"5*0/ _________________ Finnigan Xcalibur: Getting Productive with Libraries ______________ vii
Read This First
Abbreviations@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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________________ 5IFSNP


&-&$530/$03103"5*0/
Read This First
'JOOJHBO9DBMJCVS ___________________________________________________Typographical Conventions

Typographical Conventions
Typographical 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”.

5IFSNP
&-&$530/$03103"5*0/ _________________ Finnigan Xcalibur: Getting Productive with Libraries ______________ ix
Read This First
Typographical Conventions @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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.

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

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.

x ___________________Finnigan Xcalibur: Getting Productive with Libraries________________ 5IFSNP


&-&$530/$03103"5*0/
Read This First
'JOOJHBO9DBMJCVS ___________________________________________________Typographical Conventions

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

Chapter 1
Chapter Name

1.2 Second Level Topics

Third Level Topics

Fourth Level Topics

Fifth Level Topics

5IFSNP
&-&$530/$03103"5*0/ _________________ Finnigan Xcalibur: Getting Productive with Libraries ______________ xi
Read This First
Reply Cards @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

Reply Cards
Thermo 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________________5IFSNP


&-&$530/$03103"5*0/
Chapter 1
Overview 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.

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.

This chapter contains the following topics:


• Quick Reference Guide
• Specifying the Peak Detection Algorithm

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 1-1
Overview of Library Browser
Quick Reference Guide @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

1.1 Quick Reference Guide


Figure 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 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Overview of Library Browser
'JOOJHBO9DBMJCVS ______________________________________________________Quick Reference Guide

Create a Library Spectrum

Open a raw Display a Export


file in Qual spectrum spectrum to
Browser Library Browser

Create the Library Entry

Specify entry Attach a Append other


name, CAS#, Name the
structure spectra to
MW, in Library library
(optional) library
Browser

Search Libraries and Print Reports

Automatically, using .raw or .rst files

Specify search Specify sequence Batch reprocess:


parameters in in Sequence choose to print
Processing Setup Setup reports

Manually, using a single spectrum

Specify library
Print report
options; search
Open a .raw file
in Qual Browser,
and display the
spectrum
Export spectrum Specify library
to Library Browser Print reports
options; search

Collected Printed Reports


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

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 1-3
Overview of Library Browser
Specifying the Peak Detection Algorithm @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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.

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.

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.

1-4 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Overview of Library Browser
'JOOJHBO9DBMJCVS ________________________________________ 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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 1-5
Overview of Library Browser
Specifying the Peak Detection Algorithm @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

Figure 1-3. Global Mass Options dialog box

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

1-6 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Chapter 2
Creating 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.

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.

This chapter contains the following topics:


• Creating a Library Entry with Your Spectral Data
• Editing a User Library

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 2-1
Creating a Custom Library of Spectra
Creating a Library Entry with Your Spectral Data @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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.

2-2 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS __________________________________ Creating a Library Entry with Your Spectral Data

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

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:

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 2-3
Creating a Custom Library of Spectra
Creating a Library Entry with Your Spectral Data @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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

2-4 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS __________________________________ Creating a Library Entry with Your Spectral Data

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 2-5
Creating a Custom Library of Spectra
Creating a Library Entry with Your Spectral Data @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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

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.

2-6 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS __________________________________ Creating a Library Entry with Your Spectral Data

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 2-7
Creating a Custom Library of Spectra
Creating a Library Entry with Your Spectral Data @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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

2-8 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS __________________________________ Creating a Library Entry with Your Spectral Data

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

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 2-9
Creating a Custom Library of Spectra
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Editing a User Library

2.2 Editing a User Library


You can edit a user library entry that contains the MS/MS spectrum you
exported from Qual Browser.
This topic contains the following topics:
• 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________________ 5IFSNP


&-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS _______________________________________________________ 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

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 2-11
Creating a Custom Library of Spectra
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Editing a User Library

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

2-12 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ 5IFSNP


&-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS _______________________________________________________ Editing a User Library

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 2-13
Creating a Custom Library of Spectra
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Editing a User Library

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

5IFSNP
2-14 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS _______________________________________________________ Editing a User Library

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

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 2-15
Creating a Custom Library of Spectra
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Editing a User Library

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

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.

