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Creating and Searching Libraries XCALI-97062
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Contents
'JOOJHBO9DBMJCVS ________________________________________________________________________
Contents
Abbreviations .......................................................................................................................................... v
5IFSNP
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Contents
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Searching Libraries from Qual Browser and Library Browser ........................................... 4-1
4.1 Initiating a Library Search from Qual Browser......................................................................... 4-2
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Read This First
Changes to the Manual and Online Help @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Abbreviations
The following abbreviations are used in this and other manuals and in the
online Help.
A ampere
ac alternating current
ADC analog-to-digital converter
AP acquisition processor
APCI atmospheric pressure chemical ionization
API atmospheric pressure ionization
ASCII American Standard Code for Information
Interchange
b bit
B byte (8 b)
baud rate data transmission speed in events per second
°C degrees Celsius
CD compact disc
CD-ROM compact disc read-only memory
cfm cubic feet per minute
CI chemical ionization
CIP carriage and insurance paid to
cm centimeter
cm3 cubic centimeter
CPU central processing unit (of a computer)
CRC cyclic redundancy check
CRM consecutive reaction monitoring
<Ctrl> control key on the terminal keyboard
d depth
Da dalton
DAC digital-to-analog converter
dc direct current
DDS direct digital synthesizer
DEP direct exposure probe
DS data system
DSP digital signal processor
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Abbreviations@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
EI electron ionization
EMBL European Molecular Biology Laboratory
<Enter> enter key on the terminal keyboard
ESD electrostatic discharge
ESI electrospray ionization
eV electron volt
f femto (10-15)
°F degrees Fahrenheit
.fasta file extension of a SEQUEST search database file
FOB free on board
ft foot
FTP file transfer protocol
g gram
G giga (109)
GC gas chromatograph; gas chromatography
GC/MS gas chromatograph / mass spectrometer
GND electrical ground
GPIB general-purpose interface bus
GUI graphical user interface
h hour
h height
HPLC high-performance liquid chromatograph
HV high voltage
Hz hertz (cycles per second)
ICIS Interactive Chemical Information System
ICL Instrument Control Language
ID inside diameter
IEC International Electrotechnical Commission
IEEE Institute of Electrical and Electronics Engineers
in. inch
I/O input/output
k kilo (103, 1000)
K kilo (210, 1024)
KEGG Kyoto Encyclopedia of Genes and Genomes
kg kilogram
l length
L liter
LAN local area network
lb pound
LC liquid chromatograph; liquid chromatography
LC/MS liquid chromatograph / mass spectrometer
LED light-emitting diode
µ micro (10-6)
m meter
m milli (10-3)
M mega (106)
M+ molecular ion
MB Megabyte (1048576 bytes)
MH+ protonated molecular ion
min minute
mL milliliter
mm millimeter
MS mass spectrometer; mass spectrometry
MS MSn power: where n = 1
MS/MS MSn power: where n = 2
MSn MSn power: where n = 1 through 10
m/z mass-to-charge ratio
n nano (10-9)
NCBI National Center for Biotechnology Information
(USA)
NIST National Institute of Standards and Technology
(USA)
OD outside diameter
Ω ohm
p pico (10-12)
Pa pascal
PCB printed circuit board
PID proportional / integral / differential
P/N part number
P/P peak-to-peak voltage
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Typographical Conventions
Typographical conventions have been established for Thermo Electron
San Jose manuals for the following:
• Data input
• Boxed information
• Topic headings
Data Input
Throughout this manual, the following conventions indicate data input and
output via the computer:
• Messages displayed on the screen are represented by capitalizing the
initial letter of each word and by italicizing each word.
• Input that you enter by keyboard is represented in bold face letters.
(Titles of topics, chapters, and manuals also appear in bold face letters.)
• For brevity, expressions such as “choose File > Directories” are used
rather than “pull down the File menu and choose Directories.”
• Any command enclosed in angle brackets < > represents a single
keystroke. For example, “press <F1>” means press the key labeled F1.
• Any command that requires pressing two or more keys simultaneously is
shown with a plus sign connecting the keys. For example, “press
<Shift> + <F1>” means press and hold the <Shift> key and then press the
<F1> key.
• Any button that you click on the screen is represented in bold face letters
and a different font. For example, “click on Close”.
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Boxed Information
Information that is important, but not part of the main flow of text, is
displayed in a box such as the one below.
