Comet parameter: output_percolatorfile

• Controls whether to output search results in a Percolator’s tab-delimited input format.
• Valid values are 0 (do not output) or 1 (output).
• The default value is “0” if this parameter is missing.
• The created file will have a “.pin” file extension.
• Output columns are:
  • SpecID: an identifier composed of the inputBaseName_scanNumber_chargeState_resultNumber
  • Label: a value of 1 for a target peptide or -1 for a decoy peptide
  • ScanNr: spectrum scan number
  • ExpMass: experimental (measured) peptide neutral mass
  • CalcMass: calculated peptide neutral mass
  • lnrSp: natural log of the preliminary score rank (aka Sp rank)
  • deltLCn: last dCn in the output list
  • deltCn: deltaCn which is the normalized xcor difference between the top hit and next best hit
  • lnExpect: natural log of the expectation value or E-value
  • Xcorr: cross-correlation score
  • Sp: preliminary score
  • IonFrac: decimal value representing matched fragment ions count divided by total fragment ions count
  • Mass: repeat of ExpMass (this column may not even be relevant and could be deprecated in the future)
  • PepLen: length of petpide
  • Charge[n]: boolean, is this a charged n spectrum
  • enzN: boolean, is the peptide’s n-terminus consistent with the sample enzyme
  • enzC: boolean, is the peptide’s c-terminus consistent with the sample enzyme
  • enzInt: number of missed cleavages
  • lnNumSp: natural log of the number of analyzed peptides within the precursor tolerance
  • dM: normalized mass difference calculated as (ExpMass - CalcMass)/CalcMass.
  • absdM: absolute value of dM
  • Peptide: peptide sequence
  • Proteins: tab delimited list of proteins that contain the peptide

Example:

output_percolatorfile = 0
output_percolatorfile = 1