Synthetic Peptide Searching Documentation

Synthetic Peptide Searching Documentation

To search a synthetic peptide pool, please use this workflow. The parameters are nearly identical to MSGF+, but there are additional options. Specifically, users should add some background spectra that is not of the primary peptide pool to be identified. Users then will specify the “target_run_filename” as the full file name of the spectrum file to be identified. Identifications to other spectrum files are called decoys. Additionally, the set of peptides that that are in common between the target spectrum file and background spectrum files will be specified in “blacklisted_decoy_peptides_json” as a list of peptide strings in json format. Finally, users must enter the acceptable collision energies in the “acceptable_collision_energies” in a semicolon separated string format. All other collision energies are ignored.