2014/01/23

Comet version "2013.02 rev. 2".
This is a maintenance release for Comet version 2013.02.
http://comet-ms.sourceforge.net


Release notes for 2013.02 rev. 2:
- The major change with this maintenance release addresses Windows search
  performance. When searching using lots of memory (such as with small
  "fragment_bin_tol" values, the search performance was greatly reduced.
  We believe allocated memory was being swapped to disk even when there is
  more than enough memory/RAM on the host machine. This issue is addressed
  by allocating memory differently (using the VirtualAlloc function call)
  and locking memory from being paged out to disk (using the VirtualLock
  function call).
- Extend maximum protein accession string length from 40 to 512.
- Change default "remove_precursor_tolerance" value from 2.0 to 1.5.
- Skip writing out blank search hit lines for Crux-compiled text output.
- Corrects e-value calculation for decoy entries when using separate
  target/decoy searches (i.e. "decoy_search = 2").
  

Release notes for 2013.02 rev. 1:
- Fix bug for both pep.xml and pin.xml output where terminal variable
  modifications were not being written out to these two output formats.
- Fix bug where .sqt and .txt headers were not being written out to subsequent
  output files after the first output file when multiple input files are
  specified on the command line (i.e. "comet.exe *.mzXML").
- Allow whitespace in "database = " parameter value i.e. the database name
  and/or path can contain a whitespace. Note that having whitespaces in the
  database name will break some downstream tools (like TPP).
- Change Percolator pin.xml features. "dM" and "absdM" are now calculated as
  (experimental_mz - calculated_mz)/calculated_mz. Previously this feature was
  reporting (calculated_mz - experimental_mz).
- Change behavior in pep.xml output where "summary_xml" and "base_name" elements
  now include resolved full paths. Also get rid of unused xml-stylesheet
  directive.
- Increase number of significant digits to 6 for reported masses in all of the
  output formats.

 
Release notes for 2013.02 rev. 0:
- There are quite a few behind-the-scenes changes where the core search
  code has been moved into a library in preparation for interfacing with
  other tools (thanks to T. Jahan).
- Underlying changes to the code were made to facilitate integration with
  the Crux project (thanks to S. McIlwain).
- This release incorporates an update to the MSToolkit file parsing library
  (thanks to M. Hoopmann).
- Support for the mz5 file format has been dropped. mzXML, mzML, and ms2
  formats are the supported input formats.
- Comet will now report a warning for any unknown parameter due to manually
  introduced typos. In the past, these were ignored. The recommended method
  to generate a valid/current parameters file is still to use the command
  "comet.exe -p" to avoid silly errors like this.
- A new parameter "decoy_prefix" allows one to define the string pre-pended
  to the protein name for decoy matches when the decoy_search parameter is
  used.
- A new parameter "output_pinxmlfile" controls support for outputting
  Percolator-IN pin.xml files.
- The text output format has changed to add new columns and column headers.
- It was discovered that a subset of N-terminal fragment ions for internally
  generated decoy peptides were incorrectly being calculated; this has been
  corrected in this release.


Comet is an open source MS/MS database search engine released under
the Apache 2.0 license.

Current supported input formats are mzXML, mzML, ms2, and cms2.
Current supported output formats are pepXML, Percolator-IN XML, SQT, and .out files.

To run a search on an input file requires the Comet binary, a search
parameters file (comet.params), an input file, and a protein sequence
database in FASTA format.  The syntax of a search:

   comet.exe input.mzXML
   comet.exe input.ms2

Search parameters, such as which sequence database to query,
modifications to consider, mass tolerances, output format, etc. are
defined in the comet.params file.

One can generate a parameters file with the command

   comet.exe -p

Rename the created file "comet.params.new" to "comet.params".

Windows and linux command line binaries are included with this release.