2-16 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ 5IFSNP


&-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS _______________________________________________________ Editing a User Library

Figure 2-13. Spectrum Information dialog box, showing the name of


entry edited to hydrocortisoneMS2

Figure 2-14. Open dialog box

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 2-17
Creating a Custom Library of Spectra
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Editing a User Library

Figure 2-15. Attach Structure To User Spectrum 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.

2-18 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ 5IFSNP


&-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS _______________________________________________________ Editing a User Library

Figure 2-16. Spectrum Information dialog box, showing the structure


of hydrocortisone from the nistdemo library to be
included in the user-library entry

g. Click on Add to Library to display the Choose Library To Save To


dialog box. See Figure 2-17.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 2-19
Creating a Custom Library of Spectra
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Editing a User Library

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

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

2-20 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ 5IFSNP


&-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS _______________________________________________________ Editing a User Library

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

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 2-21
Creating a Custom Library of Spectra
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Editing a User Library

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

2-22 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ 5IFSNP


&-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS _______________________________________________________ Editing a User Library

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

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 2-23
Creating a Custom Library of Spectra
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Editing a User Library

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

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.

2-24 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ 5IFSNP


&-&$530/$03103"5*0/
Creating a Custom Library of Spectra
'JOOJHBO9DBMJCVS _______________________________________________________ Editing a User Library

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

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 2-25
Creating a Custom Library of Spectra
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Editing a User Library

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

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.

2-26 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ 5IFSNP


&-&$530/$03103"5*0/
Chapter 3
Searching 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.

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

This chapter contains the following topics:


• Setting Up to Search Libraries Automatically
• Reprocessing Raw Files and Printing Reports

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 3-1
Searching Libraries Automatically
Setting Up to Search Libraries Automatically @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

3.1 Setting Up to Search Libraries


Automatically
You can set up Xcalibur to search libraries automatically.
This topic contains the following topics:
• 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.
This topic contains the following topics:
• 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.

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

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.

3-2 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Searching Libraries Automatically
'JOOJHBO9DBMJCVS _____________________________________ Setting Up to Search Libraries Automatically

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

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.

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

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 3-3
Searching Libraries Automatically
Setting Up to Search Libraries Automatically @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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


option INCOS Noise

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.

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.

3-4 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Searching Libraries Automatically
'JOOJHBO9DBMJCVS _____________________________________ Setting Up to Search Libraries Automatically

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

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 3-5
Searching Libraries Automatically
Setting Up to Search Libraries Automatically @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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.

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.

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

3-6 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Searching Libraries Automatically
'JOOJHBO9DBMJCVS _____________________________________ Setting Up to Search Libraries Automatically

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

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 3-7
Searching Libraries Automatically
Setting Up to Search Libraries Automatically @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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

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.

3-8 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Searching Libraries Automatically
'JOOJHBO9DBMJCVS _____________________________________ Setting Up to Search Libraries Automatically

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

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 3-9
Searching Libraries Automatically
Setting Up to Search Libraries Automatically @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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

6. Save the Processing Method, as follows:


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

5IFSNP
3-10 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Searching Libraries Automatically
'JOOJHBO9DBMJCVS _____________________________________ Setting Up to Search Libraries Automatically

Figure 3-8. File Summary Information dialog box

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 3-11
Searching Libraries Automatically
Setting Up to Search Libraries Automatically @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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

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.

3-12 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ 5IFSNP


&-&$530/$03103"5*0/
Searching Libraries Automatically
'JOOJHBO9DBMJCVS _____________________________________ Setting Up to Search Libraries Automatically

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.

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.

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 3-13
Searching Libraries Automatically
Setting Up to Search Libraries Automatically @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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

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

3-14 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ 5IFSNP


&-&$530/$03103"5*0/
Searching Libraries Automatically
'JOOJHBO9DBMJCVS ____________________________________ 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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 3-15
Searching Libraries Automatically
Reprocessing Raw Files and Printing Reports @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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

5IFSNP
3-16 _______________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Searching Libraries Automatically
'JOOJHBO9DBMJCVS ____________________________________ Reprocessing Raw Files and Printing Reports

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

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.
In this chapter, you did the following:
• 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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 3-17
Chapter 4
Searching 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.
This chapter contains the following topics:
• Initiating a Library Search from Qual Browser
• Searching a Library by Using Library Browser
• Customizing the Library Browser Layout

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 4-1
Searching Libraries from Qual Browser and Library Browser
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Initiating 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

4-2 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Searching Libraries from Qual Browser and Library Browser
'JOOJHBO9DBMJCVS ____________________________________ 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

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 4-3
Searching Libraries from Qual Browser and Library Browser
Initiating a Library Search from Qual Browser @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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.

