Comet parameter: output_pinxmlfile

  • Controls whether to output search results in a Percolator-IN or "pin.xml" file. pin.xml files are used as inputs to Percolator.
  • When you choose to output a pin.xml file, you must also be performing a decoy_search or else the search will not run and an error will be reported.
  • The pin.xml format specifies the UniMod accession number for each modification. As this information is not available, Comet will write bogus values for the UniMod accession. Each variable modification will have the variable modification number (1 thru 6) as the UniMod accession. Each static modification will have the ASCII value of the residue as the UniMod accession. If you really care about having valid UniMod accession numbers, you'll have to handle the find and replace yourself on the produced pin.xml file.
  • Valid values are 0 (do not output) or 1 (output).
  • The default value is "0" if this parameter is missing.

output_pinxmlfile = 0
output_pinxmlfile = 1