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While fragment ion indexing code was present in release 2024.01 rev. 0, this is the first release that officially supports that functionality (and there's still much more to do). Fragment ion indexing is a method that was originally implemented by MSFragger. Documentation on using Comet's fragment ion indexing can be found here. Thanks to V. Sharma for implementing the modifications permutation code and to E. Bergstrom, C. McGann, and D. Schweppe for driving the development and testing. The new parameters below are associated with this functionality:
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Allow variable modifications to apply to a subset of proteins. For example, one can now limit mono-, di-, and tri-methylation as variable modifications to only histone proteins and not have to apply those modifications on all proteins in the human database. This functionality is controlled by the protein_modlist_file parameter. Note there will be issues for post-processing analysis, such as FDR, when applying this feature. Thanks to C. McGann for the feature request.