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*   Unexplained Peaks
In some cases, the fact that the application cannot explain a peak (because the corresponding fragment was probably formed by a compound-specific mechanism) can help in identifying characteristic structural groupings that give rise to the peak. For example, the phthalates produce a characteristic ion with m/z 149, which is formed by a highly specific mechanism. You can easily recognize the peak at m/z 149 as a contaminant from elasticized polymers. The application is not able to explain this peak because its corresponding fragment is formed by an unusual hydrogen rearrangement and cyclization, which are not supported. To distinguish between a randomly unexplained peak and a compound-specific peak, you must find examples in the library. Using a substructure search, you can retrieve compounds that contain a phthalate group as a common substructure. For additional information, see (Sub)Structure Search.
After the generation of fragments and mechanisms of the retrieved examples, the prominent peak corresponding to the phthalate group remains unexplained in the majority of cases. For example, a phthalate with a functional group at position 3, 4, 5, or 6 will have its prominent peak shifted to higher masses by the mass of this functional group. Such an unexplained, prominent peak, present in the spectra of structurally similar compounds, can be a strong indicator of a compound-specific fragmentation process. This information can serve as evidence toward identifying a substructure under investigation.

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