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.

4-4 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Searching Libraries from Qual Browser and Library Browser
'JOOJHBO9DBMJCVS ____________________________________ Initiating a Library Search from Qual Browser

Figure 4-4. Print dialog box

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 4-5
Searching Libraries from Qual Browser and Library Browser
Searching a Library by Using Library Browser@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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.

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.

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.

4-6 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Searching Libraries from Qual Browser and Library Browser
'JOOJHBO9DBMJCVS ____________________________________ Searching a Library by Using Library Browser

Figure 4-5. Library Search Property dialog box

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 4-7
Searching Libraries from Qual Browser and Library Browser
Searching a Library by Using Library Browser @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

Figure 4-6. Libraries Search Property dialog box, showing the


included libraries MS2test and nistdemo

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.)

4-8 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Searching Libraries from Qual Browser and Library Browser
'JOOJHBO9DBMJCVS ____________________________________ Searching a Library by Using Library Browser

Figure 4-7. Automation dialog box, showing option to search


libraries automatically when exporting spectra to Library
Browser

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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 4-9
Searching Libraries from Qual Browser and Library Browser
Searching a Library by Using Library Browser@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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

4-10 _______________Finnigan Xcalibur: Getting Productive with Libraries________________5IFSNP


&-&$530/$03103"5*0/
Searching Libraries from Qual Browser and Library Browser
'JOOJHBO9DBMJCVS ____________________________________ Searching a Library by Using Library Browser

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

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ 4-11
Searching Libraries from Qual Browser and Library Browser
Customizing the Library Browser Layout @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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.
In this chapter, you did the following:
• Used Qual Browser and Library Browser to search libraries
• Printed library search results

4-12 _______________Finnigan Xcalibur: Getting Productive with Libraries________________5IFSNP


&-&$530/$03103"5*0/
Chapter 5
Adding 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.
This chapter contains the following topics:
• Adding Libraries to and Deleting or Copying Libraries from the NIST
Libraries
• Converting Libraries to Another Format

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 5-1
Adding and Converting Libraries
Adding Libraries to and Deleting or Copying Libraries from the NIST Libraries @@@@@@@@@@ 'JOOJHBO9DBMJCVS

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.

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

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.

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


page

5-2 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Adding and Converting Libraries
'JOOJHBO9DBMJCVS _________________________________________ 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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ 5-3
Adding and Converting Libraries
Converting Libraries to Another Format @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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


page

5-4 5IFSNP
________________Finnigan Xcalibur: Getting Productive with Libraries________________ &-&$530/$03103"5*0/
Appendix A
Example Reports

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

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _______________ A-1
Example Reports
Reports from a Library Search Using Sequence Setup @@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS

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________________ 5IFSNP


&-&$530/$03103"5*0/
Example Reports
'JOOJHBO9DBMJCVS _________________________________ 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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ A-13
Example Reports
'JOOJHBO9DBMJCVS _______________________________ 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.

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries ______________ A-15
Index
'JOOJHBO9DBMJCVS ________________________________________________________________________

