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*   Linking Generated Fragments with a Spectrum
Use the Mass Frontier application to link generated fragments with a mass spectrum, which helps explain peaks in a spectrum. When you start a generation of fragments and mechanisms from the Database Manager window, the generated fragments are automatically linked with peaks in a spectrum according to their m/z values. After a generation, highlighted (explained) peaks are displayed in a different color—by default, red—in the original mass spectrum. Selecting a highlighted peak reveals all the mechanisms leading to it. In addition, you can automatically assign generated fragments.
To automatically assign generated fragments
In the Database Manager window, right-click the spectrum pane and choose
Auto Annotation > Generated Fragments from the shortcut menu.
The corresponding Fragments & Mechanisms window must be open.
For additional information, see Assigning Fragments to Spectral Peaks.
When an unexplained peak is likely to be an isotopic peak of an explained peak, it is depicted in a third color—by default, green. Selecting such a peak reveals all the mechanisms leading to the fragment, which can produce this isotopic profile.
You cannot predict energies and barriers in ionized molecules, which prevents the prediction of all the peaks in a mass spectrum. In addition, the fragment predictability range is usually between 50 and 90 percent. However, a prominent unexplained peak can be of special value for interpreting or identifying an unknown. An unexplained peak can indicate a compound-specific mechanism that occurs in molecules with similar structural features or with a common substructure. Several mechanisms that have been observed only in a specific group of compounds cannot be applied generally when proposing fragmentation and rearrangement pathways.
If you suspect a compound-specific mechanism of fragment formation, verify your assumption by conducting a substructure search. Then you can compare the explained and unexplained peaks in the spectra retrieved by the substructure search.

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Related Topics:
  Eliminating Generated Fragments Not Present in a Spectrum
  Simulating Fragmentation Processes in MS/MS Experiments
  Unexplained Peaks
  Bar Code Spectra
  Marking Fragments
  Specifying Precision and Isobaric Differentiation
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