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Thermo Xcalibur
Creating and Searching Libraries
Version 2.2
User Guide
XCALI-97210 Revision D
May 2011
© 2011 Thermo Fisher Scientific Inc. All rights reserved.
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The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or errorfree and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
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Release history: Revision A, January 2009; Revision B, September 2010; Revision C, January 2011
(to reflect Microsoft Windows 7 compatibility); Revision D, May 2011
Software version: Thermo Xcalibur version 2.2
For Research Use Only. Not for use in diagnostic procedures.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii
Thermo Scientific
Chapter 1
Overview of Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Library Browser Process Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
About Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Library Browser Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Library Search Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Other Search Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Name Search Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Compare Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Librarian Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Chapter 2
Adding a Spectrum to a Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Opening a Raw Data File (.raw) in Qual Browser . . . . . . . . . . . . . . . . . . . . . . . 15
Viewing a Spectrum in Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Working with Background Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Using the Subtract Background Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Subtracting Background Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Exporting Spectra from the Xcalibur Data System. . . . . . . . . . . . . . . . . . . . . . . 22
Exporting Spectra Manually from Qual Browser . . . . . . . . . . . . . . . . . . . . . . 22
Exporting Spectra Automatically from the Processing Method . . . . . . . . . . . 23
Chapter 3
Managing Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
Creating a User Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Adding Spectra to a User Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Editing a User Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Editing Spectrum Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Attaching a Chemical Structure to a Library Entry . . . . . . . . . . . . . . . . . . . . 32
Adding Additional Compounds to the User Library . . . . . . . . . . . . . . . . . . . 37
Managing the NIST Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Adding a Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Deleting a Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Copying a Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Creating and Searching Libraries User Guide
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Contents
Converting Libraries to Another Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Chapter 4
Searching Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47
Customizing a Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Including a User Library in a Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Limiting a Library Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Searching a User Library Entry by ID Number . . . . . . . . . . . . . . . . . . . . . . . 51
Setting Library Search Option Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Submitting a Spectrum to a Library Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Limiting a Library Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Applying a Molecular Weight Constraint . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Applying the Other Databases Constraint . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Applying a Name Fragment Constraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Applying Element Constraints. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Applying Mass Spectral Peak Constraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Selecting Libraries to Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Setting Up to Search Libraries Automatically . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Specifying Search Parameters in the Qual View . . . . . . . . . . . . . . . . . . . . . . . 63
Specifying Report Options for Library Searches. . . . . . . . . . . . . . . . . . . . . . . 66
Specifying Raw Data Files in Sequence Setup . . . . . . . . . . . . . . . . . . . . . . . . 70
Processing Raw Files and Printing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Initiating a Library Search from Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . 74
Searching a Library Using Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Chapter A
Library Sample Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83
Reports from a Library Search Using Sequence Setup . . . . . . . . . . . . . . . . . . . . 83
Report from a Library Search Using Qual Browser . . . . . . . . . . . . . . . . . . . . . . 94
Report from a Library Search Using Library Browser. . . . . . . . . . . . . . . . . . . . . 95
Appendix B AMDIS Compound Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .97
AMDIS Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Automated Compound Identification Using AMDIS . . . . . . . . . . . . . . . . . . . . 98
Results Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Confirm Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Appendix C Library Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103
Library Manager Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Convert Libraries Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Manage Libraries Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Library Search Options Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Search Parameters Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Libraries Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Automation Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Limits Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Library Search Constraints Page (Library View). . . . . . . . . . . . . . . . . . . . . . 111
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Spectrum Information Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Library Search Results Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121
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Creating and Searching Libraries User Guide
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P
Preface
The Thermo Xcalibur™ mass spectrometry data system includes all the software needed to
create, search, and edit libraries. This guide describes:
• How to create and edit custom libraries for MS, MS/MS, or MSn spectra
• How to manage multiple libraries
• How to search multiple libraries
To provide us with comments about this document, please click the link below. Thank you in
advance for your help.
Related Documentation
Thermo Fisher Scientific provides these documents for the Xcalibur data system:
• Xcalibur Getting Started (Quantitative Analysis)
• Acquisition and Processing User Guide
• Quantitative Analysis User Guide
• Qualitative Analysis User Guide
• Creating and Searching Libraries User Guide
• XReport User Guide
• Help from within the software
Thermo Scientific
Creating and Searching Libraries User Guide
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Preface
Safety and Special Notices
Make sure you follow the precautionary statements presented in this guide. The safety and
other special notices appear in boxes.
Safety and special notices include the following:
CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION
notice is accompanied by an appropriate CAUTION symbol.
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or may contain information that is critical for optimal
performance of the system.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
 To contact Technical Support
Phone
800-532-4752
Fax
561-688-8736
E-mail
[email protected]
Knowledge base
www.thermokb.com
Find software updates and utilities to download at mssupport.thermo.com.
 To contact Customer Service for ordering information
Phone
800-532-4752
Fax
561-688-8731
E-mail
[email protected]
Web site
www.thermo.com/ms
 To get local contact information for sales or service
Go to www.thermoscientific.com/wps/portal/ts/contactus.
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Preface
 To copy manuals from the Internet
Go to mssupport.thermo.com, agree to the Terms and Conditions, and then click
Customer Manuals in the left margin of the window.
 To suggest changes to documentation or to Help
• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.
• Send an e-mail message to the Technical Publications Editor at
[email protected]
Thermo Scientific
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1
Overview of Library Browser
This chapter gives a brief overview of Library Browser, describes how to use data exported
from Qual Browser, and describes how to build and maintain a user library.
Contents
• Library Browser Process Overview
• About Library Browser
• Library Browser Windows
Use Xcalibur Library Browser to do these tasks:
• Create spectral libraries, including MS/MS fragmentation libraries.
• Use the Library Browser to run automatic, post-acquisition library searches on MS/MS
fragmentation spectra.
• Run searches directly from the Qual Browser in the data system or automatically by batch
processing data files in the Sequence Setup window using a qualitative processing
method.
“Library Browser Process Overview” on page 2 summarizes the steps for creating, editing, and
searching custom libraries and printing reports of the results.
This chapter also provides information about how to choose a peak detection algorithm for
the Xcalibur data system to use when performing library searches.
Note Throughout this guide, the term Library Browser is used synonymously with the
term NIST MS Search (National Institute of Standards and Technology Mass Spectral
Search Program and Library System) to refer to the NIST MS Search desktop.
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Overview of Library Browser
Library Browser Process Overview
Library Browser Process Overview
Figure 1 provides a summary of the steps you perform to create, edit, and search libraries and
to print reports using the Xcalibur data system.
When using the Library Browser, create a custom user library of MS/MS or MSn spectra, one
entry at a time. To include a spectrum in a library entry, display a qualitative .raw file data in
Qual Browser. Then, in Qual Browser, you can enhance a spectrum by averaging several scans
and by subtracting background scans.
After enhancing the spectrum, you can export the spectrum to Library Browser. See “Adding
Spectra to a User Library” on page 29 for more information on this process.
After exporting the spectrum to Library Browser, you can edit the spectrum information.
For example, you can change the name of the entry or specify the molecular weight or the
CAS (Chemical Abstract Service) registry number. You can even attach a chemical structure to
the library entry or select which mass-to-charge ratios to include. See “Managing Libraries” on
page 25 for more information.
IMPORTANT For MS/MS and MSn spectra, however, do not delete any of the masses that
the data system detects because the presence of a particular mass-to-charge ratio, rather
than its intensity, is essential to identifying a compound.
Finally, the Xcalibur data system provides three ways to search libraries and print custom
reports:
• Automatically, by using raw (.raw) or result (.rst) files in Sequence Setup (See “Setting Up
to Search Libraries Automatically” on page 62 for more information.)
• Manually, by using a single spectrum in Qual Browser (See “Initiating a Library Search
from Qual Browser” on page 74 for more information.)
• Manually, by using a single spectrum exported to Library Browser (See “Searching a
Library Using Library Browser” on page 77 for more information.)
You can use the Qual view options in the Processing Setup window to specify a processing
method to print reports automatically. Then reference this processing method to specify a
sequence of files in Sequence Setup. When you process a sequence, the data system prints the
reports. Refer to the Acquisition and Processing User Guide for more information about using
Processing and Sequence Setup. You can also create processing settings to automatically add
spectra to the library.
If you manually search for search results that match a single spectrum, print the results by
using the File > Print command in Qual Browser or in Library Browser.
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1
Figure 1.
Overview of Library Browser
About Library Browser
Library Browser process overview
Create a Library Spectrum
Open a .raw file in
Qual Browser
Export spectrum to
Library Browser
Display a spectrum
Create a Library or Add to an Existing Library
Specify entry name,
CAS#, MW, in
Library Browser
Name a new library or
select an existing
library
Attach a structure
(optional)
Specify sequence in
Sequence Setup
Batch process:
choose to print reports
Append other spectra
to library
Search Libraries and Print Reports
Automatically, using .raw or .rst files
Specify search
parameters in
Processing Setup
Manually, using a single spectrum
Open a raw file in
Qual Browser and
display the spectrum
Export a spectrum to
Library Browser
Specify library options;
search
Print report
Specify library options;
search
Print reports
About Library Browser
The Xcalibur data system uses the NIST (National Institute of Standards and Technology)
Mass Spectral Search Program and Library System. This system contains up to three different
libraries:
• The 2000 version of the NIST/EPA/NIH Mass Spectral Library containing over 147000
compounds (optional)
• The NIST/EPA/NIH Mass Spectral Selected Replicates Library of 27750 spectra
(optional)
• A default user library, NISTDEMO
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Creating and Searching Libraries User Guide
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1
Overview of Library Browser
Library Browser Windows
The NIST libraries give access to
• An extensive collection of chemical names
• Chemical Abstracts Service (CAS) registry numbers
• Molecular formulas and weights
• Chemical structures
You can create user libraries using spectra
• Exported from Qual Browser
• Exported automatically by a processing method
• From other sources including text files
The program permits searches in many different ways:
• Find reference spectra most closely matching a submitted spectrum.
• Locate spectra or compounds having certain specified characteristics (for example, the
abundance of certain peaks).
• Display the mass spectra of selected molecules.
Library Browser Windows
The Library Browser contains five main windows with tabs at the bottom of the window:
• Library Search Window
• Other Search Window
• Name Search Window
• Compare Window
• Librarian Window
A description of each of these windows follows.
To display a specific window, click the appropriate tab at the bottom of the screen.
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1
Overview of Library Browser
Library Browser Windows
Library Search Window
The Library Search window of the Library Browser (see Figure 2) features eight panes:
Spec list
A “scratch pad” for storage of imported spectra and database spectra of interest
Histogram
A graphical display of the number of matches as a function of the match factor
Click a bar to change the information displayed in the other windows.
Search results (Hit list)
A list of compounds in the database with spectra that are similar to the unknown
Plot of Search Spectrum
The plot of the spectrum being investigated
Text of Search Spectrum
Text about the spectrum being investigated
Difference (Compare Result)
A graphical display of peaks from the first (often upper) spectrum and the second
(often lower) spectrum along with the difference.
Plot of Hit
The spectrum of a search result
Hit Text Information
Text concerning an item from the search results
Figure 2.
Library Search window
Compare window
Search Spectrum plot
Search Spectrum text
Spec list
Histogram
Search Results
list
Hit plot
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Hit text
Creating and Searching Libraries User Guide
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1
Overview of Library Browser
Library Browser Windows
Using the Spec List
The Library Browser stores spectra in the Spec List pane of the Library Search window when
you do either of the following:
• Export spectra from Qual Browser
• Import spectra from other sources using the File > Open command
• Get a spectrum from a library
The Browser identifies the origin of each Spec List entry with an initial letter:
(T)
Spectra that came directly from a text file such as that exported by Qual Browser
(E)
Spectra created with the Edit or New buttons in the User Library Manager window
(M)
Spectra from the NIST/EPA/NIH Main library
(R)
Spectra from the NIST/EPA/NIH Replicates library
(U)
Spectra from a user library
 To submit a Spec List spectrum to a Library Browser search
1. Set the Library Search options. See “Customizing a Search” on page 48.
2. Double-click the spectrum name.
The Browser displays all search results in the search results (Hit List) pane (see below).
Comparing a Spec List Spectrum in the Compare Pane
To transfer a Spec List entry to the Compare window, double-click the entry. See “Displaying
Spectra in the Compare Window” on page 10.
Using the Hit List
The Hit List displays a list of library spectra that match the unknown spectrum from highest
to lowest match in the Library Search window. Each search result is listed with its order
number, forward and reverse matching factors, and a library identifier:
• (M) for the Main NIST library
• (R) for the Replicates library
• (U) for a user library
Click a name from the search results to display its spectrum and structure in the Plot pane and
to display text describing the hit in the Text pane. The spectrum also appears in the Compare
window.
