Comet release 2015.02

Documentation for parameters for release 2015.02 can be found here.

release 2015.02 rev. 5 (2015.02.5), release date 2016/01/22

pepXML output: correctly report modified_peptide string; previously missing static modifications and at times terminal modifications.
MGF file parsing: fix how fragment masses are adjusted when their fragment ion charge states are present.
RAW file parsing: update MSToolkit to not report warning of unknown tokens 't' and 'E'.

release 2015.02 rev. 4 (2015.02.4), release date 2016/01/07

Additional parsing changes for better MGF support.
pepXML output: correct "mod_cterm_mass" value and escape special characters in "spectrumNativeID" values.

release 2015.02 rev. 3 (2015.02.3), release date 2015/11/24

Fix incorrect MGF parsing where blank lines in the MGF file would cause an error.
Fix n-term distance constraint variable mod searches. Thanks to U. Eckhard for reporting the above two issues.
Change output file extension to ".pin" from ".tsv" for Percolator output files.
Fix negative deltaCn values in text file output when no second hit is present.
Fix case where double decoy string is appended to the protein accession for decoy matches.

release 2015.02 rev. 2 (2015.02.2), release date 2015/10/15

Minor update to fix bug in binary modifications. The bug manifested itself in the simplest case where say two lysine residues are labeled with different modification masses and set to different binary modification groups. In this case, the second modification is not analyzed. Bug reported by Villen lab.
Known bug: when decoy searches are applied, the decoy prefix could be added multiple times for certain cases where the same decoy peptide is present in multiple decoy proteins. A fix has been implemented and will be included in the next release; let me know if you need a patched binary sooner than that.

release 2015.02 rev. 1 (2015.02.1), release date 2015/09/30

Modify behavior the binary modifications which is controlled by the third parameter entry in the variable modifications (e.g. "variable_mod01"). Instead of a binary 0 or 1 value to turn off or on each binary modification, one can now set the third parameter entry to the same value across multiple variable modifications effectively allowing an all-modified binary behavior across multiple variable modifications. See the examples at the bottom of the variable modification help pages for further explanation. NOTE: a bug was just discovered with binary modifications; a fix is imminent.
Wide mass tolerance searches, such as those performed by the Gygi lab's mass-tolerant searches, are now supported by Comet. Previous versions of Comet would crash when given large tolerances.
Update MSToolkit to support "possible charge state" cvParam in mzML files as implemented by M. Hoopmann.

release 2015.02 rev. 0 (2015.02.0), release date 2015/07/31

Associated with this release, a Windows GUI program to run Comet searches and visualize results is available. The Comet GUI supports 64-bit Windows only and can be found here.
Updated to MSToolkit revision 81 which includes .mgf input file support. Thanks to M. Hoopmann for updating MSToolkit for this.
Add a fourth option to ("override_charge") which will either use the specified charge in the input file or apply the charge states in the charge_range parameter but include the 1+ charge rule. Requested by D. Shteynberg.
Add "mass_offsets" parameter. Using this parameter, one can search spectra for peptides that have a mass offset from the experimental mass. Requested by ISB.
The "precursor_tolerance_type" parameter makes its return. It was not needed for precursor tolerances specified as ppm, which is the reason it was removed. But it is still relevant when amu and mmu are the units specified for the precursor tolerance and is now only applied in these cases.
The "use_sparse_matrix" parameter has been retired. All searches now use this internal data representation by default.
Corrected specification of terminal modifications in pep.xml output in cases when both static peptide and protein terminal modifications are specified. Reported by D. Hernandez.
Fix small bug that inadvertantly removed .cms2 input file support in previous release. Reported by MacCoss lab.

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