The file format to use for results of the search.

The FASTA protein database to search against. Only amino-acid type FASTA is supported.

If the protein database contains accessions prefixed with this string, those proteins will be considered decoys. If there are no decoy protein, this prefix will be used to generate an automatic decoy for each target protein. Set this to an empty string to disable automatic decoys.

The cleavage agent to generate in silico peptides from the protein database.

Controls which peptide termini must match the cleavage rules.

Candidate peptides with more than this number of uncleaved cleavage sites will be skipped.

Candidate peptides with more than this number of dynamic modifications will be skipped.