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Overview of Library Browser
Library Browser Windows
The Plot and Text Panes
The Plot panes display the following:
• The full spectrum or expanded views of a selected m/z range
• The compound structure (if available)
The Text panes display the following:
• Compound Information: name, formula, molecular weight, CAS number, NIST number,
ID number, and search library
• The ten largest peaks in the mass spectrum
• Synonyms or alternate names used in the library
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Overview of Library Browser
Library Browser Windows
Other Search Window
The Other Search window of the Library Browser (see Figure 3) can carry out searches based
on the following:
• Formula
• ID number
• Molecular weight
• Any peaks
• CAS Registry number
• Sequential method
• NIST library number
Launch these searches by selecting the appropriate option from the Search Type list in the top
left corner of the window or use the appropriate command from the Search menu. For more
information about modifying searches, see “Searching Libraries” on page 47.
Figure 3.
8
Other Search window
Creating and Searching Libraries User Guide
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1
Overview of Library Browser
Library Browser Windows
Name Search Window
 To search a NIST library for a compound name or a text fragment
1. In the Name Search window, type a search name into the box in the top left corner of the
window, for example, PACETO (see Figure 4).
The Xcalibur data system displays spectrum, structure, and text information in panes in
the Name Search window.
2. Right-click an entry. Choose Library Search from the shortcut menu.
The Browser loads details of the compound into the Compare window and the Plot, Text,
Compare, and Hit List panes of the Library Search window.
The default name search mode accepts both alphabetic (a–z) and numeric (0–9)
characters. Punctuation and spacing are ignored (for example, 1-butene is equivalent to
1butene). Greek characters must be spelled out (for example, alpha).
Figure 4.
Name search window
With the a to z only, no prefix option selected, the Browser accepts only alphabetic
characters and ignores common prefixes (for example, cis, trans, dl, di, and tri), numbers,
and Greek characters. In this mode, typing butene finds 1-butene and cis 2-butene.
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Overview of Library Browser
Library Browser Windows
Compare Window
The Compare window is used for the comparison of spectra only—it has no searching
capabilities. It supports comparison of any set of spectra and, unlike the Library search
window, it can show multiple spectra. There are three panes in the Compare window. The top
pane is a plot of the spectral display, the middle pane is a standard difference display pane, and
the bottom pane displays multiple spectra from the Hit List.
Figure 5.
Compare window
The Compare window uses the standard Difference Display options as follows:
Difference
Shows peaks from the first (often upper) spectrum and second (often
lower) spectrum along with the difference.
Head to Tail
Shows only the two spectra being compared. The first spectrum points
upward, the second spectrum points downward from a common axis.
Side by Side
Shows only the two spectra displayed next to each other.
Subtraction
Creates a spectrum derived by subtracting the second spectrum from the
first.
Displaying Spectra in the Compare Window
 To add spectra to the top pane
1. Double-click an entry in the Spec List of the Library Search window or select an entry in
either the Spec List or the Hit List of the Library Search window.
2. Right-click the entry and choose Copy from the shortcut menu.
3. To paste the desired spectra in the top pane, go to the Compare window and use the Paste
command on the shortcut menu.
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Overview of Library Browser
Library Browser Windows
Formatting the Compare Window
 To format the compare window
Right-click in the pane and choose Properties from the shortcut menu. The Compare
Tool Properties dialog box opens.
Figure 6.
Compare Tool Properties dialog box
You can use the Compare Tool Properties dialog box to change parameters for these
options.
• Plot page: Specify plot view parameters.
• Comp. Result: Specify compare view parameters.
• Comp. List: Specify compare list parameters:
Thermo Scientific
–
Insert best library search hits: Automatically inserts the number of hits specified
from the top of the hit list to the compare list.
–
Overwrite contents of the list: automatically overwrites the current contents of
the list with new information. If you do not select this option, data is added to
the top of the compare list.
–
No structures: puts no structures on the compare window.
–
Spectra per page: specifies the number of structures from the compare list that are
shown below the compare window.
Creating and Searching Libraries User Guide
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Overview of Library Browser
Library Browser Windows
Librarian Window
The Librarian window is the User Library manager for the Library Browser. Use it to create
User Libraries and to add spectrum files and compound information to them. Also use the
Librarian window to create, save, and edit text files, save mass spectra, and edit compound ID
information.
Figure 7.
Librarian window
The Librarian window is divided into three panes:
• A Spec List shows the names of all files under consideration, including structure and
formula if available.
• A Plot pane shows the spectrum of a file in the Spec List
• A Text pane displays any detailed text on the selected file in the Spec List
 To delete a spectrum
Click
to remove a spectrum and any associated library from the list without saving
them anywhere.
 To add a spectrum
Click
to add the highlighted spectrum on the list to a designated User library.
 To move a spectrum
Click
to remove the highlighted spectrum from the list and put it into a designated
user library.
 To delete a user library
Click
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Creating and Searching Libraries User Guide
to remove an entire user library.
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Overview of Library Browser
Library Browser Windows
Click the Add, Move, and DelLib buttons to open a dialog box listing the available user
libraries. Select the library required for the command. When adding or moving a spectrum,
type a new user library name, if required.
Figure 8.
Chose library to copy to dialog box
The dialog box also features buttons for managing individual library entries:
Click New to create a new library entry.
Click Edit to change a current library entry in the Spectrum Information dialog box.
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Adding a Spectrum to a Library
To create a library entry with MS or MS/MS (or MSn) spectral data, use the Qual Browser
window.
The procedure in this section uses steroid data. The Xcalibur data system stores the raw data
files in the C:\Xcalibur\examples\data directory.
To manually create a library entry, complete the tasks detailed below:
Contents
• Opening a Raw Data File (.raw) in Qual Browser
• Viewing a Spectrum in Qual Browser
• Working with Background Spectra
• Exporting Spectra from the Xcalibur Data System
Opening a Raw Data File (.raw) in Qual Browser
To view raw data, use the Qual Browser window. Open a data file to expand the Qual Browser
menu bar.
 To display the raw data of a steroids data file
or
1. To display the Xcalibur Home Page from your computer desktop, double-click
choose Start > Programs > Thermo Xcalibur > Xcalibur on the computer desktop.
2. To display the Qual Browser window, click
3. Choose File > Open or click
on the Xcalibur Home Page.
in the toolbar. The Open Raw File dialog box opens.
4. Browse to the location of the raw file and select the file.
5. Click Open. The chromatogram and first mass spectrum for this data file appear (see
Figure 9).
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Adding a Spectrum to a Library
Viewing a Spectrum in Qual Browser
Viewing a Spectrum in Qual Browser
To view a mass spectrum, use the interactive cells of the Qual Browser window.
 To display a mass spectrum of the raw data in a window containing four cells
1. Confirm that the data system displays a Chromatogram view similar to Figure 9. If you
cannot see the chromatogram view, do the following:
a. Select a cell. The application shows both the chromatogram and spectrum by default.
b. Choose View Spectrum.
c. Choose Grid > Delete > All Cells to remove the chromatogram.
d. Select View and clear all entries except Spectrum to expand the chromatogram to the
full size of the Qual Browser window.
e. To enlarge the window display area, click
window.
Figure 9.
in the upper right corner of the
Qual Browser window, showing the Chromatogram view of the raw file
2. Open cells to display the raw data in a grid of four cells (as shown in Figure 10):
a. To display two cells in the window, choose Grid > Insert Cells > Left.
b. To display four cells in the window, choose Grid > Insert Cells > Below.
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Adding a Spectrum to a Library
Viewing a Spectrum in Qual Browser
Figure 10 shows the following views (clockwise from lower left): Scan Filter view,
(filtered) Chromatogram view, (averaged) Spectrum view, and (unfiltered)
Chromatogram view.
Figure 10. Qual Browser window
Chromatogram view (filtered)
Spectrum view (averaged)
Scan Filter view
Chromatogram view (unfiltered)
3. To display the scan filter data, click the lower left cell and choose View > Scan Filters.
The cell lists the filters contained in the total ion current (TIC) chromatogram over a
specified time range.
4. To display a mass range chromatogram in the upper left cell
a. Make a cell active by clicking
in the upper right corner.
b. Click and hold an entry in the list. The Xcalibur application surrounds the entry with
a box and displays a page cursor.
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Adding a Spectrum to a Library
Working with Background Spectra
c. Drag the page cursor to the upper left cell and release the mouse button. The
application automatically applies the filter and displays the mass range
chromatogram.
5. To display an averaged mass spectrum in the upper right cell:
a. Make a cell active by clicking
in the upper right corner.
b. Display a mass spectrum by choosing View > 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. The
Xcalibur data system 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 10.
Working with Background Spectra
This topic explains how to remove spectra from a display so that only essential spectra are
there.
• Using the Subtract Background Tool
• Subtracting Background Spectra
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Adding a Spectrum to a Library
Working with Background Spectra
Using the Subtract Background Tool
 To change the library search list
1. To open the Subtract Background dialog box, choose Tools > Background Subtract
from the Qual Browser window.
Figure 11. Subtract Background dialog box
2. To select the input file, type the pathname of the input file in the File box or click Browse
and locate the file using the Open dialog box.
3. To choose the detector(s), identify data from the required detector source using the
Single Detector list. To use all the detectors recorded in the raw file, select the
All Detectors check box.
4. To choose a scan filter, click the Filter arrow to display filter options that are stored in
the .raw file. Then, select a filter.
5. To select the background file, type the pathname of the background file in the File box or
click Browse and locate the file using the Open dialog box.
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Adding a Spectrum to a Library
Working with Background Spectra
6. Select the scope of the subtract background file operation:
• To subtract the entire background file from the input file, select the Subtract Whole
File option.
• To subtract a single scan from the background file from each scan of the input file,
select the Subtract Single Scan (RT) option and type the retention time for the scan
in the associated box.
7. Specify alignment and scaling:
• To offset the subtraction of the background file from the input file, type the required
offset in the Alignment Offset (RT) box.
• To scale the subtraction of the background file from the input file, type the required
factor in the Scaling Factor box.
8. To specify the location of the output file, type the full path location for the output file in
the Folder box or click the Folder button and browse to the required location.
The dialog box displays the name of the output file as BG_<Input File> in the Name box.
9. To start the subtract background file operation, click Process. The dialog box closes.
To abandon the file operation and close the dialog box, click Exit.
Subtracting Background Spectra
To subtract background spectra, eliminating 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), use the Chromatogram view.
 To select two scan ranges for background subtraction
1. To select a spectrum, click
in the upper right corner of the spectrum.
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.
4. Drag the cursor away from the peak of interest and across a few scans that are
representative of the first scan range 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.
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Adding a Spectrum to a Library
Working with Background Spectra
7. Drag the cursor away from the peak of interest and across a few scans that are
representative of the second scan range to subtract (see Figure 12).
Figure 12. Qual Browser window, showing background subtracted scans in the Spectrum view (upper right)
8. To define the second range, release the mouse button.
When you release the mouse button, the data system 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.
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Adding a Spectrum to a Library
Exporting Spectra from the Xcalibur Data System
Exporting Spectra from the Xcalibur Data System
To create a library entry for a custom library, export a spectrum from the Spectrum view of
Qual Browser to the Library Browser.
To export spectra from the data system to the Library Browser, use one of these methods:
• Exporting Spectra Manually from Qual Browser
• Exporting Spectra Automatically from the Processing Method (see “Adding Spectra to a
User Library” on page 29 for more information)
Exporting Spectra Manually from Qual Browser
 To export the enhanced spectrum to Library Browser
To export an MS/MS spectrum to the Library Browser, right-click the spectrum view
(upper right cell) and choose Library > Export to Library Browser. Xcalibur
automatically displays the Library Browser (see Figure 13).
Figure 13. Library Search window
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2 Adding a Spectrum to a Library
Exporting Spectra from the Xcalibur Data System
The data system 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. The Xcalibur
application creates:
• A copy of the exported spectrum in the Xcalibur\Libspecs folder. The file is given
an .msd extension with the same filename as the original data file, although this is
truncated to eight characters (8.3 filename format).
• An index file containing details about all exported spectra.
• The data system places the exported spectrum into the Spec List (Spectrum List), and
the Library Browser immediately searches the selected libraries for matching spectra if
you check the Automation option in the Library Search Property dialog box.
To display the Library Search Property dialog box, choose Tools > Search Options.
To display the Automation option check box, click either the Search tab or the
Automation tab. See “Setting Up to Search Libraries Automatically” on page 62.
Exporting Spectra Automatically from the Processing Method
The processing method contains the Append to User Library option to automatically export a
spectrum directly into a user library. If the specified library does not exist, the Xcalibur data
system creates it.
When a spectrum is added to a user library, it contains the following basic information:
• The complete mass/intensity list
• A name formatted as <filename>#<scannumber> RT: <rt> AV: <av> NL: <nl>
for example: steroids02#1 RT: 0.01 AV: 1 NL: 2.14E3
• A comment showing the Scan Filter, such as T: + c Full ms2 363.30 [150.00 - 375.00]
• The Mol Weight and CAS Number fields are set to zero.
You might want to modify the basic information or provide the following:
• A chemical formula
• A list of synonyms
• The molecular weight
• The CAS number
• A chemical structure (in MOL, SDF, or MDL file format)
To edit a library entry, see “Editing a User Library” on page 30.
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Managing Libraries
Library Browser can create, manage, and search user libraries. Use these functions to create
reference libraries from your own spectra.
Use the Xcalibur data system to create a custom library of MS/MS spectra. The 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.
