Comet releases 2025.01

Documentation for parameters for release 2025.01 can be found here.

Download release here.

Added support for a second fragment neutral loss associated with the variable_modXX parameters. The second neutral loss is specified as a comma separated number after the first neutral loss mass. For any fragment ion that contains the modification, Comet will analyze the intact fragment ion mass (including the modification) as well as the neutral loss ion(s).
Address issue #72 where a variable (iArraySizeGlobal) wasn’t properly sized, thus causing memory issues during the search that manifested itself as a segfault at the end of the search when the memory was freed. Thanks to bfcrampton for reporting this issue.
Restored peptide index support. Comet now supports 3 modes: (a) the classic mode of directly searching a FASTA file, (b) searching against a peptide index, and (c) searching using a fragment-ion index. RTS searches through the CometWrapper.dll interface can query against either peptide index or fragment-ion index databases.
Address a bug where PEFF modifications were being applied on the wrong amino acid on N-terminal peptides after start methionine removal with the parameter “clip_nterm_methionine”. Thanks to Z. Sun for reporting this bug.
Address a bug where PEFF searches were segfaulting during the Post Analysis steps in Comet. Thanks to Z. Sun for reporting this bug.