Comet releases 2012.01

Documentation for parameters for release 2012.01 can be found here. Download release here.

release 2012.01 rev 3 (2012.01.3), release date 2013/02/04

• This is a maintenance release.
• Addresses issue with .out file generation when full/relative path is specified for input file.
• Removes full/relative paths in pep.xml output (i.e. in “summary_xml” and “spectrum” elements).
• Fixes issue where spurrious modifications are reported if no variable modification is specified in the search.
• Known issue with pep.xml modification reporting, see this post describing the problem.
• Reported issue with reading certain mzXML files. The program will segfault when reading particular scans (not known why). More details here.
• Known bug: -D command line parameter to set database does not work; you must set the database in the params file.

release 2012.01 rev 2 (2012.01.2), release date 2013/01/10

• This is a maintenance release.
• Change is in pep.xml output only.
• This release implements the “deltacnstar” score in pep.xml output which is important for things like phospho-searches containing homologous top-scoring peptides when analyzed by PeptideProphet (using the “leave alone entries with asterisked score values” option).

release 2012.01 rev 1 (2012.01.1), release date 2012/12/14

• This is a maintenance release.
• Covers most changes from the comet-ms SourceForge project revisions r24 through 34.
• Fixes/changes include correcting modified internal decoy peptides, corrects modification reporting in pep.xml output, and adds more complete headers to SQT output.
• Source and binary release files are named comet_source.2012011.zip and comet_binaries.2012011.zip, respectively.
• Known bug: in pep.xml output, the “deltacnstar” and “deltacn” parameters currently still does not implement the code logic of noting “similar” peptides. This is important for the “leave alone asterisked score values” option in PeptideProphet in conjunction with variable modification searches.

release 2012.01 rev 0 (2012.01.0), release date 2012/08/16

• This is the initial release of Comet.
• Known bug: modifications with internal decoy search will cause a segfault if the enzyme cuts n-terminal to specified residues. This bug has been fixed in the sources files in trunk as of 2012/10/09.