Contents
• Creating a User Library
• Adding Spectra to a User Library
• Editing a User Library
• Managing the NIST Libraries
• Converting Libraries to Another Format
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Managing Libraries
Creating a User Library
Creating a User Library
You can create a user library in two ways: export a spectrum from Qual Browser or view a
spectrum from the Library Browser.
 To create a user library from Qual Browser
1. To start a new user library, export a spectrum from Qual Browser. For more information
about exporting a spectrum, see “Exporting Spectra from the Xcalibur Data System” on
page 22.
2. Choose Window > Librarian.
3. In the NIST MS Search 2.0 Librarian window (see Figure 14), select a spectrum.
Figure 14. NIST MS Search 2.0 - Librarian window
4. Click Add in the Librarian window toolbar.
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Managing Libraries
Creating a User Library
 To create a library from the Library Browser window
1. Select a spectrum in the Library Browser window.
2. In the Librarian window, click
Dialog Box (see Figure 15).
in the toolbar to display the Spectrum Information
Figure 15. Spectrum Information dialog box
3. Click Add to Library to add the spectrum to a new library and name the library. The
Choose Library To Copy To dialog box opens.
4. Click the Libraries tab to display the Available Libs and the Included Libs list of libraries
(see Figure 16).
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Managing Libraries
Creating a User Library
Figure 16. Library Search Options dialog box
5. Type the name of the new user library.
6. Click OK to create the new user library and close the dialog box.
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3 Managing Libraries
Adding Spectra to a User Library
Adding Spectra to a User Library
Use the Append to User Library area, shown in Figure 17, to add processed spectra to a
specific user library.
Figure 17. Append to user library area
 To set matching criteria to avoid duplicate entries
1. Select the Enable check box.
2. Either select a user library from the User Library list or type a new library name. The
drop-down list includes all currently active user libraries.
If you type a new library name, the library is created only if a spectrum fails the matching
criteria. Enter the highest possible values in the Thresholds boxes. The failed spectrum is
appended to the library.
3. Type threshold values for Match Factor, Reverse Match Factor, and Probability%. To
confirm that all spectra are appended to the library, type 999, 999, and 100 respectively.
See “Submitting a Spectrum to a Library Search” on page 54 for an explanation of these
threshold values.
During processing and after any requested enhancement of a relevant chromatogram peak
apex scan, the Xcalibur data system submits the spectrum to a library search:
• If the top hit from a library search exceeds (or is equal to) any one of the threshold values,
the data system returns the hit list and the spectrum is not appended to the specified
library.
• If the top hit fails to reach any of the threshold values, the data system discards the hit list
(no search results are reported) and appends the searched spectrum to the specified
library. Unless otherwise specified, the library is stored in the NIST\MSSearch folder.
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Managing Libraries
Editing a User Library
Editing a User Library
To edit a user-library entry that contains an MS/MS spectrum exported from Qual Browser,
use the following procedure.
To edit a user library, complete the following tasks detailed in this section:
• Editing Spectrum Information
• Attaching a Chemical Structure to a Library Entry
• Adding Additional Compounds to the User Library
Editing Spectrum Information
 To edit MS/MS spectrum information in Library Browser
1. Open Library Browser and choose Window > Librarian. The Librarian window opens.
Because the information for an 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 18).
Figure 18. Librarian window, showing the spectrum information as a text file
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Managing Libraries
Editing a User Library
2. To display the Spectrum Information Dialog Box box (see Figure 19), click
dialog box opens, displaying information specific to the spectrum.
. The
Figure 19. Spectrum Information dialog box showing raw spectrum information
3. Give the spectrum a new name:
a. Click and drag the cursor in the Name box to highlight the entire text string.
b. Change the default text string of the spectrum to a more useful name.
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Managing Libraries
Editing a User Library
Attaching a Chemical Structure to a Library Entry
To attach a chemical structure from a list of structures to an entry in a custom library, use the
following procedure. Also use the procedure to attach a structure from a program such as
ChemDraw™. ChemDraw saves drawings of chemical structures in the .mol file format.
Because you cannot attach a structure to a text file, 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.
 To attach a structure to an entry and change the source of the entry
1. Export a spectrum to a library following the instructions in “Exporting Spectra from the
Xcalibur Data System” on page 22.
2. From the Lib. Search window, select an entry in the Spec List pane. Right-click this entry
and select Library Search. Library Browser finds the entry and copies it to the Hit List
pane (see Figure 20).
Figure 20. Library Search window, showing the results of searching a library
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Managing Libraries
Editing a User Library
3. To copy the search result to the Spec List pane:
a. Select the Hit List entry you just created. Right-click this entry and select Copy from
the shortcut menu.
b. To make the Spec List pane active, move the cursor to the Spec List pane and
left-click the mouse button.
c. To paste the entry to the Spec List window, right-click to display the shortcut menu
and choose Paste.
4. Click the Librarian tab. The Librarian window opens (see Figure 21).
Figure 21. Librarian window
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Managing Libraries
Editing a User Library
5. To save the structure of the entry from the library to the entry:
a. In the Librarian window, click
box opens (see Figure 22).
in the toolbar. The Spectrum Information dialog
Figure 22. Spectrum Information dialog box
b. To search for chemical structure files from other sources, click the Attach Struct
button. The Open dialog box opens.
c. If the structure you want is not available in the Open dialog box folders, click Cancel
to search other libraries. The Attach Structure to User Spectrum dialog box opens
(see Figure 23).
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Managing Libraries
Editing a User Library
Figure 23. Attach Structure to User Spectrum dialog box
d. Select a library name in the Get Structure From area and click Open Library.
e. Type the name of the compound to search for in the Substring Search box. Then
click Substring Search. Library Browser scans the library and finds the MS data and
the structure for your entry.
f.
Thermo Scientific
To accept the structure and return to the Spectrum Information dialog box (see
Figure 24), click Accept.
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Managing Libraries
Editing a User Library
Figure 24. Spectrum Information dialog box, showing the structure to add
g. Click Add to Library to display the Choose Library to Save to dialog box (see
Figure 25).
Figure 25. Choose library to save to dialog box
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Managing Libraries
Editing a User Library
h. To save the structure to the library, click OK. The application closes the Choose
Library to Save to dialog box and opens the Librarian window. The source of the
entry appears as the new library name.
6. Highlight the entry in the Spec List. The Text File designation appears in the Plot pane.
7. To delete the entry, click
in the toolbar.
A warning appears.
8. Click OK to close the warning dialog box.
9. Click the Lib. Search tab to return to Library Browser’s Library Search window.
10. Double-click the entry in the Spec List.
The Xcalibur application attaches the chemical structure to the library entry.
Adding Additional Compounds to the User Library
To add compounds to a user library, use the Qual Browser window.
This procedure describes exporting spectra to Library Browser using unenhanced spectra. For
more information, see “Working with Background Spectra” on page 18 and the previous
section, “Attaching a Chemical Structure to a Library Entry” on page 32. Apply the
procedures from these related sections to unenhanced spectra, when possible, before you do
the procedure in this section.
 To add library entries from Qual Browser to a user library
in the task bar at the
1. To display the Qual Browser window, click
bottom of the monitor screen.
2. To display an MS/MS spectrum of a relevant peak:
a. Click
active.
in the Spectrum view (upper right cell) in Qual Browser to make the cell
b. Move the cursor to the Chromatogram view in the lower right cell. Click and hold
just to the left of the second chromatographic peak.
c. To average the scans you select, drag the cursor horizontally across the peak. The
Xcalibur data system displays the spectrum in the Spectrum view.
3. Right-click the mass spectrum to display a shortcut menu.
4. To export the spectrum, choose Library > Export to Library Browser. The data system
displays a message box, as shown in Figure 26.
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Managing Libraries
Editing a User Library
Figure 26. Export Message box
5. To add the entry to the top of the Clipboard window, click Prepend.
6. To edit the spectrum information
a. Display the Librarian window by choosing Window > Librarian in Library Browser.
b. Select the unedited entry in the Spec List pane as shown in Figure 27.
Figure 27. Librarian window, showing a spectrum in a list of entries
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c. Click
Managing Libraries
Editing a User Library
. The Spectrum Information dialog box opens.
d. Select all of the text in the Name box and type a name for the entry.
e. Click Add to Library. The Choose Library to Save to dialog box opens.
f.
To copy the new spectrum entry to the selected library, click OK. (The entry
Text File in the Librarian window does not change.)
7. To copy and paste the library entry from the Hit List pane to the Spec List pane (see
Figure 28):
Figure 28. Library Browser panes, showing the results of a search from the Spec List panel
a. In Library Browser, choose Window > Lib. Search to display the Library Search
window.
b. Select a file in the Spec List pane. Right-click this entry and choose Library Search.
If Library Browser finds the entry, the application copies it to the Hit List pane.
c. Select the search results entry from the Hit List. Right-click this entry and choose
Copy from the shortcut menu.
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Managing Libraries
Editing a User Library
d. To make the Spec List pane active, move the cursor to the Spec List pane and left
click the mouse button.
e. To paste the entry to the Spec List window, right-click to display the shortcut menu
and choose Paste.
8. Choose Window > Librarian to display the Librarian window (see Figure 29).
Figure 29. Librarian window, showing the entry from the source file highlighted
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9. To delete the entry, highlight the entry from the source file and click
(see Figure 30).
Managing Libraries
Editing a User Library
in the toolbar
Figure 30. Librarian window, showing added entries
10. Close the windows and return to the Xcalibur Home Page:
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.
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Managing Libraries
Managing the NIST Libraries
Managing the NIST Libraries
To add, delete, or move a library from the NIST libraries list, use the Manage Libraries page
in the Xcalibur Library Manager dialog box. This section shows you how to complete the
following tasks:
• Adding a Library
• Deleting a Library
• Copying a Library
 To open the Xcalibur Library Manager
1. If the Xcalibur Home Page is not already open on the computer, choose Start > All
Programs > Thermo Xcalibur > Xcalibur. Verify that the home page is open in the
Roadmap view.
2. To open the Library Manager Dialog Box, choose Tools > Library Manager. The
Library Manager opens on the Manage Libraries page by default (see Figure 31).
Figure 31. Manage Libraries page
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3 Managing Libraries
Managing the NIST Libraries
Adding a Library
When you add a library to the NIST libraries list, either copy the library file to the local
computer or link to the library at a remote location without copying files.
 To add a library
1. In the Library Manager Dialog Box, click Add. The Add Library dialog box opens (see
Figure 32).
Figure 32. Add Library dialog box
2. In the Add Library dialog box, type the path for the new library file in the Source field or
click Browse to bring up the Browse for Folder dialog box and find the desired file.
3. Select one of the two options:
• Copy the library to the local computer
• Link to the library from either a remote location or computer
Note Because libraries can be large, you can often save time by selecting the Link
option rather than the Copy option.
4. Click OK. The data system adds the desired library to the NIST Libraries list in the
Xcalibur Library Manager dialog box.
5. If you have no more tasks to complete with the Library Manager, click Exit.
Deleting a Library
 To delete a selected library in the NIST Libraries list
1. In the Xcalibur Library Manager dialog box, select a library to delete from the
NIST Libraries list.
2. Click Delete. The system prompts you to confirm the deletion. To delete the selected
library, click Yes.
3. If you have no more tasks to complete with the Library Manager, click Exit.
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Managing Libraries
Managing the NIST Libraries
Copying a Library
You can copy a selected library to another directory on the computer or network by using the
Archive feature.
 To copy a library
1. In the Library Manager Dialog Box, select a library to copy from in the library name in
the NIST Libraries list.
2. Click Archive. The Archive Library dialog box opens (see Figure 33).
Figure 33. Archive Library dialog box
3. In the Archive Library dialog box, type the path for the copied library file in the
Destination field or click Browse to bring up the Browse for Folder dialog box and find
the desired location.
4. To copy the desired library to the remote location, click OK.
5. If you have no more tasks to complete with the Library Manager, click Exit.
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3 Managing Libraries
Converting Libraries to Another Format
Converting Libraries to Another Format
To convert all or any portion of a library to another format, use the Convert Libraries Page in
the Library Manager Dialog Box (see Figure 34). Also, use this page to copy a library to
another location.
Figure 34. Convert libraries page
 To convert a library from one format to another
1. In the Xcalibur Library Manager dialog box, type the following information in the
Source Library Details area:
• Select the type of source library, based on the file extension, from the Type
drop-down list.
• Type the path to the source library in the Library field or click Browse to open the
Browse for Folder dialog box and find a file.
• To convert only certain entries from the source library, type the number range of the
entries to convert in the Process Entries field. For example, to convert only entries
#100 to #200, type 100-200.
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Managing Libraries
Converting Libraries to Another Format
2. Enter the following information in the Target Library Details area:
• Select the type of target library based on the file extension, from the Type drop-down
list.
• Type the path to the target library in the Library field or click Browse to open the
Browse for Folder dialog box and find a folder.
Note When you select NIST as the target library type, the default target library is
the library folder for Xcalibur software: C:\NIST02\MSSEARCH\.
