Comet releases 2016.01

Documentation for parameters for release 2016.01 can be found here. Download release here.

release 2016.01 rev. 3 (2016.01.3), release date 2017/05/02

• Bug fix: peptides with variable modifications would have their precursor mass calculated using fragment ion masses. This is an issue when the precursor mass type and fragment mass types are different e.g. average masses for the precursor calculation and monoisotopic masses for the fragment ion calculations. Thanks to D. Zhao for identifying the bug.
• Update MSToolkit to latest version. This encapsulates the bug fix mentioned below as well as better support for ETD+SA scans. Thanks to P. Pedrioli for originally implementing the ETD+SA fixes.
• Incorporate r981 which was missing edge cases in internal binary mass search.
• pepXML output fix: declare aminoacid_modification before any instance of terminal_modification per schema. Thank to L. Mendoza for reporting this issue.

release 2016.01 rev. 2 (2016.01.2), release date 2016/04/06

• Reverts the modification encoding in the “output_txtfile” output back to reporting variable modification mass differences (e.g. DLSTM[16.0]HK) instead of the actual modified residue mass values (e.g. DLSTM[147]HK).
• Known bug: there’s an issue with raw file parsing where the charge state and precursor mass might not be correctly read. Mike Hoopmann made an update to the MSToolkit file parsing library to fix this. I’ve decided not to make a new release (branching and tagging the code and assigning a new version string). Please download the comet_source_2016012.zip or comet_binaries_2016012.zip files again to obtain the patched program. These zip files were updated on 10/13/2016. Thanks to A. Sharma for reporting the bug.

release 2016.01 rev. 1 (2016.01.1), release date 2016/03/29

• Fixes a bug where variable terminal modifications on decoy peptides are not properly generated leading to possible program crash due to calculating fragment ions that are too large for the decoy peptide. Reported by Villen lab.
• Fixes a bug where peptide mass comparisons are failing, leading to duplicate peptides being stored and reported as separate entries. Reported by S. Michalakopoulos.
• For text and pepXML output, the peptide rank for ties (two peptides with exact same xcorr) now have the same rank instead of the rankings always being sequential.
• The 2016.01 release also changed how modifications are reported in the text output. Instead of mass differences (e.g. DLSTM[16.0]HK), the modification annotation now shows the modified residue mass (e.g. DLSTM[147]HK).

release 2016.01 rev. 0 (2016.01.0), release date 2016/03/15

• Known bug: when using a decoy search and variable n- or c-terminal modifications, Comet could segfault/crash due to accessing an array out of bounds. This is due to the modfications not being properly translated to the decoy peptide which could result in calculated fragment ion masses that are too large. A fix is implemented and will be part of the next release. Until the next release is available, email me if you would like a patched binary.
• Add direct selenocysteine support by retiring parameter entry “add_U_user_amino_acid” and adding “add_U_selenocysteine” per doi:10.1021/acs.jproteome.5b01028.
• Allow negative numbers for the “num_threads” parameter; will subtract that many threads from # CPU cores. For example, to use 3 threads for a 4-core CPU or 7 threads for an 8-core CPU, set “num_threads = -1”. This allows your computer to have a CPU core free when running searches. Requested by D. Shteynberg.
• Fix bug in the expectation score calculation when “print_expect_score = 0” and pep.xml, pin, and txt files are specified (but not .out files). Under this scenario, the cross correlation histogram was not being fully accumulated which is what is used to calculate the E-value. This fix should result in more accurate E-values. Reported by A. Cheng. (Note “print_expect_score” was intended to only affect “.out” output.)
• For Comet compiled for Crux, return the missing modified peptide column in the text output.
• Update deltaCn calculation for non top-ranked peptides or .pep.xml, .pin and .txt outputs. The deltaCn values for the top ranked hits do not change. The lower hit entries had incorrect values associated with them (normalized xcorr difference between consecutive entries instead of the normalized xcorr difference from the top hit, the latter which is correct). Reported by M. Hoopmann.
• This version of Comet will run with comet.params files generated from version 2015.02. If you use these parameter files, you will receive a warning message about an unknown parameter “add_U_user_amino_acid” that you can safely ignore. Set “add_U_user_amino_acid = 150.95363” for selenocysteine support with the old parameters file.