Topic Headings
The following headings are used to show the organization of topics within a
chapter:
Chapter 1
Chapter Name
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Reply Cards @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Reply Cards
Thermo Electron San Jose manuals contain one or two reply cards. All
manuals contain a Customer Registration / Reader Survey card and some
contain a Change of Location card. These cards are located at the front of each
manual.
The Customer Registration / Reader Survey card has two functions. First,
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The Change of Location card allows us to track the whereabouts of the
instrument. Fill out and return the card if you move the instrument to another
site within your company or if you sell the instrument. Occasionally, we need
to notify owners of our products about safety or other issues.
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Overview of Library Browser
Quick Reference Guide @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
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Overview of Library Browser
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Specify library
Print report
options; search
Open a .raw file
in Qual Browser,
and display the
spectrum
Export spectrum Specify library
to Library Browser Print reports
options; search
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Overview of Library Browser
Specifying the Peak Detection Algorithm @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Note: For new Processing Methods only, you can choose either the ICIS, the
Genesis, or the Avalon Xcalibur peak detection algorithm as the default
setting for each type of detector. From the Roadmap view of the Home Page,
choose Tools > Configuration and select the appropriate default option
on the Peak Detection page.
5. Specify mass tolerance and mass precision as follows. See Figure 1-3.
a. Select Display > Mass Options. The Global Mass Options dialog
box is displayed.
b. Specify a mass tolerance bandwidth in the Mass Tolerance text box to
calculate spectrum averages, to add and subtract spectra, and to
convert profile data to centroid data. Specify the units of mass
tolerance as mmu or ppm.
c. Specify a mass precision number from 0 to 5 in the Decimals text
box. Xcalibur applies a number of decimal places to mass intensity
values for data processing calculations.
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Overview of Library Browser
'JOOJHBO9DBMJCVS ________________________________________ Specifying the Peak Detection Algorithm
Figure 1-2. Xcalibur - Qual Browser display of the Chrom view shortcut menu. Specify which
algorithm Xcalibur uses to find and measure peaks.
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Chapter 2
Creating a Custom Library of Spectra
You can create a custom library of MS/MS spectra by using the Xcalibur data
system. The Xcalibur data system includes a subset of the NIST mass spectral
library called nistdemo. The NIST/EPA/NIH Main Library contains more than
100,000 compounds whose MS-type spectra were obtained primarily in
electron ionization (EI) scan mode. You might want to create a custom library
that includes MS/MS spectra or spectra of MSn analyses.
Note. Refer to the online Help for more information, as follows: Choose
Help on the menu bar in any Xcalibur window. If you need assistance
specifically for Library Browser, choose Help > Help Topics on the
Library Browser menu bar.
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The procedure in this topic uses steroid data. The raw data files are included
with your Xcalibur data system in the directory C:\Xcalibur\examples\data.
This topic contains the following topics:
• Opening a Raw Data File (.raw) in Qual Browser
• Viewing a Spectrum in Qual Browser
• Subtracting Background Spectra
• Exporting a Spectrum to Library Browser
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Figure 2-1. Open Raw File dialog box, showing the selection of
steroids 14.raw
5. Select the Add: Window option button, and then click on Open to display
the data for the steroids. (Figure 2-1)
Leave the Qual Browser window open, and go on to the next topic: Viewing a
Spectrum in Qual Browser.
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Figure 2-2. Qual Browser window, showing the Chromatogram view of steroids14.raw
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Figure 2-3. Qual Browser window, showing the following views (clockwise from lower left): Scan
Filter view, (filtered) Chromatogram view, (averaged) Spectrum view, and (unfiltered)
Chromatogram view
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4. Drag the cursor across a few scans that are representative of the first scan
range you want to subtract.
5. Release the mouse button to define the first range. The label on the cursor
changes to -2.
6. Click and hold on a baseline region on the other side of the peak of
interest.
7. Drag the cursor across a few scans that are representative of the second
scan range you want to subtract. See Figure 2-4.
8. Release the mouse button to define the second range.
When you release the mouse button, Xcalibur subtracts an average of the
selected scans and redraws the Spectrum view. The Spectrum view header
shows the number of subtracted scans. For example,
SB: 12 0.52-0.56, 0.92-0.99 indicates the following:
• Qual Browser has applied background subtraction to the spectrum by
using a 12-scan average.
• Retention time ranges used in the subtraction are 0.52 to 0.56 min and
0.92 to 0.99 min.