When you select ICIS/GCQ/ITS 40 or MassLab as the target library type, the
Title field becomes active.
• Type the title for the converted library in this field.
3. Make the following choices in the Options area, if desired:
• Select either the Create/Replace option or the Append option. Create/Replace is
selected by default.
When you select NIST as the source library type, the Include Replicate Entries from
the NIST Library in the Target Library check box becomes active.
• Click this check box to copy replicate entries.
When you select the Include Replicate Entries check box, the Replicate Library field
is active. The default replicate library is C:\NIST02\MSSEARCH\REPLIB.
• To use a different replicate library, type the path to the desired library in the Replicate
Library field or click Browse to open the Browse for Folder dialog box and find a
folder.
4. To begin the conversion process, click Convert. The Conversion Status box displays
sequential chronological (top to bottom) messages such as:
Started the conversion on SEP 3, 1999 at 10:01, please wait
Finished the conversion on SEP 3, 1999 at 10:02
Converted 570 entries
5. If you have no more tasks to complete with the Library Manager, click Exit to close the
Xcalibur Library Manager dialog box.
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Searching Libraries
After you create a custom library of spectra, you can search it or other libraries. Set up libraries
to search them automatically or search them manually from Qual Browser or Library Browser.
Contents
• Customizing a Search
• Setting Library Search Option Parameters
• Submitting a Spectrum to a Library Search
• Limiting a Library Search
• Selecting Libraries to Search
• Setting Up to Search Libraries Automatically
• Processing Raw Files and Printing Reports
• Initiating a Library Search from Qual Browser
• Searching a Library Using Library Browser
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Customizing a Search
Customizing a Search
The Library Browser automatically loads all exported spectra into the Spec List window.
Initiate a library search by double-clicking the appropriate entry. The search uses the settings
defined in the Library Search Options Dialog Box (see Figure 35).
Figure 35. Library Search Options dialog box
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Customizing a Search
Including a User Library in a Search
The default library for a search is the NIST/EPA/NIH main library (mainlib), if it is present.
Otherwise, the default is a demonstration user library, nistdemo. You can add other libraries to
the search and change the order of searching on the Libraries page of the Library Search
Options dialog box (see Figure 36).
Figure 36. Libraries page of the Library Search Options dialog box
To access this page, click the Libraries tab of the Library Search Options dialog box. The
Libraries page is divided into two panes:
Thermo Scientific
Available Libs
Lists libraries defined within the Library Browser.
Included Libs
Lists the libraries used by the Library Browser in searches, in the search
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Searching Libraries
Customizing a Search
 To change the search order of included libraries
Use the up and down arrows.
 To include a library in the search
1. Select the library name in the Available Libs list.
2. Click Add.
 To exclude a library from a search
1. Select the library name in the Included Libs list.
2. Click the Delete button (large red X).
Limiting a Library Search
To examine or modify search constraints, click the Constraints tab of the Library Search
Options dialog box.
Constraints are divided into six categories:
• Molecular Weight
• Name Fragment
• Elements Value
• Elements Present
• Peaks
• Other Databases
For details about limiting a library search, see “Library Search Constraints Page (Library
View)” on page 111.
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Customizing a Search
Searching a User Library Entry by ID Number
To search entries in existing libraries, search for a library spectrum by Formula, ID Number,
Molecular Weight, Any Peaks, CAS Number, Sequential Method, NIST Number, or Name.
Use ID Search if other information is not available or to find a spectrum exported from a
processing method.
 To search a library by ID Number
1. To open the ID Number Search dialog box (see Figure 37), choose Search > ID Number
from any Library window.
Figure 37. ID Number Search dialog box
The Library Statistics area shows the number of available spectra.
2. To consider all spectra, specify a range in the ID Number box that is equal to or larger
than the ID range shown in the Library Statistics area.
3. Select the appropriate user library in the Library drop down list.
4. Click Search. The Xcalibur data system writes all entries within the specified range to the
Lib. Search area.
5. To copy a spectrum to be edited into the Spec List from the Library Search window, select
the spectrum name in the Hit List and use the mouse to drag the selection to the Spec List
window.
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Setting Library Search Option Parameters
Setting Library Search Option Parameters
Use the Library Search Options page (see Figure 38) to specify how the library search is
carried out.
 To set Library Search Option parameters
1. Open the Search Parameters Page of the Search Properties dialog box:
From the Qual Browser window, choose Actions > Library > Options or right-click
within a Spectrum view and select Library > Options from the popup context menu.
Click the Library Search Options tab.
Figure 38. Library Search Options page from Qual View
2. To submit processed spectra to an identity search, select an Identity option in the
Search Type area.
Figure 39. Search type area default settings
3. Choose one of the three Identity search types:
• Select the Normal option to use a normal identity search.
• Select the Quick option to use a quick identity search.
• Select the Penalize Rare Compounds option if you want a modified normal identity
search.
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Setting Library Search Option Parameters
4. To submit processed spectra to a similarity search, select the Similarity option. Then
choose one of the three Similarity search types:
• Select the Simple option to use a Simple Similarity search.
• Select the Hybrid option to use a Hybrid Similarity search.
• Select the Neutral Loss option if you want a Neutral Loss Similarity search.
The difference between the two search types is primarily in the weightings of the
spectrum as a function of mass.
5. To limit the number of search results to be returned by a library search and reported in
the results file, type a number in the Maximum Number of Hits box.
Figure 40. Options area default settings
6. If you know the molecular weight of your target analyte and want to restrict the search to
library compounds of the same molecular weight, select the Search with MW = check
box and type the molecular weight in the associated box.
7. To include mass defect values for library searches, select the Enable check box in the
Mass Defect area.
8. Select a sorting method for hits in the results file in the Options area. The Options area
shown in Figure 40 contains three ways to customize the library search. The Reverse
Search and Search with MW = options are normally not active.
• To have the Xcalibur data system sort hits by Reverse Match Factor, select the
Reverse Search check box.
• To have the Xcalibur data system sort hits by the Forward Match Factor, clear the
Reverse Search check box.
9. To add new spectra to a user library:
a. In the Append to User Library area check box, select Enable.
b. From the User Library list, select the target user library.
c. Type a threshold value for Match Factor in the Match Factor box.
d. Type a threshold value for Reverse Match Factor in the Reverse Match Factor box.
e. Type a threshold value for Probability % in the Probability % box.
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Submitting a Spectrum to a Library Search
10. To save the new settings and close the dialog box, click OK.
Note Do not use the Search with MW= option when you have already clicked the
Molecular Weight option on the Library Search Constraints page.
Submitting a Spectrum to a Library Search
 To submit a spectrum in a Qual Browser spectrum view to a library search
1. To open a Chromatogram view:
a. Click
in the cell where you want to open the Chromatogram view.
The Xcalibur application changes the icon to
b. Choose View > Chromatogram or click
to indicate that it is the active cell.
on the toolbar.
2. To open a Spectrum view:
a. Click
in the cell where you want to open the Spectrum view.
The application changes the icon to
b. Choose View > Spectrum or click
to indicate that it is the active cell.
on the toolbar.
3. To display or enhance a spectrum, choose from these options:
• With the spectrum cell pinned, click the chromatogram at the point of interest
(a peak apex, for example).
• To view a spectrum averaged across a peak, drag the cursor through the
chromatogram peak of interest. For more information on this step, refer to “Selecting
a One-Dimensional Range on a Plot” in Chapter 3 in the Qualitative Analysis User
Guide.
• Enhance the spectrum, if necessary, by using background subtraction. For more
information on this step, see “Working with Background Spectra” on page 18.
4. Select the search libraries and other search options. For more information, see “Setting
Library Search Option Parameters” on page 52.
5. To start the library search, choose one of these options:
• Choose Actions > Library > Search
• Click
on the toolbar
• Right-click the Spectrum View and select Library > Search from the context menu
Qual Browser displays the results of the library search in a Library Search Results window.
For more information about this window, see “Library Search Results Window” on
page 119.
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Limiting a Library Search
Limiting a Library Search
For processing efficiency, constrain a library search using some of the options on the
Library Search Constraints page (these are all normally not active). For example, you can
exclude certain high intensity ions that appear in many compounds or that are present in the
spectrum background. You can target a search to a particular range of molecular weights or to
compounds containing certain elements.
The Library Search Constraints page (see Figure 41) contains five groups of options to
constrain the library search. To display the Library Search Constraints page, from the Qual
view of the Processing Setup window, select the Library Search Constraints tab. See the
following sections to set these constraints.
• Applying a Molecular Weight Constraint
• Applying the Other Databases Constraint
• Applying a Name Fragment Constraint
• Applying Element Constraints
• Applying Mass Spectral Peak Constraint
Figure 41. Library Search Constraints page from Qual View
Set parameters and save your settings by clicking OK. To save your settings as a default for
future searches, click Save as Default.
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Limiting a Library Search
Note Using Library Search Constraints requires specific knowledge about the target
compounds in the chromatogram. This knowledge is not always possible in automated
processing.
Applying a Molecular Weight Constraint
 To limit the library search to compounds with a specific molecular weight or
molecular weight range
1. Select the Enable check box in the Molecular Weight area (see Figure 42).
Figure 42. Molecular weight area
2. To type a molecular weight or molecular weight range, use the Range box. To specify a
range, use the format low mass - high mass. The valid range is 1 to 999999. All search
results must satisfy the specified molecular weight range.
Note This constraint is not available if you have already clicked the Search with
MW= option on the Library Search Options page.
Applying the Other Databases Constraint
 To limit the library search to entries in the NIST library that are also featured in other
databases
1. Select the Enable check box in the Other Databases area (see Figure 43). NIST library
entries contain references to other commercial databases if they contain information
about the compound.
Figure 43. Other databases area
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Limiting a Library Search
2. Select one or more databases from the available list. To use a database constraint, select its
check box. If you do not want to use a database constraint, make sure its check box is
clear.
Fine
Commercially Available Fine Chemical Index
TSCA
Toxic Substances Control Act Inventory
RTECS
Registry of Toxic Effects of Chemical Substances
EPA
EPA Environmental Monitoring Methods Index
USP
US Pharmacopoeia/U.S.A.N.
HODOC
CRC Handbook of Data of Organic Compounds
NIH
NIH-NCI Inventory File
EINECS
European Index of Commercial Chemical Substances
IR
NIST/EPA Gas Phase IR Database
The data system only reports search results if they feature in one or more, but not
necessarily all, of the selected databases.
Applying a Name Fragment Constraint
 To limit the search to compounds with a specific name or name fragment
1. Select the Enable check box in the Name Fragment area.
The Name box accepts a text string (up to 39 characters) to represent a fragment of a
compound name; for example, “cyclo”. The library search filters search results and only
returns those containing the specified text in their names. The entry is not case sensitive;
for example “CYCLO” returns compounds containing the fragments “cyclo”, “Cyclo”,
“CYCLO” and any other case permutations.
Figure 44. Name fragment area
2. Type a name fragment in the Name box.
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Limiting a Library Search
Applying Element Constraints
To constrain the library search to compounds with specific element profiles, select the Enable
check box in the Element Constraints area. There are two methods:
• Individual Element
• Elements in Compound
 To use the Individual Elements constraints
1. Click the Element box. Type the required element abbreviation.
Use this area to set specific criteria about the elements required in a library search result
(hit). For example, the entries shown in Figure 45 would only return search results for
compounds that contain more than five fluorine atoms and exactly three chlorine atoms.
Figure 45. Element constraints area
You do not need to provide a complete elemental profile. The library search returns
compounds if they satisfy all the specified criteria regardless of any other elements
present. Use this option to specify which elements you do not want to be in a library hit.
For example, C = 0 confirms that no search results contain carbon.
When a contradiction occurs, for example, C < 2, and C > 4, the data system displays an
error dialog box. Correct the contradiction to proceed.
2. In the same row, click the Condition list. Click the arrow and select from the three
available conditions: < (less than), > (greater than), or = (equal to).
3. In the same row, click the Value box. Type the required number of elements for the
element constraint condition.
4. Repeat Steps 1 - 3 on the next available row to add further elements to the table.
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Limiting a Library Search
 To use the Elements in Compound constraints
1. Select the Elements box and type the IUPAC approved abbreviation for each element
(see Figure 45) that must be present in returned search results. Separate each element in
the list (of up to 30 characters) by the character specified as the list separator character.
Refer to “Changing the List Separator Character” in Chapter 2 in the Acquisition and
Processing User Guide for more information.
2. Select the All option to have the returned search results contain all, and only, the listed
elements. For example “C, H, O” would return HCHO but not CO2, CH4, or CH2Cl2.
3. Select the Some option to have the returned search results contain at least one of the
specified elements and no elements other than those listed. For example “C, H, O” would
return CO2, CH4, and HCHO but not CH2Cl2 (Cl not allowed).
If you leave the box blank, the data system does not apply the Elements in compound
constraint function. If you type an invalid element, the data system reports an error when
the edit field loses focus.
If there are no contradictions, you can use the two types of elemental constraints together. For
example, if the Individual Element area contains “C=0” or “C<1" in and the Elements In
Compound box contains “C” when the All option has been selected, the data system displays
an error dialog box. Correct the contradiction to proceed.
