Comet parameter: max_duplicate_proteins
- This parameter defines the maximum number of proteins (identifiers/accessions)
to report. If a peptide is present in 6 total protein sequences, there is one
(first) reference protein and 5 additional duplicate proteins. This parameter
controls how many of those 5 additional duplicate proteins are reported.
- If "decoy_search = 2"
is set to report separate target and decoy results, this parameter will be
applied to the target and decoy outputs separately.
- Valid values are any integer greater than or equal to 0.
- If set to "-1", there will be no limit on the number of reported additional proteins.
- The default value is "20" if this parameter is missing.
Example:
max_duplicate_proteins = 0 // one reference protein reported, no additional duplicates
max_duplicate_proteins = 10 // one reference protein reported along with ten additional duplicates