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Command-Line Arguments

-d data filepaths (string; comma separated; required)
-minprecz minimum assumed precursor charge state (integer; default=2)
-maxprecz maximum assumed precursor charge state (integer; default=4)
-at MS/MS absolute intensity threshold (double; default=-1.0)
-rt MS/MS relative threshold (double; percent of base peak; default=-1.0)
-mp maximum number of MS/MS peaks (integer; default=400)
-acs assign charge states (boolean; default=true)
-di de-isotope (boolean; default=true)
-db FASTA or UniProt XML database filepath (string; required)
-noup no UniProt modifications if using UniProt XML database (flag; default=[missing])
-ad append decoys; create target-decoy database on-the-fly (boolean; default=false)
-p protease (string; required)
-mmc maximum number of missed cleavages allowed (integer; default=2)
-imb initiator methionine behavior (string; cleave, retain, or variable; default=variable)
-fm fixed modifications (string, semicolon separated; default=[none])
-vm variable modification (string, semicolon separated; default=[none])
-mvmi maximum variable modification isoforms per base peptide sequence (integer; default=1024)
-precmtv precursor mass tolerance value (double; default=2.1)
-precmtu precursor mass tolerance units (string; Da or ppm; default:Da)
-precmt precursor mass type (string; monoisotopic or average; default:monoisotopic)
-pmc precursor monoisotopic mass correction (boolean; default=false)
-minpmo minimum precursor monoisotopic correction offset (integer; default=-3)
-maxpmo maximum precursor monoisotopic correction offset (integer; default=1)
-prodmtv product mass tolerance value (double; default=0.015)
-prodmtu product mass tolerance units (string; Da or ppm; default:Da)
-prodmt product mass type (string; monoisotopic or average; default:monoisotopic)
-fdr maximum false discovery rate (double; percentage; default=1.0)
-cmu consider modified peptides as unique (boolean; default=false)
-mt maximum threads (integer; default=[processor count])
-mmu minimize memory usage (boolean; default=false)
-o output folder path (string; default=[current directory])