Comet 2022.01 rev. 0 is now available.

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Jimmy Eng

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May 2, 2022, 1:14:55 PM5/2/22
to Comet ms/ms db search support
Comet 2022.01 rev. 0 is now available.
  • Add support for the VariantComplex entries in PEFF databases. These are annotated as “sequence_substitution” elements in the pep.xml output. This functionality was implemented by M. Hoopmann and was actually present in the 2021.02 release.
  • For the .pin output, decoy entries are now annotated with the “-1” decoy label under the “Label” column. Previously, the decoy annotations were supported only with Comet’s internal decoy searches. With this change, for “decoy_search = 0” searches (aka a user supplied target-decoy database), any database entry that matches the “decoy_prefix” text will be annotated with the “-1” decoy label.
  • Add hidden parameter entry “clip_nterm_aa” which skips the N-term residue of every peptide. For example with trypsin digestion, tryptic peptides are generated then the n-term residue is removed before analysis. Feature requested by J. Luo. “Hidden” parameters are those that do not appear in the example params file downloadable from the website or generated by running “comet -p”.
  • Add hidden parameter entry “minimum_xcorr” which sets the minimum xcorr cutoff. By default, this cutoff is set to 0.0 (specifically 1e-8); for Crux compiled Comet, the default minimum xcorr is -999. Any peptide must score higher than this cutoff to be reported in the output. Feature requested by I. Smith.
  • Bug fix: address memory leak in the ThreadPool code during search cleanup that caused segfaults under Linux. Thanks to D. Shteynberg and M. Hoopmann for the fix.
  • Bug fix: correctly support the clip_nterm_methionine parameter in conjunction with PEFF searches is implemented with this release. Previous versions (including the 2021.02) did not correctly handle this combination.
  • Bug fix: address memory pool issue present since 2021.01.0 for database indexing with num_threads set to “1”. Thanks to A. Kertesz-Farkas for reporting the bug.
  • Bug fix: move static “aminoacid_modification” elements before “terminal_modification” elements in the pep.xml output to conform to the schema. Thanks to D. Shteynberg for report the bug.
  • There are no parameters changes so this version will work with comet.params files annotated as being for versions 2022.01, 2021.01 and 2020.01.
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