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*   Assigning Fragments to Spectral Peaks
Use the Mass Frontier application for the automated prediction of fragments from a structure. If you start the generation of fragments from Database Manager window and the active record contains a structure (an MS1 structure for Spectral Tree), the application automatically links the generated fragments with peaks in the spectra according to their m/z values. For additional information, see Linking Generated Fragments with a Spectrum.
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To predict fragments from a structure
1.
Choose Tools > Fragments and Mechanisms from the Mass Frontier main menu.
Note  The selected record must contain an MS1 structure in the spectral tree.
The Reaction Restrictions dialog box opens.
2.
For details about using the Reaction Restrictions dialog box, see Fragments and Mechanisms Module.
The Fragments & Mechanisms window displays possible fragments for each explained peak.
The application links the generated fragments with peaks in the spectrum (spectra in the spectral tree) according to their m/z values. On the Spectrum page, the explained peaks are highlighted in red. See Linking Generated Fragments with a Spectrum.
3.
To display the mechanisms leading to an explained peak, click Mechanisms in the Fragments & Mechanisms window and then do one of the following:
In the Fragments & Mechanisms window, select the m/z value of a peak.
–or–
a.
A yellow triangle indicates the active peak.
b.
The Fragments & Mechanisms window displays all mechanisms leading to the selected peak.
Fragments & Mechanisms window
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To automatically assign generated fragments to peaks
1.
Choose Tools > Fragments and Mechanisms from the Mass Frontier main menu.
The Reaction Restrictions dialog box opens.
2.
For details about using the Reaction Restrictions dialog box, see Fragments and Mechanisms Module.
The Fragments & Mechanisms window opens. This window must remain open to assign the fragments to peaks in the Database Manager window.
3.
4.
Right-click the Spectrum page and choose Auto Annotation > Generated Fragments from the shortcut menu.
The Auto Fragment Annotation of Peaks dialog box opens.
5.
The application reports the number of new fragments that are added to the spectrum.
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To manually assign a fragment structure to a peak
1.
Click the Assign Structure to m/z Value button, , in the Database Manager toolbar.
Note  Do not confuse this button with its generic equivalent in the Mass Frontier toolbar, which opens a Structure Editor that does not automatically connect the fragment to its spectral peak.
The Structure Editor – Database Manager dialog box opens.
2.
For detailed instructions for using the Structure Editor, see Structure Editor Module.
3.
Based on the fragment m/z value, the application automatically connects your structure to its spectral peak in the Spectrum pane.
4.
5.


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Related Topics:
  Using the Database Manager Window
  Using the Info Page
  Using the Mass Differences Page
  Using the Compare Spectra Page
  Using the Compare Trees Page
  Working with Spectral Records
  Displaying Isotope Patterns
  Exchanging Mass Spectral Data Between Modules
  Using the Library Pane
  Processing Data-Reduced Chromatograms
  Using the Search Utilities
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