Applying Mass Spectral Peak Constraint
The Mass spectral peak constraint feature builds a profile of ions and their abundances to be
matched against library entries during the search.
 To apply mass spectral peak constraints
Select Enable in the Mass Spectral Peak Constraints area. The search algorithm only
returns search results matching the specified constraints.
Figure 46. Example of a relative mass spectral peak constraint
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Limiting a Library Search
 To specify how the data system applies the From and To parameters in the Mass
spectral peak constraints table
1. To evaluate all table entries as a percentage of the base (largest) ion in the spectrum, select
the Absolute option.
2. To treat the first entry as an absolute Normal or Loss type, select the Relative option. The
software considers subsequent entries in the table relative to the first.
3. In the Mass Spectral Peak Constraints table, click the first available Type list. Click the
arrow and select from the four available conditions: Normal, Loss, Rank or Maxmass.
4. In the same row, select the m/z box. In a Normal, Rank or Maxmass type constraint, use
this box to type the m/z value of the mass spectral peak to be constrained. In a Loss type
constraint, use this box to type the value of a neutral loss.
5. In the same row, select the From box. In a Normal, Loss or Maxmass type constraint, use
this box to type the minimum abundance of the constrained mass spectral peak. In a
Rank type constraint, use this box to type the lowest position of the ion in an intensity
ordered list of spectral peaks.
6. In the same row, select the To box. In a Normal, Loss or Maxmass type constraint, use
this box to type the maximum abundance of the constrained mass spectral peak. In a
Rank type constraint, use this box to type the highest position of the ion in an intensity
ordered list of spectral peaks.
7. Repeat steps 3-6 on the next available row to add further peaks to the Mass Spectral Peak
Constraints table.
If you specify the same number in both fields, the designated ion must have that rank in
the retrieved spectrum.
Note If you switch between Absolute and Relative modes, the Xcalibur data
system prompts you with a warning dialog box before clearing all rows in the
grid.
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Selecting Libraries to Search
Selecting Libraries to Search
To select a library to search, click
on the Library Search Options page (see
Figure 38 on page 52). The Search List page of the Search Properties dialog box opens
(see Figure 47). This dialog box lists the names and search order of libraries to be used in
library search processing. The list on the left of the dialog box shows the available libraries.
The list on the right of the dialog box shows the selected libraries in their search order.
Figure 47. Search List view
The Xcalibur data system generates the Available Libraries list dynamically. Each time you
open the Search Properties dialog box, the current list of libraries available on the system at
that time appears. This current list might display libraries that do not exist on the
system—they might have been selected on another system or deleted or renamed since the
method was created.
When you click OK in the Search List view, all libraries in the Selected Libraries list are
checked. If any of them do not exist, a warning dialog box opens.
 To include a library in the search list
1. To open the Search Properties dialog box, choose from these options:
• From the Qual Browser window, choose Actions > Library > Options and click the
Search List tab.
• Right-click within a Spectrum view, select Library > Options from the shortcut
context menu, and click the Search List tab.
• Click Search List
page 52).
on the Library Search Options page (see Figure 38 on
2. Select the library name in the Available Libraries list.
3. Click Add to add the library to the Selected Libraries list in the final position.
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Setting Up to Search Libraries Automatically
 To change the search order of selected libraries
Select the library name in the Selected Libraries list:
• Click Top to move the library to the top of the list.
• Click Up to move the library up one position.
• Click Down to move the library down one position.
• Click Bottom to move the library to the last position.
 To exclude a library from the search list
1. Select the library name in the Selected Libraries list.
2. Click Remove to transfer the library to the Available Libraries list.
3. Click OK to save the new settings and close the dialog box.
Setting Up to Search Libraries Automatically
 To set up method files in the data system that search libraries automatically
1. Use the Xcalibur Processing Setup window to create a processing method file (.pmd).
2. Use the Sequence Setup window to process data files in a sequence list (.sld) with the
processing method that you created. For more information about setting up sequences
and processes, refer to the Processes and Sequences User Guide.
To set up for automatic searching, complete the following procedures:
• Specifying Search Parameters in the Qual View
• Specifying Report Options for Library Searches
• Specifying Raw Data Files in Sequence Setup
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Setting Up to Search Libraries Automatically
Specifying Search Parameters in the Qual View
To search libraries automatically, set up the Qual view in the Processing Setup window. For
this example, use steroids data.
Note Using the Library Search Constraints page requires specific knowledge about the
target compounds in the chromatogram. It is not always possible to use this knowledge to
refine automated processing.
 To specify parameters for a qualitative library search in the Qual view
1. To open the Processing Setup window, from the Xcalibur Home Page, click
.
2. Open a raw data file in the Qual view:
a. To display the Identification page for Quan view, choose File > New.
b. To display the Qual view, click
.
c. To display the Open Raw File dialog box, choose File > Open Raw File.
d. To display the raw data, select a raw file and click Open (see Figure 48).
Figure 48. Processing Setup window
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3. Select a detector type on the Identification page.
4. Select a peak detect algorithm in the Peak Detect list to specify how the data system finds
and processes chromatogram peaks.
ICIS
This 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.
Genesis
This algorithm is the original Xcalibur peak detection algorithm and has
been provided for backward compatibility with Xcalibur 1.0 data system
studies.
Avalon
This algorithm supports detectors other than MS and detects negative
chromatographic peaks and shoulders more accurately than Genesis or
ICIS.
5. In the Filter list, select a scan filter.
6. To accept current changes to the Identification page, click OK.
7. To set advanced parameters, click the Advanced button (see Figure 49).
Note For the following procedure, the ICIS Advanced Parameters dialog box opens.
If you choose another peak detect method, a different Advanced Parameters dialog
box opens. Fill in the values that are appropriate for the method.
a. Confirm that the INCOS Noise option is selected in the Noise Method area.
Figure 49. ICIS Advanced Parameters dialog box
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Setting Up to Search Libraries Automatically
Note The Xcalibur data system generates the Available Libraries list dynamically.
Each time you open the Search List dialog box, The application lists the libraries
available on the system at that time.
Libraries listed in the Selected Libraries list, on the other hand, might not exist on
the system. They might have been selected on another system or deleted or
renamed since the processing method was created.
b. To close the dialog box and return to the Processing Setup window, click OK.
8. To apply changes to the Identification page, click OK.
9. Specify the name of the library to search:
a. To display search type options, click the Library Search Options tab.
b. To display the list of available libraries, click Search List (see Figure 50).
Figure 50. Search List dialog box
c. To select a library to search, highlight the library name in the Available Libraries list
and click Add to move the library name to the Selected Libraries list.
d. Click OK to select that library and return to the Qual view of the Processing Setup
window.
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Setting Up to Search Libraries Automatically
Specifying Report Options for Library Searches
To produce and print reports automatically, specify report options from the Reports view of
the Processing Setup window after specifying library search characteristics.
Note For more information about creating custom report templates using Microsoft™
Word, refer to the XReport User Guide.
 To display the raw file data in the format of a custom report template
1. Click
on the View bar in the Processing Setup window or choose View > Reports.
The Reports view appears (see Figure 51).
Figure 51. Reports view
2. If the Apply Changes? dialog box opens, read the
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message and click Yes.
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Setting Up to Search Libraries Automatically
3. Click the Enable cell in the Sample Reports area. When a check box appears, select the
check box to make Row 1 active (see Figure 52).
Figure 52. Reports view with Row 1 active
4. Specify the sample brackets in Row 1:
a. To exclude the bracket for standards from the report, click Yes in the Std column and
clear the check box.
b. To exclude the bracket for quality control samples, click Yes in the QC column and
clear the check box.
c. Click Yes in the Other column and clear the check box.
5. Specify the name of a Report Template (.doc) in Row 1:
a. To display the Browse for Sample Report Template dialog box, double-click the
Report Template Name cell.
b. Scroll to select a report template.
c. To select the report template, and display the filename in the Report Template Name
cell, click Open.
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6. To apply changes to the Reports view, click OK. Figure 53 shows the Reports view and a
specified Report Template Name.
Figure 53. Processing Setup window
7. Save the processing method:
a. Choose File > Save As. The File Summary Information dialog box opens (see
Figure 54).
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Figure 54. File Summary Information dialog box
b. Type file summary information in the Description box and click OK. The Save As
dialog box opens.
c. In the Save As dialog box, type a name the processing method (see Figure 55).
Figure 55. Save As dialog box
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d. To save the method and return to the Reports view, click Save.
8. To close the Processing Setup window and return to the Xcalibur Home Page, choose
File > Exit.
Specifying Raw Data Files in Sequence Setup
To search libraries and print reports automatically, specify the raw files containing the data to
process.
 To display the Sequence Setup window and open a sequence list (.sld)
1. To display the Sequence Setup window, click
on the Xcalibur Home Page.
2. To display the Open dialog box, choose File > Open.
3. Scroll to select a sequence file and double-click to display the list of samples (see
Figure 56).
Figure 56. Sequence Setup window
4. To exclude samples from the list, highlight rows to exclude and choose Edit > Delete
Row. The data system displays a message box to confirm the Delete Row command.
Click Yes (see Figure 57).
Figure 57. Sequence Setup window after excluding rows
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Note Use Sequence Setup to create a sequential list containing a variety of sample
types or brackets. However, when performing qualitative analysis, the type is usually
unknown.
5. To view the Sample Type column, click the left side of the horizontal scroll bar at the
bottom of the workspace. Double-click the Row 1 cell in the Sample Type column to
display a drop-down list. Then, scroll up to select Unknown.
6. Expand the width of the Path column to confirm that the directory is the one
storing the raw files. For example, raw files containing steroids data are found in
C:\Xcalibur\examples\data.
7. To select the processing method, double-click the Row 1 cell in the Processing Method
column. Browse to select the processing method. Figure 58 shows the edited list of two
files contained in steroid.sld.
Figure 58. Sequence Setup window
8. Repeat Steps 4 and 5 for all other rows of the sequence. Step 6 is repeated automatically
for subsequent rows.
9. To save the sequence list file, choose File > Save As. The File Summary Information
dialog box opens. Type a description in the Comment box and click OK.
Figure 59. File Summary Information dialog box
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Processing Raw Files and Printing Reports
The Save As dialog box opens.
10. Type a name in the File Name box to name the sequence.
11. Click Save to save the sequence list and return to the Sequence Setup window.
Processing Raw Files and Printing Reports
To batch process raw data and print reports automatically, use Sequence Setup. Whether you
are processing or reprocessing the data, the results are the same. This guide refers to processed
data whether the action is processing or reprocessing.
 To process a list of raw files and print library search reports
1. To display the Sequence Setup window, click
on the Xcalibur Home Page.
2. To select the rows in the current sequence to process, in Sequence Setup, click and hold
on the row number in the first row to process and drag the cursor to the bottom row. The
Xcalibur application highlights the selected rows.
on the tool bar or choose Actions > Batch Reprocess. The Batch Reprocess
3. Click
Setup dialog box opens (Figure 60).
Figure 60. Batch Reprocess Setup dialog box
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Processing Raw Files and Printing Reports
4. Confirm that the Process Rows box lists all row numbers (for example 1-2). If the
numbers are missing, double-click the box and type the row numbers.
5. Select
any of the following check boxes.
• Quan
– Peak Detection & Integration
– Calibration
– Quantitation
• Qual
– Peak Detection & Integration
– Spectrum Enhancement
– Library Search
• Reports
– Print Sample Reports
– Print Summary Reports
• Programs
• Create Quan Summary Spreadsheet
• Advanced Options
• Replace Sample Info
6. To initiate batch processing of the selected samples, click OK. If the data system displays
a Save your changes box, as shown in Figure 61, click Yes.
Figure 61. Message box
7. To display the Processing Status window (see Figure 62), click the Queue Manager task
in your computer task bar.
Figure 62. Processing Status window
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Two beeps signal the end of the batch processing.
8. Check your printed reports to see that they provide the information you wanted.
Initiating a Library Search from Qual Browser
 To perform a library search from the Qual Browser window
1. Click
on the Xcalibur Home Page to display the Qual Browser window.
2. To open a raw file that contains steroids data, choose File > Open or click
toolbar. The Open Raw File dialog box opens.
in the
3. Browse to a raw file and click Open.
4. View a spectrum. For procedure details, see “Viewing a Spectrum in Qual Browser” on
page 16. Figure 63 shows four views (clockwise from lower left): Scan Filter view,
(filtered) Chromatogram view, (averaged) Spectrum view, and (unfiltered)
Chromatogram view.
Figure 63. Qual Browser window
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Initiating a Library Search from Qual Browser
5. Select one or more libraries to search:
a. Right-click the Spectrum view (upper right). A shortcut menu appears.
b. To display the Search Properties dialog box (see Figure 64), choose
Library > Options from the shortcut menu.
Figure 64. Search Properties dialog box with selected library
c. Confirm that any libraries you want to search are listed in the Selected Libraries list.
d. Click OK to save the settings, close the dialog box, and return to the Qual Browser
window.
