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options. the Unspecified Charge list.
Revision A XCALI-97350
© 2011 Thermo Fisher Scientific Inc.
All rights reserved.
Creating a Spectral Tree from Multiple MSn Spectra in The component symbol turns green,
a Single Direct-Infusion Sample File and the spectral tree appears.
c. Click Calculate.
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3. After creating the library, close the Mass Frontier Server Manager.
4. To make the new library accessible to the application, close the Predicting Fragmentation and
Mass Frontier application and restart it. Automatically Annotating Spectra
Tip To remove a user library, go to the Mass Frontier Server The Mass Frontier Fragmentation Library™ uses 24 general
Manager, right-click the user library and select Uninstall Library. ionization, fragmentation, and rearrangement rules and
approximately 31 000 fragmentation schemes collated from
Step 2. Copy the Spectral Tree to the Database published literature to automatically predict fragmentation,
rearrangement, and resonance mechanisms from a chemical
1. In the Chromatogram Processor window, select component 1.
structure. The structure can include ions and isotopically labeled
2. In the Mass Frontier main toolbar, click the Copy button, ,
compounds.
and select Copy MS Tree.
3. In the Mass Frontier main toolbar, click the Database Manager You can start the fragmentation process from the Structure Editor
button, . A new Database Manager window opens. window, the Database Manager window, or the Fragments &
4. In the Mass Frontier main toolbar, click the Paste button, , Mechanisms window. When you start the process from the Database
and choose Tree. Manager window, the Mass Frontier application automatically links
the generated fragments in the Fragments & Mechanisms window
with the corresponding spectrum in the Database Manager window.
In the spectrum, peaks that have the same m/z values as the generated
fragments appear in red, different from the original spectrum in blue.
You can select a red peak to see all the pathways leading to the peak.
The following procedure shows how to predict the fragmentation
pathways for the buspirone structure, compare the theoretical
fragmentation to the data from the experimental direct-infusion
sample, and then automatically annotate a spectrum.
Step 1. Generate Possible Fragmentation and
Rearrangement Pathways
1. Make sure the Database Manager window that contains the
spectral tree from the direct-infusion sample is still open, and
Tip In the Database Manager toolbar, click the Show Spectral then open the buspirone.mol structure as shown in the next
Tree button, , to switch the spectral tree pane in the window. figures.
a. Click the Open button in the Mass Frontier toolbar, and then choose Structure.
b. Select buspirone.mol and click Open. The file is in the following folder:
… \Documents and Settings\All Users\Shared Documents \HighChem
\Mass Frontier 7.0\Structures
Leave the Database Manager window open for the next procedure,
which compares the theoretical fragmentation of a buspirone
structure to the experimental direct-infusion buspirone sample.
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The application displays the molecular structure in the structure 4. In the Fragments & Mechanisms window, view the results:
pane and the molecular mass and formula on the Work page. a. Click the Fragments tab to show only the Fragments,
or click the Mechanisms tab to show both
Tip In the Database Manager toolbar, click the Show mechanisms and fragments.
Structure button, , to switch the structure pane in the
window.
Molecular mass and formula Molecular structure b. In the spectrum, click a red peak.
b. Select the
Both option.
c. Select the
Active check
boxes for all
libraries.
d. Click OK. The Fragments & Mechanisms window displays the possible
fragments and mechanisms for the selected red peak.
In the spectrum, the red peaks are “explained” peaks that can be
linked to the generated fragments from the buspirone structure
based on m/z values. The blue peaks in the spectrum cannot be
linked to the generated fragments.
The Mass Frontier application generates all the m/z values for the
given reaction restrictions settings and displays the results in the
Fragments & Mechanisms window.
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2. In the Fragments & Mechanisms window, change which
m/z values appear as follows: Performing Component Detection
a. Click the Show m/z Values for Explained Peaks Only button. You can choose from several algorithms when performing component
Only the fragments for m/z values that can be linked with a spectrum
(explained peaks) appear.
detection on data from a Data Dependent MSn experiment. Thermo
b. Click the button again to display results for all the m/z values. Fisher Scientific recommends the JCD algorithm for most of your
LC/MS experiments.
Y To perform component detection
1. In the Mass Frontier toolbar, click the Chromatogram Processor
button, .
2. In the Open Chromatogram dialog box, select the buspirone.raw
file in the following folder and click Open.
…\Documents and Settings\All Users\Shared Documents
\HighChem\Mass Frontier 7.0\Chromatograms
3. In the Chromatogram Processor toolbar, click the Components
Detection & Spectra Deconvolution button, , and
choose JCD.
4. In the J-Component Detection Algorithm dialog box, set these
Step 3. Automatically Annotate the Spectra parameters:
1. In the Database Manager window, right-click the spectrum and
choose Auto Annotation > Generated Fragments.
c. Click Calculate.
d. Click Close.
a. Click Default to
reset the parameter
values.
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5. Click the Hit Selector button, , to view the matched library
Matching Components to Library Entries entry in the Hit Selector window.
You can match the components detected in the buspirone.raw file
against the library entries.
Y To match components to library entries
1. In the Chromatogram Processor window TIC pane, zoom in on
the components between retention time 10.00 and 12.00.
a. In the Mass
Frontier toolbar,
click the Copy
button and
choose List of
Fragments.
b. In the
Chromatogram
Processor
window, click
the FISh
button.
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d. In the FISh Filter: Input
Fragments dialog box, Useful Window Icons
click the Paste button
to paste the copied The Mass Frontier 7.0 application consists of more than a dozen
fragments from the frequently used windows. The next table shows the icons of these
Clipboard, and then
click OK. windows and their corresponding definitions.
Getting Help
For additional information, consult the following:
• For more details about using the Mass Frontier application, refer
to the videos and the Help available from the Mass Frontier Help
menu or the Mass Frontier User Guide.
• For the latest service release of the software, visit
www.highchem.com/downloads/mass-frontier.
• For upcoming application notes and posters, visit
www.thermo.com.
4. In the Chromatogram Processor window, view the FISh result. • For Technical Support:
Pink peaks represent matched ions.
Phone: 1-800-532-4752
View the filtered chromatogram by FISh in pink.
Fax: 1-561-688-8736
E-mail: us.techsupport.analyze@thermofisher.com
For international contacts, go to
http://www.thermo.com/cda/contactus/home
You can combine the FISh results with other functions in the
application to perform further data manipulation. For example,
locate the corresponding components based on the retention time
and precursor information and add them to a user-created library.