Search_enzyme_sense_1 = C # First enzyme's cutting terminal. Search_enzyme_nocut_1 = # First enzyme's protecting amino acid.Īllowed_missed_cleavage_1 = 2 # First enzyme's allowed number of missed cleavages per peptide. Search_enzyme_cut_1 = KR # First enzyme's cutting amino acid. Search_enzyme_name_2 = # Name of the second enzyme. Search_enzyme_name_1 = stricttrypsin # Name of the first enzyme. Min_sequence_matches = 2 # Minimum number of sequence-specific (not Y) ions to record a match Only used if b~/y~ are specified in the fragment_ion_series list Remainder_fragment_masses = # masses for b~/y~ ions (multiple values separated by /). # ion_series_definitions = # User defined ion series. # and mass offset searches) (0 for OFF, 1 for ON).ĭelta_mass_exclude_ranges = (-1.5,3.5) # Exclude mass range for shifted ions searching.įragment_ion_series = b,y # Ion series used in search, specify any of a,b,c,x,y,z,b-18,y-18,b~,y~,Y (comma separated). Localize_delta_mass = 0 # Include fragment ions mass-shifted by unknown modifications (recommended for open Precursor_mass_mode = selected # One of isolated/selected/corrected. Allowed values are single letter codes (e.g. Restrict_deltamass_to = all # Specify amino acids on which delta masses (mass offsets or search modifications) can occur. Mass_offsets = 0 # Creates multiple precursor tolerance windows with specified mass offsets. Isotope_error = 0/1/2 # Also search for MS/MS events triggered on specified isotopic peaks. d formats.ĭecoy_prefix = rev_ # Prefix of the decoy protein entries. Write_uncalibrated_mgf = 0 # Write uncalibrated MS2 scans (0 for No, 1 for Yes). Write_calibrated_mzml = 0 # Write calibrated MS2 scans (0 for No and 1 for Yes). Use_all_mods_in_first_search = 0 # Use all variable modifications in first search (0 for No, 1 for Yes). Precursor_true_units = 1 # True precursor mass tolerance units (0 for Da, 1 for ppm).įragment_mass_tolerance = 20 # Fragment mass tolerance (window is +/- this value).įragment_mass_units = 1 # Fragment mass tolerance units (0 for Da, 1 for ppm).Ĭalibrate_mass = 2 # Perform mass calibration (0 for OFF, 1 for ON, 2 for ON and find optimal parameters). Precursor_true_tolerance = 20 # True precursor mass tolerance (window is +/- this value). Precursor_mass_units = 1 # Precursor mass tolerance units (0 for Da, 1 for ppm).ĭata_type = 0 # Data type (0 for DDA, 1 for DIA, 2 for DIA-narrow-window). Precursor_mass_upper = 20 # Upper bound of the precursor mass window. Precursor_mass_lower = -20 # Lower bound of the precursor mass window. Num_threads = 0 # Number of CPU threads to use.ĭatabase_name = test.fasta # Path to the protein database file in FASTA format.
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