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 returned 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.
• This parameter is currently not supported by the index database generation and searches against an indexed database. For a target-decoy search against an indexed database, please include decoy sequences in the input FASTA database prior to the index generation.

Example:

decoy_search = 0
decoy_search = 1
decoy_search = 2