Comet

Comet parameter: decoy_search

• This parameter controls whether or not an internal decoy search is performed.
• If your database already has decoy sequences, you should not instruct Comet to generate its own internal decoy peptides. In this case, set this parameter to 0. This parameter is intended to be applied only when a database composed of target sequences is searched.
• For every target peptide that is scored, Comet will generate a corresponding decoy peptide to score. This guarantees an exact 1:1 target to decoy ratio.
• 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