Comet parameter: decoy_search

  • This parameter controls whether or not an internal decoy search is performed.
  • Comet generates decoys by reversing each target peptide sequence, keeping the N-terminal or C-terminal amino acid in place (depending on the "sense" value of the digestion enzyme specified by search_enzyme_number). For example, peptide DIGSESTK becomes decoy peptide TSESGIDK for a tryptic search and peptide DVINHKGGA becomes DAGGKHNIV for an Asp-N search.
  • Valid parameter values are 0, 1, or 2:
    • 0 = no decoy search (default)
    • 1 = concatenated decoy search. Target and decoy entries will be scored against each other and a single result is performed for each spectrum query.
    • 2 = separate decoy search. Target and decoy entries will be scored separately and separate target and decoy search results will be reported.
  • The default value is "0" if this parameter is missing.

Example:
decoy_search = 0
decoy_search = 1
decoy_search = 2