Release of Crux v1.37

[Bill Noble]

The Crux development team is pleased to announce the release of the newest version of Crux.  Changes in this version are listed below.  The software is available at

    http://noble.gs.washington.edu/proj/crux/

Questions or suggestions can be sent to crux-...@googlegroups.com.

Bill Noble
Department of Genome Sciences
University of Washington

Major enhancements

• Added crux barista, a tool for inferring protein identifications.
• Reimplemented crux q-ranker with new outputs and command-line syntax.
• Percolator and compute-q-values now compute and report posterior error probabilities, in addition to q-values.
• crux create-index now generates and store decoy peptides in the index. Decoys can still be generated on-the-fly when searching .fasta files.

Minor changes

• A pair of options, cterm-fixed and nterm-fixed, allow fixed terminal peptide modifications, i.e., a mass shift applied to every peptide on either or both termini.
• A bug in the spectrum processing code was fixed, which was erroneously eliminating a few of the highest m/z fragment peaks. Xcorrs have changed slightly as a result.
• Simplified the --mz-bin-width and --mz-offset parameters so that --xcorr-var-bin is no longer needed.
• Indexes now store information about any static mods used when they were created.
• In the tab-delimited output files the 'matches/spectrum' column gives the number of target peptides compared to the spectrum and the decoy file has an additional column, 'decoy matches/spectrum' that gives the number of decoy peptides compared to the spectrum. These two numbers may differ when decoys are not generated on-the-fly.