Comet releases 2022.01

Documentation for parameters for release 2022.01 can be found here.

Download release here.

release 2022.01 rev. 2 (2022.01.2), release date 2022/09/12

This is a minor release that addresses these issues:

• MSToolkit update to 20e99ce. Thanks to M. Hoopmann for addressing the MGF issue in the MSToolkit repo. Addresses issue 23.
• Add user message/warning when “spectrum_batch_size = 0” is set. Addresses issue 27.
• Add/return expectation value scores within real-time search interface.
• Known bug: When applying add_Cterm_protein, the static modificaton is not applied for the peptide mass calculation for peptides that contain a variable modification. This bug has been addressed with commit c0b6187. Thanks to M. Hoopmann for reporting the issue.

release 2022.01 rev. 1 (2022.01.1), release date 2022/07/25

This is a minor release that addresses these issues:

• Fix mzid output; all known errors were addressed so that files now validate. Thanks to J. Uszkoreit and M. Riffle for assisting with this process.
• The parameter entry “output_mzidentmlfile” has been extended to allow control of whether the protein sequences in the <Seq> element are reported in the output mzid file.
• When running a regular search not using Comet’s internal decoy peptides, any protein sequence that begins with the parameter string set in “decoy_prefix” will be annotated as a decoy entry in the mzid output. This is the same behavior as the Percolator pin output for annotating decoy matches when searching against a user supplied target-decoy database.
• A search with a single variable modification entry “79.99 STY” will run faster than if the modifications were specified separately, e.g. “79.99 S”, “79.99 T”, and “79.99 Y” as three separate variable modification entries. Comet will now automatically reduce/combine separate variable modifications to a single entry if possible. Thanks to C. Bielow/OpenMS for suggesting the optimization.

release 2022.01 rev. 0 (2022.01.0), release date 2022/05/02

• 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.