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Initiating a Library Search from Qual Browser
6. To start the library search, right-click the Spectrum view (upper right). From the shortcut
menu, choose Library > Search to submit the spectrum to a library search.
The Xcalibur application displays library spectra (search results) that match the spectrum
in a four-pane Library Search Results view (see Figure 65).
Figure 65. Library Search Results view cascaded with the Raw Data view
The interactive cells of the Library Search Results view show the following library search
results, displayed clockwise from the upper left quadrant:
• Hits list (search results)
• Molecular structure, including formula, molecular weight, name, and library index
number
• Difference spectrum (Raw Data minus Library Entry)
76
–
Peaks above the X-axis are relatively more intense in the spectrum than in the
library entry.
–
Peaks below the X-axis are relatively more intense in the library entry than in the
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Searching a Library Using Library Browser
• Comparison of the sample spectrum and the library entry
7. To print the library search report, choose File > Print Preview. The Print dialog box
opens (see Figure 66).
Figure 66. Print dialog box
8. Select options for your print display.
9. To close the dialog box and preview the results, click OK.
10. To display the Print dialog box again, click Print and click OK.
11. Click OK in the second Print dialog box to print the results. See “Library Sample
Reports” on page 83 for an example of library search results initiated from Qual Browser.
12. Click
to close the Library Search Results view.
Searching a Library Using Library Browser
To search a library, use the Library Browser window.
 To perform a library search on a spectrum exported from Qual Browser
1. Click
in the Spectrum view (upper right) in the Qual Browser window to activate the
window.
2. Right-click the Spectrum view to display the shortcut menu.
Note To display data files in Library Browser, export them from Qual Browser. You
can export a spectrum into Library Browser from Qual Browser after opening a raw
file (.raw) or a result file (.rst) in Qual Browser.
3. Choose Library > Export to Library Browser to open the Library Browser windows
automatically.
When you export a spectrum to Library Browser, the data system automatically does the
following:
• Copies information about the exported spectrum into the C:\Xcalibur\Libspecs
directory. The data system gives the file an extension of .msd and truncates the
filename to the first eight characters of the original filename.
• Creates an index file containing details about the exported spectrum.
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When Library Browser opens, the Xcalibur data system automatically does the following:
• Picks up the index file.
• Locates the exported .msd spectrum files and lists them in the Spec List pane.
4. To define search parameters in Library Browser, choose Tools > Library Search Options
to display the Library Search Property dialog box (see Figure 67).
Figure 67. Library Search Property dialog box
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Searching a Library Using Library Browser
5. Click the Libraries tab to display the list of available and included libraries (see
Figure 68). Use this dialog box to specify which libraries to search and the search order.
Figure 68. Libraries dialog box
• To add a library to the search list, select its name in the Available Libs list and
click Add.
• To exclude a library from the search list, select its name in the Included Libs list and
click .
• Click the Search tab and observe the Automation check box in the Other Options
area (Figure 67).
• If the check box is checked for Automation, go to Step 5b save the parameters and
close the Library Search Options dialog box.
• If the check box is not checked, go to Step 5a to set automation options.
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Searching a Library Using Library Browser
a. To set automation options for searches, click the Automation tab and select the
Automatic Search On check box.
The following figure shows possible settings for the option to automatically search
libraries when exporting spectra to Library Browser.
Figure 69. Automation page
b. Click OK to save your options, close the dialog box, and return to the Library
Browser windows. This action sets automatic searching as the default option the next
time you open the Library Browser.
6. Double-click 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 (see Figure 70).
• Hit List History drop-down list shows the results of the search.
• Hit List pane contains a list of spectral results.
• Structures panes (tab) display the chemical structure of the compound associated
with the highlighted entry.
• Text panes display compound names, a mass/intensity list, and a scan filter of the
highlighted entry.
• Plot panes display a single mass spectrum of a selected entry.
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• Compare pane displays the difference between two spectra and presents them in
various ways.
The following figure shows the library search results for a raw spectrum.
Figure 70. Library Browser default window
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7. Right-click an entry in the Hit List pane to copy it to the first position in the Spec List
pane (see Figure 71).
Figure 71. Library Browser default window, showing file copying from Hit List to Spec List panes
8. To print the search results, click Print in the tool bar. See “Library Sample Reports” on
page 83 for an example of library search results initiated from Library Browser.
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Library Sample Reports
This appendix contains samples of possible results using Xcalibur Library Browser.
Contents
• Reports from a Library Search Using Sequence Setup
• Report from a Library Search Using Qual Browser
• Report from a Library Search Using Library Browser
Reports from a Library Search Using Sequence Setup
The Xcalibur data system prints reports library search reports automatically from Sequence
Setup. Click the report name to view an example report:
• Library Search Report #1
–
Spectrum of Raw Data #1
–
Spectrum of Raw Data #2
–
Spectrum of Raw Data #3
–
Spectrum of Raw Data #4
• Library Search Report #2
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Spectrum of Raw Data #1
–
Spectrum of Raw Data #2
–
Spectrum of Raw Data #3
–
Spectrum of Raw Data #4
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Report from a Library Search Using Qual Browser
Report from a Library Search Using Qual Browser
The following is an example report of a library search that you can print from Qual Browser.
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Report from a Library Search Using Library Browser
Report from a Library Search Using Library Browser
This section includes an example report of a library search that you can print from
Library Browser.
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B
AMDIS Compound Identification
This topic appendix describes using AMDIS to automate compound identification. The
Automated Mass Spectral Deconvolution & Identification System (AMDIS) is a computer
program developed to reduce the effort involved in identifying compounds by GC/MS while
maintaining the level of reliability associated with traditional analysis. AMDIS extracts spectra
for individual components from GC/MS data and uses these spectra to identify compounds
by matching these spectra with spectra in a reference library.
Contents
• AMDIS Overview
• Automated Compound Identification Using AMDIS
AMDIS Overview
AMDIS uses an extension of the published model peak approach1 as the basis for the
calculations used to extract pure component spectra from complex chromatograms. The
model peak approach uses selected ion chromatograms as models for component shape.
Based on the shape, individual mass spectral peak abundance profiles are extracted to produce
a purified spectrum.
AMDIS was developed at NIST with the support of the Defense Threat Reduction Agency
(DOD). NIST reports that the model peak method was successfully used for target
compound identification in a large-scale EPA study2.
The first version of AMDIS was released September 1996, and AMDIS has been distributed
at no additional cost along with the NIST Mass Spectral Database since January 1998.
AMDIS is included with the Xcalibur software and is also available through the NIST
internet site: www.nist.gov/srd/.
1
Dromey, R. G; Stefi, M. J.; Reindfleisch, T. C; Duffield, A. M. Extraction of Mass Spectra Free of Background
and Neighboring Component Contributions from Gas Chromatography/Mass Spectrometry Data. Anal. Chem.
1976 48 (9) 1368-1375.
2 Shackelford, W. M.; Cline, D. M.; Faas, L; Kurth, G. An evaluation of Automated Spectrum Matching for
Survey Identification of Wastewater Components by Gas Chromatography-Mass Spectrometry. Analytica Chim.
Acta 1983 146 25-27.
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AMDIS Compound Identification
Automated Compound Identification Using AMDIS
Automated Compound Identification Using AMDIS
AMDIS does the following:
• Performs an automated search of the NIST library
• Displays dual chromatographs
• Performs batch analyses
• Builds user defined libraries using either user provided GC/MS files or the NIST Mass
Spectral Database
• Provides compound class identification
• Tracks results of routine performance runs
• Uses a library of mass spectra with or without retention indices to identify compounds in
a data file
AMDIS has two main windows:
• Results Window
• Confirm Window
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Results Window
The Results window contains only search results and is most commonly used for routine
analyses (see Figure 72).
Figure 72. AMDIS Results window
The Results window is divided into three areas: the Control panel (top left), the Results pane
(top right), and the Library and Settings pane. See Table 1.
Use the Library and Settings pane to
• Examine the library
• Compare the library spectrum with the extracted spectrum
• Examine the settings for the analysis
• View the retention index standards and internal standards
• Examine the QA/QC report or the S/N for the run
• Set options for the printed results
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AMDIS Compound Identification
Automated Compound Identification Using AMDIS
Table 1. Library and Settings pane parameters
Area
Function/options
Control panel (button names)
Analyze
Open a window to select the type of analysis, the data file
to be analyzed, the target library file, and the calibration
data or library.
Help
Open Help for the Results window.
Done
Close the window.
Confirm
Open the Confirm window.
Print
Print different reports and information.
Load Results
Select and display the results of a previous analysis.
Results pane (area functions)
R.T.
View the retention time for each chemical.
N Identifications
View the name of the compound found.
Component
View the component parameters for the deconvoluted
chromatographic peak.
Match
View the match factors between the mass spectrum of the
component and that of the library.
Library and Settings pane (views)
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Library
Examine the library
Spectra
Compare the library spectrum with the extracted
spectrum
Settings
Examine the settings for the analysis
Standards
View the retention index standards and internal standards
QA/QC or S/N
Examine the QA/QC report or the S/N for the run
Options
Set options for the printed results
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Confirm Window
The Confirm window shows the data used in identification in more detail than the Results
window does (see Figure 73).
Figure 73. AMDIS Confirm window
The Confirm window is divided into the Menu Bar/Button Bar (top), Chromatogram (top
most graphical display), Component Profile (middle graphical display), Component/Target
Information list (middle numeric display), and Component/Target Mass Spectra (bottom
graphical display).
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Automated Compound Identification Using AMDIS
Table 2. Confirm window areas and their functions and options
Area
Function/options
Menu bar
File, Analyze, Mode, View, Library, Options, Window, Help
Toolbar
Run, Rescale, Info, [arrow images]
Chromatogram display
View the ion chromatograms for each ion.
Chromatogram profile
View the total ion current and the largest mass chromatogram peaks over the region
actually used in the deconvolution of the component.
Component/Target
Information
View either component or target data.
Component/Target
Mass Spectra display
View the raw mass spectrum (scan) and the deconvoluted spectrum at a given retention
time. Once data has been analyzed, this display also shows the mass spectra of the
component and the library.
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Library Reference
The Library function in the Xcalibur data system provides different reference windows whose
elements are defined here. For information about Library windows, see “Library Browser
Windows” on page 4.
Contents
• Library Manager Dialog Box
• Library Search Options Dialog Box
• Spectrum Information Dialog Box
• Library Search Results Window
Library Manager Dialog Box
Use the Library Manager dialog box to manage NIST libraries used with the NIST search
software and to convert libraries between the ICIS/GCQ/ITS 40, MassLab, NIST, and
ANDI-MS formats.
Xcalibur Library Manager supports the following conversions:
To
From
ICIS/GCQ/ITS 40
ICIS/GCQ/ITS 40
MassLab
ANDI-MS
NIST





MassLab

ANDI-MS


NIST




Note The Xcalibur data system does not directly support INCOS, LAB-BASE, or
JCAMP library conversions. However, MassLab data system users have a conversion
program to convert from a LAB-BASE user library to a MassLab user library. In addition,
a conversion tool exists in ICIS (a UNIX system) that can convert a LAB-BASE user
library to a MassLab user library.
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Library Manager Dialog Box
The Library Manager dialog box has the following pages:
• Convert Libraries Page
• Manage Libraries Page
Convert Libraries Page
Use the Convert Libraries page to convert one type of source library to another type of library
at a target location and to copy a library to another location.
Note Library convertion times range from minutes to hours, depending on the number of
files and size of the files.
Table 3. Convert Libraries page parameters (Sheet 1 of 2)
Parameter
Description
Source Library Details
Type [Source]
Choose the source library file type that you want to convert to another file type.
Select any of the following file types: ICIS/GCQ/ITS 40 (*.lib, .lbr), MassLab (*.idb),
ANDI-MS (*.cdf ), NIST, or AutoMass (*.spr, *.prs, *.nam, *.hdr).
Library/Browse [Source]
Choose the source library that you want to convert. To change the library, click Browse
and select the path to the source library on your computer or network.
Process Entries [Source]
Specify the number range of the library entries that you want to convert from the source
library. If you leave the box empty, the Xcalibur data system converts all entries. The
format is First Entry-Last Entry. For example, to convert library entry #100 through
library entry #200, type 100-200 in the Process Entries box.
Target library details
Type [Target]
View the target library file type when converting the source library.
If you select source library file type ICIS/GCQ/ITS 40, MassLab, ANDI-MS, or NIST,
you can select from the following target library file types: ICIS/GCQ/ITS 40
(*.lib, .lbr), MassLab (*.idb), NIST, or ANDI-MS (*.cdf ).
If you select source library file type AutoMass, you can only select the NIST target
library file type.
If you select the library type NIST, the Xcalibur data system displays the path to the
NIST library folder in the Library box. You specified this location when you installed
NIST.
Library/Browse [Target]
104
View the file folder to store the converted library file. To change the folder,
click Browse and select the target folder on your computer or network.
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Library Manager Dialog Box
Table 3. Convert Libraries page parameters (Sheet 2 of 2)
Parameter
Description
Title [Target]
Type in a title for the ICIS/GCQ/ITS 40 library or for the Mass Lab library that you
create during the conversion. You can add a title to the new library using any format.
