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. This means up to 21 proteins, one reference and twenty additional, will be reported for each search result.

Example:

max_duplicate_proteins = 0
max_duplicate_proteins = 10