Comet parameter: output_mzidentmlfile

• Controls whether to output search results in an mzIdentML file.
• Valid values are:
  • 0 (do not output)
  • 1 (output mzid file)
  • 2 (output mzid file and includes protein sequences in the <Seq> tags; this is available as of version 2022.01.1)
• The default value is “0” if this parameter is missing.
• Note, the mzIdentML format has these issues:
  • It appears as if the mzIdentML format expects decoy entries to exist in the input FASTA file; at least that seems to be the expectation in the documentation that I’ve read. When running an internal decoy search, Comet’s mzIdentML output will report decoy protein references even though they do not exist in the underlying FASTA file. The reported decoy protein, like in the other output formats, is generated by appending the decoy prefix to the protein accession that the decoy peptide was generated from. I have no idea if the mzIdentML format allows for this or not.
  • Within the “FragmentTolerance” element, the requirement of fragment “search tolerance plus value” (MS:1001412) and “search tolerance minus value” (MS:1001413) make no sense in the context of spectral correlation matching used in Comet, SEQUEST and other tools that perform the cross-correlation score. A fragment bin value and bin offset are needed to encapsulate the corresponding fragment settings in Comet. Currently 1/2 of the “fragment_bin_offset” value is reported for the search tolerance plus/minus values since the format is not able to properly represent this aspect the search parameters.

Example:

output_mzidentmlfile = 0
output_mzidentmlfile = 1
output_mzidentmlfile = 2   (for version 2022.01.1 and later)