Leave the Qual Browser window open, and go on to the next topic: Exporting
a Spectrum to Library Browser.
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Figure 2-4. Qual Browser window, showing background subtracted scans in the Spectrum view
(upper right)
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Editing a User Library
Figure 2-6. Librarian window, showing the spectrum information as a text file
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Editing a User Library
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Editing a User Library
Figure 2-10. Libraries page of the Library Search Property dialog box,
showing the library ms2test added to the Included Libs
list box
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4. Select steroids14 in the Spec List pane. Right click on this entry and
select Library Search. Library Browser finds the entry
hydrocortisoneMS2 and copies it to the Hit List pane. See
Figure 2-11.
5. Copy the hit to the Spec List pane, as follows:
a. Select the Hit List entry hydrocortisoneMS2. Right click on this entry
and select Copy from the shortcut menu.
b. Move the cursor to the Spec List pane, and then left click the mouse
button to make the Spec List pane active.
c. Right click to display the shortcut menu and select Paste to paste the
entry hydrocortisoneMS2 to the Spec List window.
6. Choose the Librarian tab to open the Librarian window. See
Figure 2-12.
Figure 2-11. Library Search window, showing the results of searching the library ms2test
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Editing a User Library
Figure 2-12. Librarian window, showing the ms2test library entry hydrocortisoneMS2
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Editing a User Library
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Editing a User Library
Figure 2-18. Warning bar that appears after you delete an entry from
the Spec List
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Editing a User Library
Figure 2-20. Librarian window, showing a steroid spectrum in the list of ms2test library entries
6. Copy and paste the library entry deoxycorticosteroneMS2 from the Hit
List pane to the Spec List pane. See Figure 2-21.
a. Choose Window > Lib. Search in Library Browser to display the
Library Search window.
b. Select steroids14 in the Spec List pane. Right click on this entry and
select Library Search. Library Browser finds the entry
deoxycorticosteroneMS2 and copies it to the Hit List pane.
c. Select the Hit List entry deoxycorticosteroneMS2. Right click on this
entry and select Copy from the shortcut menu.
d. Move the cursor to the Spec List pane, and then left click the mouse
button to make the Spec List pane active.
e. Right click to display the shortcut menu and select Paste to paste the
entry deoxycorticosteroneMS2 to the Spec List window.
Figure 2-21. Library Browser panes, showing the results of a search from the Spec List pane
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Editing a User Library
Figure 2-22. Librarian window, showing the entry from the source Text File highlighted
Figure 2-23. Librarian window, showing the entries from the source ms2test only
9. Click on the Qual Browser button in the task bar at the bottom of your
monitor screen to redisplay the Qual Browser window.
10. Repeat Steps 2 through 7 (above) to append the third steroid entry
methyltestosteroneMS2 to the Library Manager list.
11. Repeat Steps 2 through 6 (above) to append the fourth steroid entry
progesteroneMS2 to the Library Manager list.
The Library Search window of the Library Browser should appear similar
to Figure 2-24.
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Editing a User Library
Figure 2-24. Library Search window, showing the Compare Result pane containing the MS/MS
spectra of four steroids
12. Close the windows, and return to the Xcalibur Home Page, as follows:
a. Choose File > Exit to close Library Browser and return to Qual
Browser.
b. Choose File > Exit again to close the Qual Browser window and
return to the Xcalibur Home Page.
In this chapter, you did the following:
• Created a user library containing four MS/MS spectra
• Edited a library entry to include compound structure
Go to the next chapter: Searching Libraries Automatically.
After you create your custom library of spectra, you can search it and/or other
libraries automatically. You need to set up method files in Xcalibur windows
to search libraries automatically:
• Use the Xcalibur Processing Setup window to create a Processing Method
file (.pmd).
• Use the Sequence Setup window to reprocess data files in a sequence list
(.sld) with the Processing Method that you created.
Note. If you need more information about setting up methods, refer to online
Help.
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Note. To use the Library Search Constraints page, you need to have specific
knowledge about the target compounds in your chromatogram. This is not
always possible in automated processing
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3. Ensure that the MS option is selected in the Type list box of the Detector
group box and that ICIS is selected in the Peak Detect list box.
4. Specify a scan filter on the Identification page, as follows:
a. Click on the down arrow of the Filter combo box to display the scan
filters in steroids14.raw.
b. Click on one of the filters to select it.
