Hi Sud, I think you can just use this parameter with Comet:
search_enzyme_number = 0 # choose from list at end of this params file
where 0 is defined at the bottom of the comet.params:
[COMET_ENZYME_INFO]
0. Cut_everywhere 0 - -
1. Trypsin 1 KR P
This tends to be a very computationally expensive search, so limiting your sequence database to a modest size would be beneficial.
Eric
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