Index

Librarian window, 2-10, 2-16, 2-22, 2-24, 2-25


A Libraries To Search And The Search Order dialog box,
4-8
adding an entry to a library, procedure, 2-12
Library Browser windows, 2-9
adding libraries to the NIST libraries list, 5-2
Library Search Property dialog box, 2-14
adding plots to a view, 2-4
Library Search Results view, 4-4
algorithms (note), 3-3
Library Search window, 2-15, 2-23, 2-26
appending additional compounds to the user library,
Message box
procedure, 2-21
Saving Sequence List, 3-16
appending spectra, Message box (figure), 2-21
Spec List, 2-21
Attach Structure To User Spectrum dialog box (figure),
Open dialog box, 2-17
2-18
Open Raw File dialog box, 2-3
attaching a chemical structure to a library entry,
Peak Detection page, 1-5
procedure, 2-13
Print dialog box, 4-5
Automation dialog box (figure), 4-9
Processing Setup window, Qual view, 3-3
Avalon peak detection algorithm, 1-4
Processing Status window, 3-17
Qual Browser window, 2-4, 2-6, 2-8, 4-2
B Reports view
enabling row 1, 3-8
background, subtracting, procedure, 2-6 specifying report template, 3-10
brackets (note), 3-13 Save As dialog box, 3-12
Browse For Sample Report Template dialog box, (figure), Search List dialog box, 3-5
3-9 Search Properties dialog box, 4-3
Sequence Setup window, 3-13, 3-14
C Spectrum Information dialog box, 2-11, 2-17, 2-19
User Search Options dialog box, 4-7
Choose Library To Save To dialog box Xcalibur Configuration dialog box, 1-5
figure, 2-12, 2-20 File Summary Information dialog box (figure), 3-11
Chromatogram view (figure), 2-4
Configuration dialog box, Xcalibur (figure), 1-5 G
converting libraries to another format, 5-3
copying libraries from the NIST libraries list, 5-2 Genesis peak detection algorithm, 1-4
creating a custom library of spectra, procedure, 2-1
creating a library entry with your spectral data, 2-2
custom reports, example, 3-8
I
ICIS
D peak detection algorithm, 1-4
specifying (figure), 1-5
deleting libraries from the NIST libraries list, 5-2 ICIS Advanced Parameters dialog box (figure), 3-4
detecting peaks INCOS Noise option button (figure), 3-4
ICIS algorithm (note), 3-3
specifying ICIS algorithm (figure), 1-5
L
E layouts, customizing in Library Browser, 4-12
Librarian window (figure), 2-10, 2-16, 2-22, 2-24, 2-25
exporting a spectrum to Library Browser, procedure, 2-9 libraries
adding entries to, 2-12
F adding to the NIST libraries list, 5-2
appending compounds to, 2-21
figures appending entries to (figure), 2-22
Attach Structure To User Spectrum dialog box, 2-18 attaching structures to
Automation dialog box, 4-9 figure, 2-18, 2-19
Batch Reprocess Setup dialog box, 3-16 procedure, 2-13
Browse For Sample Report Template dialog box, 3-9 converting to another format, 5-3
Choose Library To Save To dialog box, 2-12, 2-20 copying from the NIST libraries list, 5-2
Chromatogram view, 2-4 creating entries in, 2-2
File Summary Information dialog box, 3-11 deleting from the NIST libraries list, 5-2
ICIS Advanced Parameters dialog box, 3-4 managing (figure), 2-10

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries __________________ I
Index
________________________________________________________________________ 'JOOJHBO9DBMJCVS