5. Click on OK to accept changes to Identification page.
Note. For more information about the algorithms that Xcalibur uses to
perform library searches, refer to the online Help.
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Note. Xcalibur generates the Available Libraries list dynamically. Each time
you open the Search List dialog box, Xcalibur lists the libraries available on
your system at that time.
Libraries listed in the Selected Libraries list, on the other hand, might not
exist on your system. They might have been selected on another system or
deleted or renamed since the Processing Method was created.
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Figure 3-3. Search List dialog box, showing the selected library
MS2test
c. Highlight MS2test in the Available Libraries list box, and then click
on Add to move the library name to the Selected Libraries list box.
d. Click on OK to select MS2test, and return to the Qual view of
Processing Setup.
Leave the Qual view open, and go to the next topic: Specifying Report
Options for Library Searches.
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Specify that you want to display the data in steroids14.raw in the format of a
custom report template, as follows:
1. Click on the Reports button on the View bar in the Processing Setup
window, or choose View > Reports to display the Reports view. See
Figure 3-4.
Note. If the Apply Changes? dialog box displays, read the message , and
then click on Yes.
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2. Click on the Enable cell in the Sample Reports group box to display a
check box . Then, select the check box to enable Row 1. See
Figure 3-5.
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Figure 3-5. Processing Setup window, showing the Reports view with Row 1 enable
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c. Click on Open to select the report template, and display the filename
in the Report Template Name cell.
5. Click on OK to apply your changes to the Reports view. See
Figure 3-7.
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Figure 3-7. Processing Setup window, showing the Reports view and a specified Report
Template Name
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b. Type in the Description text box, and then click on OK to display the
Save As dialog box.
c. Name the Processing Method, as follows:
C:\Xcalibur\examples\methods\steroidsMS2.pmd. See Figure 3-9.
(Ensure that you save the Processing Method to the specified
directory because you will need to retrieve it later.)
d. Click on Save to save the method, and return to the Reports view.
7. Choose File > Exit to close the Processing Setup window, and return to
the Xcalibur Home Page.
Go to the next topic: Specifying Raw Data Files in Sequence Setup.
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Figure 3-9. Save As dialog box, showing the Processing Method file
steroidsMS2.pmd
2. Open a sequence list file into the Sequence Setup window, as follows:
a. Choose File > Open to display the Open dialog box.
b. Scroll to select the Sequence file
C:\Xcalibur\examples\methods\steroid.sld, and then double-click to
display the list of samples. See Figure 3-10.
3. Specify to include only two samples in the list, as follows:
a. Highlight Rows 1 through 10, and then choose Edit > Delete Row
to leave three samples remaining in the sequence. Xcalibur displays a
message box to confirm the Delete Row command. Click on Yes.
b. Highlight Row 3, and then choose Edit > Delete Row to leave two
samples remaining in the sequence. Xcalibur displays a message box
to confirm the Delete Row command. Click on Yes. See Figure 3-11.
Figure 3-10. Sequence Setup window, showing a list of two files contained in steroid.sld
4. If necessary, click on the left side of the horizontal scroll bar at the bottom
of the workspace to display the Sample Type column. Double-click on the
Row 1 cell in the Sample Type column to display a drop-down list box.
Then, scroll up to select Unknown.
5. If necessary, expand the width of the Path column to ensure that the
directory is the one in which your raw files are stored. For example, raw
files containing steroids data are found in C:\Xcalibur\examples\data.
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Figure 3-11. Sequence Setup window, showing a list of two files contained in steroid.sld
Figure 3-12. Sequence Setup window, showing the edited list of two files contained in steroid.sld
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Reprocessing Raw Files and Printing Reports @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Figure 3-14. Message box, asking if you want to save changes to the
sequence list
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Searching Libraries Automatically
'JOOJHBO9DBMJCVS ____________________________________ Reprocessing Raw Files and Printing Reports
Figure 3-15. Processing Status window, showing two samples in the queue
7. Go to your printer to get your printed reports (one for each sample). See
that they resemble those shown in Appendix A: Example Reports.
8. Choose View > Roadmap View to close Sequence Setup and display
the Roadmap View.
In this chapter, you did the following:
• Set up a Processing Method in Processing Setup to search libraries
automatically
• Reprocessed a sequence of data files in Sequence Setup
• Printed library search results of raw data automatically
Go to the next chapter: Searching Libraries from Qual Browser and
Library Browser.
