Comet releases 2014.01

Documentation for parameters for release 2014.01 can be found here. Download release here.

release 2014.01 rev. 1 (2014.01.1), release date 2014/06/03

• Known issue: when using “precursor_tolerance_type = 1” to specify the tolerance is applied on the precursor m/z peak, Comet has been errantly calculating the mass tolerance on the deconvoluted peptide mass and then additionally scaling this tolerance by the charge state. This inflates the precursor tolerance by N-fold where N is the precursor charge state (so a 10 ppm tolerance ends up being 20 ppm for 2+ precursors and 30 ppm for 3+ precursors). The fix is to always specify “precursor_tolerance_type = 0”. This parameter will be deprecated in the next release.
• Known issue: using custom amino acids (B, J, U, X, Z) fails.
• Known issue: high-res ms/ms searches (using small “fragment_bin_tol” values) are ~2x slower than 2014.01.0 due to an unnecessary array initialization that was added in this maintenance release.
• Known issue: Using -N command line option adds full path to "spectrum" attribute in Windows.
• Known issue: Using -N command line option, the pep.xml "base_name" attribute has full path to the output file instead of to the input file.
• Re-use temporary arrays during spectral preprocessing for better memory management running under Windows, implemented by M. Hoopmann.
• New parameter “override_charge” instructs Comet to override the listed precursor charge state in the input file with that specified by the “charge_range” parameter, implemented by D. Shteynberg.
• Update MSToolkit to version r68 to support non-consecutive mzXML scans.
• Bug fix: synchronize normal and sparse matrix xcorr scores when decoys are generated to fill in the xcorr distribution for the expectation score calculation, reported by D. Tabb.
• Bug fix: buffer overflow issue on some linux distributions when retrieving host name, reported by K. Tamura.
• Bug fix: close spawned threads, reported by M. Riffle.
• Bug fix: corrected “sample_enzyme” reporting in pep.xml output, reported by L. Mendoza.
• Bug fix: remove extra tab in txt output, reported by A. Kertesz-Farkas.
• Bug fix: output file name gets mangled when .out files are used and the input is specified using a full path, reported by C. Hoogland.

release 2014.01 rev. 0 (2014.01.0), release date 2014/03/25

• Known issue: the sample_enzyme information in pep.xml output is completely broken.
• Known issue: there is a memory leak in the program. Avoid invoking Comet with a ton of input files on the command line.
• Known issue: report of inconsistent results using “sparse_matrix = 0” and “sparse_matrix = 1” searches. I believe this is due to decoy xcorr score generation, affecting E-values, in cases where there is a low number of candidate peptide matches.
• Known issue: it’s been reported that results are inconsistent depending on the number of threads used in a search (Windows). Some numbers deviate in the 3rd/4th decimal point.
• Add “output_suffix” parameter option which appends a suffix to the base name of pep.xml, pin.xml, txt, and sqt output files.
• Add Native ID attribute to pep.xml output when searching mzML files. This entails an update to the MSToolkit file parsing library which was made by M. Hoopman.
• Report the name of the file that’s being searched in the runtime output.
• Avoid creating empty/stub output files in the case where an input file has been moved away during a search. These first four features were based on requests by D. Tabb.
• Change how E-values are calculated when “decoy_search = 2” is applied. This setting performs a separate target and decoy search as if two different databases were searched separately resulting in two sets of search results. In the past, the E-value calculations for the target hits were calculated on the underlying target xcorr score distribution only. And the decoy E-value calculations were based only on the decoy xcorr score distribution. Now, the target and decoy score hits contribute to one xcorr score distribution that is used to calculate the target and decoy E-values per suggestion by the Noble lab.
• Sort results by scan number; previously results were reported in order of increasing peptide mass. With results sorted by scan number, this allows more efficient analysis using quantification tools that cache spectral data in memory. Requested by D. Shteynberg.
• Bug fix: Change in spectral processing to handle edge case where the last peak in some spectra are excluded from the analysis.
• Bug fix: Correct a bug that required order of two loops to be swapped. Before this fix, a small number of fragment ions possibly do not get considered for particular peptide/spectrum/charge combinations. Thanks to A. Kertesz-Farkas for identifying these last two issues.
• For Windows binary only: revert previous memory changes (using VirtualAlloc and VirtualLock functions) as there were negative consequences associated with unexpected out of memory errors.
• For Crux compiled version only: modify text output, primarily changing column order using changes submitted by S. McIlWain.
• For Crux compiled version only: report all peptide hits, including those with negative xcorr scores.
• As the “output_suffix” is the only new parameter entry which most researchers likely won’t use, this version of Comet will also run with comet.params files from version 2013.02.