Note This box in the Target library details area only becomes active when you select
an ICIS/GCQ/ITS 40 or MassLab library.
Add the library to the
Add the converted library to the NIST software for use with the Xcalibur application.
NIST software for use with
xcalibur
Options
Target library action:
Create/Replace
Create a new library in the target directory or to replace an existing library. You can also
append (add) the new (converted) entries to a previously created target library.
Target library action:
Append
Append (adds) the new (converted) entries to a previously created target library. You can
also create a new library in the target directory or to replace an existing library.
Include replicate entries
from the NIST library in
the target library
Include replicate entries in the target library. Otherwise, leave the box unchecked.
Replicate library/browse
Specify the location of a replicate library. To change the replicate library, click Browse
and select the folder for the replicate library on your computer or network. If you
specify a replicate library, the Xcalibur data system adds replicate entries into the
appropriate replicate library.
Note This check box is only active if you are converting from a NIST library to
another format.
If you select the library type NIST, the Xcalibur data system displays the path to the
NIST replicate library folder in the Library box. You specify this location when you
install NIST software.
Button
Convert
Start the library conversion you have specified using the Convert Libraries page. The
Xcalibur application opens the Library Conversion Status dialog box and displays the
Conversion Status progress bar and the Conversion Status box. The Status bar displays
messages such as the following:
Processed 100% of the entries, continuing on
The Conversion Status box displays sequential chronological (top to bottom) messages
such as the following:
• Started the conversion on SEP 3, 1999 at 10:01, please wait
• Finished the conversion on SEP 3, 1999 at 10:02
• Converted 570 entries
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Library Manager Dialog Box
Manage Libraries Page
Use the Manage Libraries page to add a library to the NIST libraries list or to delete a library
from the NIST libraries list. You can also copy a library to another location.
Table 4. Manage Libraries page parameters (Sheet 1 of 2)
Parameter
Description
NIST Libraries
NIST Libraries list
View all of the NIST libraries currently available on your computer or network. You can add
libraries to this list, delete libraries from this list, and copy libraries on the list to another
location.
Buttons
Add
Add a library to the NIST Libraries list. The Add Library dialog box opens.
The Add Library dialog box has the following parameters:
• Parameter
• Description
• Source
Use this button to specify the location of the library that you want to add.
–
Copy the library to the local computer: Select this option to copy the selected
library to your computer.
–
Link to the library from either a remote location or computer: Select this option to
access the library remotely.
Note Because libraries can be large, you might save time by using the Link option rather
than the Copy option.
Click OK when you have selected the library you want to add and selected Action options.
Delete
Delete the library that you have previously selected in the NIST Libraries list. Select the
library that you want to delete from the NIST Libraries list. Click Delete. The
Delete Library message box opens with the following message:
Are you sure you want to delete the selected NIST library?
Click Yes. The Xcalibur data system removes the library from the list.
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Library Search Options Dialog Box
Table 4. Manage Libraries page parameters (Sheet 2 of 2)
Parameter
Description
Archive
Copy a selected library to another directory on your computer or network. Select the library
that you want to copy to another directory. Click Archive. The Archive Library dialog box
opens.
The Archive Library dialog box has the following parameters:
• Parameter
• Description
• Destination: Specify the location for the selected library.
Use Browse to select a destination for the selected file. Click OK. The data system makes a
copy of the selected NIST library and stores it in the selected directory.
Library Search Options Dialog Box
Use the Library Search Options dialog box to select and order the libraries used during library
searching. You can also change the way that the search is carried out.
The Library Search Options dialog box contains these pages:
• Search Parameters Page
• Libraries Page
• Automation Page
• Limits Page
• Library Search Constraints Page (Library View)
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Library Search Options Dialog Box
Search Parameters Page
Use the Search Parameters page to select the type of library search, limit the search by a
molecular weight constraint, and determine how the results of the search are returned.
Table 5. Search Parameters page parameters (Sheet 1 of 2)
Parameter
Description
Spectrum Search Type
Define the type of library search applied to spectra. There are two main options: Identity
and Similarity. The difference between the two search types is primarily in the weightings of
the spectrum as a function of mass.
Identity
Apply an Identity search algorithm for library matching of spectra. A Normal Identity
search is the default option.
Similarity
Apply a Similarity search algorithm for library matching of spectra.
Normal
Apply a Normal Identity search algorithm for library matching of spectra. This is the default
option. A Normal Identity search is suited to low quality or unusual spectra. The search
algorithm uses a standard pre-screen search filter.
Quick
Apply a Quick Identity search algorithm for library matching of spectra. Use this option
when you are sure the spectrum or compound exists in the library. The search algorithm
uses a fast pre-screen search filter.
Spectrum Search Options
Reverse Search
Specify that the Xcalibur data system sorts matching library spectra (hits) by the
Reverse Search Match Factor. By default, the data system sorts search results by the
Forward Match Factor.
Penalize Rare
Compounds
Reduce the match factors of hit compounds present in few databases. This option is
effective only when you have selected one or more of the NIST databases (such as
MAINLIB). It has no effect on spectra in user libraries or other commercial libraries.
Each reference spectrum in a NIST library contains a record of other commercial databases
containing information about the compound. A compound is considered rare if it is present
in a limited number of these databases. If you select the Penalize Rare Compounds option,
search result compounds present in few or no other databases other than the NIST libraries,
will have their match factors reduced (the maximum penalty is 50 out of 1000). This, in
effect, leads to a relative increase in the match factors of common compounds, placing them
higher in the hit list than exotic isomers with near identical spectra.
Pre-search
Default
Off
Turn off the pre-search option.
MW
Restrict the search to library entries with a particular molecular weight. Type the molecular
weight in the associated box.
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Library Search Options Dialog Box
Table 5. Search Parameters page parameters (Sheet 2 of 2)
Parameter
Description
Other Options
Automation
Indicate whether automatic library searching is enabled.
AutoReport
Print reports of the results of library searching with user spectrum.
Apply Limits
Set limits of m/z and peak abundance for spectral comparison.
Use Constraints
Set additional constraints on the search.
Libraries Page
Use the Libraries page to specify the libraries used and the search order for them. It is possible
to keep different lists of active libraries for each of the search modes.
Table 6. Libraries page parameters
Parameter
Description
Library Lists
Available Libraries
List the libraries that are currently excluded from searching during processing. The Xcalibur
data system regenerates this list when you open the dialog box.
Included Libraries
List the libraries that are currently included in searches during processing. The order of the
libraries defines the order in which they are searched by the data system.
Buttons
Remove
Transfer a library from the Selected Libraries list to the Available Libraries list.
Up
Move a library in the Selected Libraries list up one position (earlier in the search order).
Down
Move a library in the Selected Libraries list down one position (later in the search order).
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Library Search Options Dialog Box
Automation Page
Use the Automation page to specify values for an automated library search.
Table 7. Automation page parameters
Parameter
Description
Number of hits to print
Set the number of spectra to be printed per page. The default value of 2 prints the
unknown and the top two matches on a single sheet of paper.
Include spectrum plot in
report
Include spectrum, text of intensities, and masses in report.
Draw structure in plots
Add a molecular structure to the spectrum plot, if this is available.
Apply maximum
spectrum length
Provide an upper mass limit for printed spectrum.
Return focus to caller
upon completion
Used in the context of an instrument control program calling the search program.
Automatic search on
Carry out a library search automatically in Library Browser when a spectrum is
exported from Qual Browser.
Limits Page
Use the Limits page to define limits for a library search.
Table 8. Limits page parameters
Parameter
Description
Apply limits
Apply limits to the library search.
Minimum Abundance
Specify the minimum level of abundance before including in a search.
Minimum m/z
Specify the minimum level of abundance before excluding from a search.
Maximum m/z
Specify the maximum level of abundance before excluding from a search.
Set Default
Set parameter values as the default for future searches.
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Library Search Options Dialog Box
Library Search Constraints Page (Library View)
Use the Constraints page to define additional constraints on the search. For example, limit the
search to only compounds with names containing specified letters (such as “ol” for alcohols),
or specify that only certain elements can be present in the compound.
Limit a library search to increase processing efficiency. For example, you might want to
exclude certain high intensity ions that appear in many compounds or that are present in the
spectrum background. You can target a search to a particular range of molecular weights or to
compounds containing certain elements. This view is available both in the Library Browser
and the Qual Browser.
Table 9. Library Search Constraints Page parameters (Sheet 1 of 7)
Parameter
Description
Molecular Weight
Limit the library search to compounds with a specific molecular weight or molecular
weight range by selecting the Molecular Weight Enable check box.
Range
Type a molecular weight or molecular weight range in the box (for example, 200-250).
During a search, the Xcalibur data system only compares processed spectra with
reference data derived from compounds with a molecular weight within the specified
range.
Name Fragment
Limit the library search to compounds with a specific name or name fragment by
selecting the Name Fragment Enable check box.
Name
Thermo Scientific
Type a text string (up to 39 characters) to represent a fragment of a compound name;
for example, “cyclo”. During the library search, the Xcalibur data system filters search
results and only returns those containing the specified text in their names. The entry is
not case sensitive, so “CYCLO” returns compounds containing the fragments “cyclo”,
“Cyclo” and “CYCLO”.
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Library Search Options Dialog Box
Table 9. Library Search Constraints Page parameters (Sheet 2 of 7)
Parameter
Description
Elements Value
Individual Element Table
Set specific criteria about the elements required in a library hit. Each row in the table
represents an element constraint.
There are three parts to each constraint:
• Element: An IUPAC-approved abbreviation for an element, for example “Cl” for
chlorine
• Condition: A mathematical operator, < (less than), > (greater than), or = (equals)
• Value: A numerical value representing the number of atoms of the specified
element required to satisfy the constraint.
In the example shown here, the Xcalibur data system only returns search results for
compounds that contain more than five fluorine atoms or exactly three chlorine atoms.
You do not need to provide a complete elemental profile. The library search returns
compounds if they satisfy all the specified criteria regardless of any other elements
present.
[Row Number]
Enter a new item in the last unused row in the table (indicated by an asterisk). Each
numbered row represents an item in the table.
Element
Type the IUPAC-approved abbreviation for the element you want to use an element
constraint. It is used in conjunction with the Condition list and Value box in the same
row within the Individual Element table.
To enter an element constraint, click the box and type the required abbreviation. For
example, to apply carbon as an element constraint, type “C”. The data system adds a
new row to the table for further entries.
Condition
Enter a condition for an element constraint in this box. The Xcalibur data system uses
this condition in conjunction with the Condition list and Value box in the same row
within the Individual Element table. Valid conditions are:
< (less than)
> (greater than)
= (equals)
To type an element constraint condition, click the box to activate the list. Click the
down arrow and select the required abbreviation.
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Library Search Options Dialog Box
Table 9. Library Search Constraints Page parameters (Sheet 3 of 7)
Parameter
Description
Value
Type a numerical value for an element constraint in this box. The Xcalibur application
uses this value in conjunction with the Condition list and Value box in the same row
within the Individual Element table.The value represents the number of atoms of the
specified element required by library compounds to satisfy the constraint.
To type an element constraint value, click the box and type the required number (the
valid range is 0 to 99).
Elements Present
Select to constrain the library search to compounds containing specific elements using
the Individual Element or Elements in Compound methods.
You can use the two types of elemental constraints together, but make sure there are no
contradictions. For example, you might put “C=0” in the Individual Element group
and then list “C” in the Elements in Compound box. When a contradiction occurs, a
warning dialog box opens.
Elements In Compound
Elements
Specify a list of elements that must be present in search results. To enter an element list,
click the box and type the IUPAC-approved abbreviation for each element. Separate
each element in the list (of up to 30 characters) by a comma.
All
Specify that the Xcalibur data system should return search results containing all, and
only, the listed elements. For example “C, H, O” would return HCHO but not CO2,
CH4, or CH2Cl2. Compare these results with the Some option.
Some
Specify that the Xcalibur data system return search results that contain at least one of
the specified elements and no elements that are unlisted. For example, “C, H, O” would
return CO2, CH4, HCHO but not CH2Cl2. Compare these results with the All
option.
Clear
Delete the text in the Elements in Compounds box.
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Library Search Options Dialog Box
Table 9. Library Search Constraints Page parameters (Sheet 4 of 7)
Parameter
Description
Mass Spectral Peak Constraints
Build a profile of ions and ion abundances to be matched against library entries during
the search. The search algorithm only returns search results matching the specified
constraints.
Mass spectral peak
constraints table
Set specific criteria about the mass spectral peaks required in a library hit. Each row in
the table represents an individual mass spectral peak constraint. There are four
components to each constraint represented by the table columns:
Type: Normal, Loss, Rank, or Maxmass
m/z: In a Normal, Rank, or Maxmass type constraint, use this box to type the m/z value
of the mass spectral peak to limit. In a Loss type constraint, use this box to type the
value of a neutral loss.
From: In a Normal, Loss, or Maxmass type constraint, type the minimum abundance
of the constrained mass spectral peak in this box. In a Rank type constraint, type the
lowest position of the ion in an intensity ordered list of spectral peaks in this box.