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Chapter 4
Searching Libraries from Qual Browser
and Library Browser
You can search libraries from the Qual Browser window or by using the
Library Browser windows. You can search for hits on one spectrum at a time,
and then print the search results on the single spectrum. Appendix A:
Example Reports contains examples of reports you can print by following
the procedures in this chapter.
This chapter contains the following topics:
• Initiating a Library Search from Qual Browser
• Searching a Library by Using Library Browser
• Customizing the Library Browser Layout
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Initiating a Library Search from Qual Browser
Figure 4-1. Qual Browser window, showing the following views (clockwise from lower left):
Scan Filter view, (filtered) Chromatogram view, (averaged) Spectrum view,
(unfiltered) Chromatogram view
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Searching Libraries from Qual Browser and Library Browser
'JOOJHBO9DBMJCVS ____________________________________ Initiating a Library Search from Qual Browser
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Figure 4-3. Qual Browser window, showing the Library Search Results view cascaded with the
Raw Data view. Refer to the text above for a description of the contents of each cell.
The interactive cells of the Library Search Results view show the following
library search results, displayed clockwise from the upper left quadrant, as
follows.
• Hits list
• Molecular structure, including formula, molecular weight, name, and
library index number
• Difference spectrum (Raw Data minus Library Entry)
• Peaks above the X-axis are relatively more intense in your spectrum than
in the library entry.
• Peaks below the X-axis are relatively more intense in the library entry
than in your sample spectrum.
• Comparison of your sample spectrum and the library entry
6. Print the results of the search, as follows:
a. Choose File > Print Preview to display the Print dialog box. See
Figure 4-4.
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'JOOJHBO9DBMJCVS ____________________________________ Initiating a Library Search from Qual Browser
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Note. You can display data files in Library Browser only by exporting them
from Qual Browser. You can export a spectrum into Library Browser from
Qual Browser after you open a raw file (.raw) or a result file (.rst) in Qual
Browser.
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Searching Libraries from Qual Browser and Library Browser
'JOOJHBO9DBMJCVS ____________________________________ Searching a Library by Using Library Browser
b. Click on the Libraries tab to display the Available Libs: and the
Included Libs. libraries. See Figure 4-6. This dialog box allows you
to specify the libraries you want to search and in what order you want
to search them.
• If you want to add a library to the search list, click on its name in
the Available Libs: list box, and then click on Add.
• If you want to exclude a library from the search list, click on its
name in the Included Libs: list box, and then click on Exclude.
In this example include both MS2test and nistdemo. Click on OK to save the
settings, close the dialog box, and return to a Library Browser window.
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'JOOJHBO9DBMJCVS ____________________________________ Searching a Library by Using Library Browser
5. Double-click on the entry in the Spec List pane to begin a library search.
The interactive panes of Library Browser change to display the results of
the search, as follows. See Figure 4-8.
• Hit List History drop-down list shows the results of the search.
• Hit List pane contains a list of spectral results.
• Structure panes (tab) display the chemical structure of the compound
associated with the highlighted entry.
• Text panes display compound names, a mass/intensity list, scan filter
of the highlighted entry. (Refer to the online Help in Library Browser
for more information.)
• Plot panes display a single mass spectrum of a selected entry.
• Compare pane displays the difference between two spectra and
presents them in various ways.
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Figure 4-8. Library Browser default window, showing the library search results on the raw
spectrum that you exported from Qual Browser
Figure 4-9. Library Browser default window, showing file copying from Hit List to Spec List
panes
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Library Manager allows you to add libraries to a NIST library file and to
convert libraries from one format to another. You can open the Xcalibur
Library Manager dialog box from the Tools menu of the Xcalibur
HomePage – Roadmap view.
This chapter contains the following topics:
• Adding Libraries to and Deleting or Copying Libraries from the NIST
Libraries
• Converting Libraries to Another Format
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Adding and Converting Libraries
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Note. Because libraries can be large, you might save time using the Link
option rather than the Copy option.
The Delete button allows you to delete a library in the NIST Libraries list.
The Archive button allows you to copy a selected library to another directory
on your computer or network.
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Appendix A
Example Reports
This appendix contains examples of results you can obtain by using Xcalibur
Library Browser software.
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Example Reports
'JOOJHBO9DBMJCVS _______________________________ Report from a Library Search Using Library Browser
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Index
'JOOJHBO9DBMJCVS ________________________________________________________________________
Index
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Index
________________________________________________________________________ 'JOOJHBO9DBMJCVS
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