## 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`