naming, 2-12 printing reports


searching in Library Browser, 4-10
from Library Browser, 4-6 in Qual Browser, 4-4
from Qual Browser, 4-2 in Sequence Setup, 3-15
specifying which to search, 2-14 procedures
specifying, in Processing Setup (figure), 3-5 accessing online Help (note), 2-1
specifying, to search in Qual Browser (figure), 4-3 adding an entry to a library, 2-12
Libraries To Search And The Search Order dialog box adding libraries to the NIST libraries list, 5-2
(figure), 4-8 appending additional compounds to the user library,
Library Browser 2-21
contents, 4-9 attaching a chemical structure to a library entry, 2-13
customizing layouts, 4-12 converting libraries to another format, 5-3
definition, 1-1 copying libraries from the NIST libraries list, 5-2
exporting a spectrum to, 2-9 creating a custom library of spectra, 2-1
figure, 2-9 creating a library entry with your spectral data, 2-2
library search customizing Library Browser layout, 4-12
Processing Method search list (note), 3-4 deleting libraries from the NIST libraries list, 5-2
Library Search Property dialog box (figure), 2-14 exporting a spectrum to Library Browser, 2-9
Library Search Results view (figure), 4-4 naming a library, 2-12
Library Search window (figure), 2-15, 2-23, 2-26 opening a raw data file in Qual Browser, 2-2
overview of Library Browser, 1-1
M printing reports in Sequence Setup, 3-15
reprocessing raw files in Sequence Setup, 3-15
mass defect, 4-9 searching libraries from Library Browser, 4-6
mass-to-charge ratios list (figure), 2-11 searching libraries from Qual Browser, 4-2
Message box setting up Qual view to search a library, 3-2
appending spectra (figure), 2-21 specifying ICIS for peak detection, 1-4
Saving Sequence list (figure), 3-16 specifying raw data files in Sequence Setup, 3-12
specifying report options for library searches, 3-6
specifying report options in Processing Setup, 3-2
N specifying search parameters in Processing Setup, 3-2
subtracting background spectra, 2-6
naming libraries viewing a spectrum in Qual Browser, 2-3
figure, 2-12 Processing Setup window
procedure, 2-12 Qual view (figure), 3-3
NIST MS Search (note), 1-1 Reports view, 3-6
notes Processing Status window (figure), 3-17
algorithm, 3-3
custom report templates, 3-6
displaying files in Library Browser, 4-6 Q
Library Browser definition, 1-1
Merlin, 3-6 Qual Browser
online Help access, 2-1 exporting a spectrum to Library Browser, 2-9
Sequence Setup window, 3-13 figure, 2-4, 2-6, 2-8
target compounds Qual Browser window (figure), 4-2
using Library Search Constraints page, 3-2 Qual view
user libraries, 3-4 in Processing Setup (figure), 3-3
setting up, to search a library, 3-2
qualitative analysis, reprocessing data, 3-15
O Quick Reference Guide, 1-2
online Help access (note), 2-1
Open dialog box (figure), 2-17 R
Open Raw File dialog box (figure), 2-3
opening a raw data file in Qual Browser, procedure, 2-2 reports
overview of Library Browser, 1-1 designing custom (note), 3-6
example of custom, 3-8, A-2
printing
P in Library Browser, 4-10
in Qual Browser, 4-4
Peak Detection page (figure), 1-5 in Sequence Setup, 3-15
peak detection, specifying ICIS algorithm (figure), 1-5 template name, specifying (figure), 3-10
plots, adding to a view, 2-4
Print dialog box (figure), 4-5

II___________________Finnigan Xcalibur: Getting Productive with Libraries________________ 5IFSNP


&-&$530/$03103"5*0/
Index
'JOOJHBO9DBMJCVS ________________________________________________________________________

Reports view Spectrum view (figure), 2-6, 2-8, 4-2


enabling row 1 (figure), 3-8 status, processing (figure), 3-17
specifying report template (figure), 3-10 structures, attaching to library entry
reprocessing in Sequence Setup, 3-15 figure, 2-18, 2-19
procedure, 2-13
S subtracting background spectra, procedure, 2-6

Save As dialog box, (figure), 3-12 U


Scan Filter view (figure), 2-6, 2-8, 4-2
search libraries User Search Options dialog box (figure), 4-7
Automation dialog box, 4-9
Spectral Import Options dialog box, 4-8
Search List dialog box (figure), 3-5
V
Search Properties dialog box (figure), 4-3 viewing a spectrum in Qual Browser, procedure, 2-3
search results in Library Browser, 2-15 views
searching libraries Chromatogram, 2-6, 2-8, 4-2
from Spec List (figure), 2-23 cursor actions in, 2-3
in Library Browser, 2-14 Library Search Results in Qual Browser, 4-4
Sequence Setup window Scan Filter, 2-6, 2-8, 4-2
figure, 3-13, 3-14 Spectrum, 2-6, 2-8, 4-2
note, 3-13 using interactively, 2-3
Sequence Setup, specifying files, 3-12
Spec List, searching from (figure), 2-23
specifying peak detection with the ICIS algorithm, 1-4 W
Spectral Import Options dialog box, 4-8
Warning box (figure), 2-20
spectrum
as text file (figure), 2-10 X
background subtracting (figure), 2-8
imported from Qual Browser (figure), 2-9 Xcalibur Configuration dialog box (figure), 1-5
Spectrum Information dialog box
figure, 2-11, 2-17, 2-19

5IFSNP
&-&$530/$03103"5*0/ _______________ Finnigan Xcalibur: Getting Productive with Libraries _________________ III