To: In a Normal, Loss, or Maxmass type constraint, type the maximum abundance of
the constrained mass spectral peak in this box. In a Rank type constraint, type the
highest position of the ion in an intensity ordered list of spectral peaks in this box.
[Row Number]
114
Enter a new item in the last unused row in the table, indicated with an asterisk. Each
numbered row represents an item in the table.
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Library Search Options Dialog Box
Table 9. Library Search Constraints Page parameters (Sheet 5 of 7)
Parameter
Description
Type
Specify the type of ion constraint.
Normal: Applies to a specific ion represented by its m/z value. The From and To values
represent the abundance of the ion.
Loss: Describes a neutral loss from a molecular ion. In this case, the m/z value (limited
to 64) represents the mass of the ‘lost’ neutral group, for example, for methyl m/z = 15.
For this constraint to be matched, a library spectrum must contain the following:
• A fragment ion at an m/z value 15 less than the molecular ion
• An abundance in the specified From and To range
Rank: Tests the order of an ion in the spectrum in terms of relative abundance. Ions
are ranked from the largest (the base peak) to the 16th. A compound matches a Rank
constraint if its library spectrum contains a mass spectral peak with these criteria:
• At the specified m/z value
• Ranked between the specified From and To rank positions
If you specify the same number in both fields, the designated ion must have that
rank in the retrieved spectrum.
Maxmass: Sets a constraint on the m/z value of the most significant high mass ion.
Library search results must feature the following:
• An ion at the specified m/z value
• No significantly larger masses at higher m/z values.
• An abundance in the specified From and To range
m/z
In a Normal, Rank, or Maxmass type constraint, type the m/z value of the mass spectral
peak to be constrained in this box. The Xcalibur application discards a library hit if it
does not contain a mass spectral peak at the specified m/z value.
In a Loss type constraint, use this box to type the value of a neutral loss. The application
discards a library hit if it does not feature a fragment ion at an m/z value appropriate to
the specified neutral loss (in relation to the molecular ion).
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Library Search Options Dialog Box
Table 9. Library Search Constraints Page parameters (Sheet 6 of 7)
Parameter
Description
From
In a Normal, Loss, or Maxmass type constraint, type the minimum abundance of the
constrained mass spectral peak in this box. In a Rank type constraint, you use this box
to type the lowest position of the ion in an intensity ordered list of spectral peaks.
You can specify the same number in both From and To boxes. In this case, the Xcalibur
data system discards a library hit unless the designated mass spectral peak is present in
exactly the specified abundance or rank in the retrieved spectrum.
To
In a Normal, Loss, or Maxmass type constraint, type the maximum abundance of the
constrained mass spectral peak in this box. In a Rank type constraint, type the highest
position of the ion in an intensity ordered list of spectral peaks in this box.
You can specify the same number in both From and To boxes. In this case, the Xcalibur
data system discards a library hit unless the designated mass spectral peak is present in
exactly the specified abundance or rank in the retrieved spectrum.
Absolute
Specify how the Xcalibur data system applies the From and To parameters in the
Mass Spectral Peak Constraints table.
Select the Absolute option if you want the application to evaluate all table entries as a
percentage of the base (largest) ion in the spectrum. Values must be between 0 and
100%. For example, if you type 10 and 50 in the From and To fields of a Normal type
constraint, the application discards any search results in which the specified mass
spectral peak is not present at an abundance of between 10 and 50%.
In the case of Normal and Loss type constraints, the abundance values can also be
Relative.
Relative
Specify how the Xcalibur data system applies the From and To parameters in the
Mass Spectral Peak Constraints table.
Select the Relative option if you want the application to treat the first entry as an
absolute Normal or Loss type. The application considers subsequent entries in the table
relative to the first. In the following example, library search results must contain the
following:
• An ion at m/z 125 with an abundance between 10 and 50% of the base ion
• An ion at m/z 250 with an intensity between 50% and 999% of the observed
intensity of the first ion in the list
• Relative mode is not available for Rank or Maxmass types.
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Library Search Options Dialog Box
Table 9. Library Search Constraints Page parameters (Sheet 7 of 7)
Parameter
Description
Other Databases
Selection Criteria
Limit the library search to entries in the NIST library also featured in other databases.
Each entry in the NIST library contains a list of other commercial databases containing
information about the compound.
The Xcalibur application reports search results featuring in one or more of the selected
databases (a hit does not have to feature in all the selected databases).
Fine
Report search results from reference compounds or spectra also to be found in the
commercially available Fine Chemical Index.
TSCA
Report search results from reference compounds or spectra also to be found in the
Toxic Substances Control Act Inventory (TSCA).
RTECS
Report search results from reference compounds or spectra also to be found in the
Registry of Toxic Effects of Chemical Substances (RTECS).
EPA
Report search results from reference compounds or spectra also to be found in the
Environmental Protection Agency (EPA) Environmental Monitoring Methods Index.
USP
Report search results from reference compounds or spectra also to be found in the
US Pharmacopoeia (USP)/U.S.A.N.
HODOC
Report search results from reference compounds or spectra also to be found in the
CRC Handbook of Data of Organic Compounds (HODOC).
NIH
Report search results from reference compounds or spectra also to be found in the
NIH-NCI Inventory File.
EINECS
Report search results from reference compounds or spectra also to be found in the
European Index of Commercial Chemical Substances (EINECS).
IR
Report search results from reference compounds or spectra also to be found in the
NIST/EPA Gas Phase IR Database.
Clear All
Clear all the check boxes in the Other Databases area.
Button
Save As Default
Thermo Scientific
Validate and save the settings on the current page as default settings. The Xcalibur
application uses these settings for all new processing methods, overriding the previous
default values permanently.
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Spectrum Information Dialog Box
Spectrum Information Dialog Box
Use the Spectrum Information dialog box to type or to change information stored with a
library spectrum. The dialog box displays information for the spectrum selected in the
Spec List in the Librarian window.
Figure 74. Spectrum Information dialog box
Table 10. Spectrum Information dialog box parameters (Sheet 1 of 2)
118
Parameters
Action
Name
Type a name for the spectrum.
Formula
Type the chemical formula, for example, C12H8Cl6O.
Other Names
Type synonyms for the compound.
Comments
Type any comments about the spectrum.
Mol. Weight
NIST MS Search assigns a molecular weight based on the
formula. If no formula is available, type the molecular weight.
ID Number
View the ID number assigned to the library entry.
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Library Search Results Window
Table 10. Spectrum Information dialog box parameters (Sheet 2 of 2)
Parameters
Action
CAS Number
View the CAS number for the compound. (You need not enter
this information.)
Peaks
View the number of peaks in the mass list.
Buttons
Add to Library
Add the edited spectrum and structure to an existing or new
library.
Replace
Replace the spectrum in the library from which it came.
Add to List
Add the edited spectrum to the Spec List.
Attach Struct
Obtain a structure from other libraries.
Clipboard Struct
Attach a structure from the clipboard, if present.
To edit the mass list, use the Peaks Info area.
Library Search Results Window
Qual Browser displays this window in its workspace when you submit a spectrum in a
Spectrum View to a library search or when you open a result file containing library search
results from qualitative processing.
The Library Search Results window displays matching library spectra (hits) in a four-pane
arrangement. Clockwise from the top left, the four panes are as follows:
Hit List
The Hit List lists the best matches found during the library search. Three factors describe the
accuracy of the match to your spectrum:
SI
A direct matching factor for the unknown and the library spectrum.
RSI
A reverse search matching factor ignoring any peaks in the unknown that are
not in the library spectrum.
Prob
A probability factor based on the differences between adjacent hits in an SI
ordered list.
With the SI and RSI matching factors, a perfect match results in a value of 1000. As a general
guide 900 or greater is an excellent match; 800-900, a good match; and 700-800, a fair
match. A matching factor less than 600 is a poor match. Unknown spectra with many peaks
tend to yield lower match factors than otherwise similar spectra with fewer peaks.
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Library Search Results Window
The probability factor is a complex parameter based on the SI matching factor and the
difference between adjacent matches. If a hit has an SI match factor > 900 and the next best
hit has a match factor of 300, the probability of the compound being correctly identified is
high. Conversely, if several hits are returned with very similar SI matching factors, the
probability of a correct assignment is low.
Molecular Structure
Shows the formula, structure, molecular weight, name and library index number of the
currently selected hit in the Hit List.
Difference Spectrum
Compares the submitted spectrum with the currently selected library spectrum in the Hit
List. Peaks above the X-axis are relatively more intense in the sample than the library entry.
Negative peaks are relatively more intense in the library entry than in the sample spectrum.
Comparison
Displays the submitted spectrum above the currently selected library spectrum in the Hit List.
Note Avoid making positive assignments based solely on the statistical result of a library
search. The Xcalibur data system might identify a compound with an unusual structure
(or, more importantly, an unusual mass spectrum) in a definitive way. More usually, your
unknown might be a member of a class of compounds with very similar mass spectra. The
ability of Qual Browser or any search system to distinguish between them is limited. In
many cases, the best that the search algorithm can do is identify a class of compounds that
have similar mass spectra — and usually similar structure. In most cases, you should seek
confirmation by other analysis techniques.
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I
Index
A
adding a library to the NIST Libraries list 43
adding plots to a view 16
adding spectra to a user library 29
AMDIS 97
append to user library 23, 29
attaching a chemical structure to a library entry 32
automated compound identification 97
EPA Environmental Monitoring Methods Index database 57
European Index of Commercial Chemical Substances
database 57
exporting spectrum to Library Browser 22
F
Fine Chemical Index database 57
H
B
hits list, using 6
background, subtracting 20
I
C
Compare window 10
compound identification, automated 97
constraining a library search 50, 55
Constraints tab 50
converting libraries to another format 45
copying a library from the NIST Libraries list 44
CRC Handbook of Data of Organic Compounds database
57
creating a library entry with your spectral data 15–16, 42–45
custom reports, example 67
D
deconvolution, automated 97
deleting a library from the NIST Libraries list 43
dialog boxes
Library Browser
ID Number Search 51
Library Search Options 49
Spectrum Information 118
Search Properties for libraries 61
E
element constraints 58
elements in compound 59
Thermo Scientific
ID Number Search dialog box 51
L
Librarian window 12
libraries
adding, to NIST Libraries list 43
attaching structures to
figure 35–36
converting to another format 45
copying, from NIST libraries list 44
creating entries in 15–16, 42–45
deleting, from NIST Libraries list 43
searching
from Library Browser 77
from Qual Browser 74
Library Browser
about 3
contents 80
exporting spectra to 22
figure 22
library search
constraining 50
Library Browser 6
options in Library Browser 49
processing method search list 61
selecting libraries 49
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Index: M
Library Search Constraints page
element constraints 58
elements in compound 59
figure 55
mass spectral peak constraints 59
molecular weight 56
name fragment 57
Library Search Options dialog box 28
Library Search Options page
append to user library 29
figure 52
options 53
library search processing 61
Library Search Property dialog box
See Library Search Options dialog box
Library Search Results window 119
Library Search window 5
limiting a library search 50, 55
M
Mass spectral peak constraints 59
Match factor threshold 29
molecular weight, constraining a library search 56
Q
Qual view
Library Search Constraints page 55
Library Search Options page 52
qualitative analysis, reprocessing data 72
R
Registry of Toxic Effects Chemical Substances database 57
reports
example of custom 67
printing
in Library Browser 82
in Qual Browser 77
in Sequence Setup 72
reverse search, match factor threshold 29
S
N
Name Fragment constraint 57
Name search window 9
Names window 9
National Institute of Standards and Technology 1, 3
NIH-NCI Inventory File database 57
NIST Browser 3
NIST MS Search 3
NIST/EPA Gas Phase IR database 57
O
opening a raw data file in Qual Browser 15
Other Search window 8
overview of Library Browser 1
P
Plot pane 7
printing reports
in Library Browser 82
in Qual Browser 77
in Sequence Setup 72
probability threshold 29
Processing method, exporting a spectrum 23
122
Processing Setup
Qual view
Library Search Constraints page 55
Library Search Options page 52
Search List page of Search Properties dialog box 61
Processing Setup window, Reports view 66
Creating and Searching Libraries User Guide
search libraries
Automation dialog box 80
search results in Library Browser 32
search results, using the hit list 6
search, customizing 48
Sequence Setup window, figure 70
Sequence Setup, specifying files 70
Spec List
submitting a search from 6
transferring spectrum to Compare pane 6
Spectral Import Options dialog box 80
Spectrum Information dialog box 118
subtracting background spectra 20
T
Text pane, information 7
thresholds, append to user library option 29
Toxic Substances Control Act Inventory database 57
U
US Pharmacopoeia database 57
Thermo Scientific
Index: V
user libraries
appending spectra 29
creating 25
finding Xcalibur data 51
including in a search 49
maintenance 13
selecting 61
V
viewing a spectrum in Qual Browser 16
views
cursor actions in 16
using interactively 16
X
Xcalibur Library Manager Dialog Box
Convert Libraries Page 104
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123
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