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Fragments

Description

This module performs feature annotation by matching single MS/MS fragments against a library of annotated MS/MS fragments. Therefore, matches can help to annotate features and identify molecules. The annotation algorithm works as follows:

  • For each feature, iterate through fragments and compare them against a library of annotated fragments.
  • If the m/z values of a fragment and a library fragment match (are inside a specified mass deviation), annotate the feature.

Parameters

  • mass_dev_ppm: the maximum allowed mass deviation difference to constitute a match

Limitations

  • Fragment matches can often be spurious (a single fragment m/z can correspond to many different molecule substructures) or can result from random noise. Therefore, they must not be trusted blindly.
  • Currently, only positive ion mode fragments are supported.
  • Currently, only y2- and b2 fragments resulting from (proteinogenic) peptides are supported (all calculated as [M+H]+ adducts). More information can be found on fermo_core_extras.