Comet 2024.01 rev 0 is now available

[Jimmy Eng]

Comet 2024.01 rev. 0 is now available.

• Release notes:  https://uwpr.github.io/Comet/releases/release_202401.html
• Parameters:  https://uwpr.github.io/Comet/parameters/parameters_202401/
• Download:  https://github.com/UWPR/Comet/releases

Updates in this major release include:

• Add the parameters “peptide_mass_tolerance_lower” and “peptide_mass_tolerance_upper” to allow the specification of non-symmetric precursor mass tolerances. This means that “peptide_mass_tolerance” is retired and you should start with a fresh comet.params with this release and not re-use an old parameters file.  You can download a new comet.params from the Parameters page above or generate it using the "-p" (and now "-q") command line options.
• Add support for up to 15 variable modifications with the addition of “variable_mod10” through “variable_mod15”. Please do not attempt to search with 15 (or even 9) variable mods without using some serious constraints unless you are the most patient person in the world.
• Add support for what I will term an “exclusive” modification where only one from the set of exclusive variable modifications can appear in a peptide. You would want to apply this option to rare modifications that are unlikely to co-exist and be identified along with another rate modification in the same peptide. Denoting which variable modifications are an “exclusive” modification is accomplished by setting field 7 in the “variable_mod##” parameters to “-1”. The exclusive modification can still apply to multiple residues (controlled by the 4th field) and can exist in conjunction with other variable modifications that are not denoted as being exclusive. This reduces the complexity and search times when analyzing many modifications by not requiring all permutation/combinations of modifications to be analyzed. Requested by E. Deutsch.
• Change “isotope_error” options 4 thru 7. Those options now correspond to 4 = -1/0/1/2/3, 5 = -1/0/1, 6 = -3/-2/-1/0/1/2/3, 7 = -8/-4/0/4/8.
• Add the parameter “resolve_fullpaths” to allow the control of whether or not to resolve the full path base_names in the pepXML output. Default behavior is to resolve those full paths. This parameter allows the user to control leaving the paths as-is. Requested by M. Riffle.
• Fix calculating good E-value scores for extremely sparse spectra. This occurs for sparse spectra as any match to any single peak looks like an outlier from the majority of peptides that match no peaks. This is handled by putting a constraint on the linear regression step of the E-value calculation.
• Simplify the spectral processing for Sp scoring (preliminary score) by just taking the raw binned spectra and normalizing the max intensity to 100.
• Change the convention for the dCn (delta Cn) score for single hit results i.e. those results where only a single peptide is scored/reported. In the past, these single peptide hits received a dCn score of 1.0 but now these single peptide hits will receive a dCn score of 0.0.
• Update to the MSToolkit library to fix a scan numbering bug when spectra are not numbered. Implemented by the talented M. Hoopmann.
• Update the index search, including the CometWrapper.dll interface used for real time search (RTS), to use fragment ion indexing. It is still a work in progress and not all functionality has been implemented (so do not use it unless you want to be a beta tester). Documentation will be added when it is ready for general use. The fragment ion indexing is used as a pre-filter to the full cross-correlation scoring and is not fast compared to other search tools. Thanks to V. Sharma for implementing the modifications permutation code and the E. Bergstrom, C. McGann, and D. Schweppe for development/testing feedback.
• Added “set_X_residue” parameters which allow user to redefine the base mass of each amino acid residue e.g. set_A_residue to modify the base mass of alanine. Making use of static modifications can effectively accomplish the same thing so there is a very limited use case for this new feature. Feature requested by m.f.abdollahnia via the Comet google group.
• Implemented returning multiple results, instead of just the top hit peptide, for each RTS spectrum query through the CometWrapper.dll interface. Code was contributed by our Thermo collaborators J. Canterbury and W. Barshop and integrated by C. McGann.
  
• “comet -p” now generates a slightly simplified comet.params.new file. Some lesser used parameters are left out of that file. “comet -q” will generate a comet.params.new file with a more complete list of supported search parameters.
• Fixed issues with the mzIdentML output as reported by R. Marissen in issue #45.
• Fixed the inconsistent Sp rank numbers between runs, reported by keesh0 in issue #46.
• Fixed bug with counting the number of missed cleavages for enzymes that cut before (N-terminal of) the residue, reported by cpaul32015 in issue #47.

[Jimmy Eng]

I pulled this release.  Hopefully it'll be back up in a day or so once I can address an issue I just discovered.

[Jimmy Eng]

Release is up again; everything is functioning correctly now as far as I'm aware.

[Jimmy Eng]

I just re-tagged the 2024.01.0 release to address Windows searches failing.  Addressed with commit f00df0c.

On Monday, May 6, 2024 at 2:45:34 PM UTC-7 Jimmy Eng wrote: