Comet releases 2014.02

Documentation for parameters for release 2014.02 can be found here. Download release here.

release 2014.02 rev. 2 (2014.02.2), release date 2014/09/25

• This release addresses a potential bug in SQT output where an infinite loop printing out the “StaticMod” header line occurs when static modifications are specified and no variable modifications are specified.

release 2014.02 rev. 1 (2014.02.1), release date 2014/09/18

• Report missing variable modifications in pep.xml header.
• Note the version string in the code/binaries was not updated to properly reflect version “2014.02 rev. 1”; the version string unfortunately still states “2014.02 rev. 0”.

release 2014.02 rev. 0 (2014.02.0), release date 2014/09/16

• This release implements a change to how variable terminal modifications are specified. Both n- and c-terminal variable modifications are now specified the same way as amino acid modifications by using the letters ‘n’ and ‘c’ respectively i.e. “42.010565 nK” for acetylation. When reporting results, the peptide strings will look something like “K.nDIGSESTEDK.A” for an n-terminal modification and “K.DIGSESTEDKc.A” for a c-terminal modification. Previously, an n- or c-terminal modification was denoted by replacing the separation periods with brackets (] and [ respectively). Definitely look at the parameter help page for any of the variable mods (for example “variable_mod01”) to see a description of the new options in these parameters as well as example uses.
• When searching a small database or using restrictive parameters such that only a small number of candidate peptides are analyzed, Comet will now require (and generate) 1000 xcorr scores for the E-value calculation, up from 500. This corrects a couple of reported examples where poor scoring identifications from sparse searches received artificially low E-values.
• Implement a memory pool that’s shared between threads for the re-use of an array (pbDuplFragment). This change gives upwards of ~35% performance improvement in addition to better memory use from constantly creating and destroying the arrays. Implemented by T. Jahan.
• When auto-detecting the number of threads to spawn, Comet will now set this number to the value stored in the environment variable NSLOTS if that environment variable is set. This environment variable can be used by cluster management software such as SGE. Code changes submitted by J. Egertson.
• Extended the number of variable modifications from 6 to 9.
• Added minor Makefile changes to support compiling under msys/mingw; contributed by J. Slagel.
• Bug fix: correct initialization in custom amino acids (B, J, U, X, Z).
• Bug fix: Removed an unnecessary array initialization introduced in version 2014.01.1. This caused searches to be upwards of 2X slower; most noticeable when using small “fragment_bin_tol” values.
• Bug fix: addressed a couple of esoteric pep.xml output issues (paths and such) when using the -N command line option.
• Bug fix: fix the StaticMod output string in SQT format header (H) line; was not printing out the modification residue and these header lines were not present in the decoy output.
• Bug fix: fix the “override_charge”, parameter. The charge ranges were being searched but these were in addition to the existing charge states specified in the input file. The logic has been corrected so that only the specified charge range will be searched.
• New parameters: All of the variable_modXX parameters (for example “variable_mod01”) have been modified to add two new options for an optional terminal distance constraint and which terminus that distance constraint is applied to. And the nubmer of variable mods has been extended to 9. The modification character codes for mods 1 through 9 are: *#@^~$%!+
• New parameter “output_percolatorfile”. Percolator, I believe as of version 2.08, no longer supports the Percolator-in or pin.xml format. The supported input format is now a tab-delimited file hence the parameter name change.
• Removed the parameter “output_pinxml”. See the replacement parameter “output_percolatorfile”.
• Removed the parameter “precursor_tolerance_type”. The implementation of this parameter had a bug and it turns out this parameter was simply not needed.
• Update MSToolkit to version r72.