# comet_version 2020.01 rev. 0 # Comet MS/MS search engine parameters file. # Everything following the '#' symbol is treated as a comment. database_name = /some/path/db.fasta decoy_search = 0 # 0=no (default), 1=concatenated search, 2=separate search peff_format = 0 # 0=no (normal fasta, default), 1=PEFF PSI-MOD, 2=PEFF Unimod peff_obo = # path to PSI Mod or Unimod OBO file num_threads = 0 # 0=poll CPU to set num threads; else specify num threads directly (max 128) # # masses # peptide_mass_tolerance = 3.0 peptide_mass_units = 0 # 0=amu, 1=mmu, 2=ppm mass_type_parent = 1 # 0=average masses, 1=monoisotopic masses mass_type_fragment = 1 # 0=average masses, 1=monoisotopic masses precursor_tolerance_type = 0 # 0=MH+ (default), 1=precursor m/z; only valid for amu/mmu tolerances isotope_error = 0 # 0=off, 1=0/1 (C13 error), 2=0/1/2, 3=0/1/2/3, 4=-8/-4/0/4/8 (for +4/+8 labeling) # # search enzyme # search_enzyme_number = 1 # choose from list at end of this params file search_enzyme2_number = 0 # second enzyme; set to 0 if no second enzyme num_enzyme_termini = 2 # 1 (semi-digested), 2 (fully digested, default), 8 C-term unspecific , 9 N-term unspecific allowed_missed_cleavage = 2 # maximum value is 5; for enzyme search # # Up to 9 variable modifications are supported # format: <0=variable/else binary> # e.g. 79.966331 STY 0 3 -1 0 0 97.976896 # variable_mod01 = 15.9949 M 0 3 -1 0 0 0.0 variable_mod02 = 0.0 X 0 3 -1 0 0 0.0 variable_mod03 = 0.0 X 0 3 -1 0 0 0.0 variable_mod04 = 0.0 X 0 3 -1 0 0 0.0 variable_mod05 = 0.0 X 0 3 -1 0 0 0.0 variable_mod06 = 0.0 X 0 3 -1 0 0 0.0 variable_mod07 = 0.0 X 0 3 -1 0 0 0.0 variable_mod08 = 0.0 X 0 3 -1 0 0 0.0 variable_mod09 = 0.0 X 0 3 -1 0 0 0.0 max_variable_mods_in_peptide = 5 require_variable_mod = 0 # # fragment ions # # ion trap ms/ms: 1.0005 tolerance, 0.4 offset (mono masses), theoretical_fragment_ions = 1 # high res ms/ms: 0.02 tolerance, 0.0 offset (mono masses), theoretical_fragment_ions = 0, spectrum_batch_size = 15000 # fragment_bin_tol = 1.0005 # binning to use on fragment ions fragment_bin_offset = 0.4 # offset position to start the binning (0.0 to 1.0) theoretical_fragment_ions = 1 # 0=use flanking peaks, 1=M peak only use_A_ions = 0 use_B_ions = 1 use_C_ions = 0 use_X_ions = 0 use_Y_ions = 1 use_Z_ions = 0 use_Z1_ions = 0 use_NL_ions = 0 # 0=no, 1=yes to consider NH3/H2O neutral loss peaks # # output # output_sqtfile = 0 # 0=no, 1=yes write sqt file output_txtfile = 0 # 0=no, 1=yes write tab-delimited txt file output_pepxmlfile = 1 # 0=no, 1=yes write pepXML file output_mzidentmlfile = 0 # 0=no, 1=yes write mzIdentML file output_percolatorfile = 0 # 0=no, 1=yes write Percolator pin file print_expect_score = 1 # 0=no, 1=yes to replace Sp with expect in out & sqt num_output_lines = 5 # num peptide results to show sample_enzyme_number = 1 # Sample enzyme which is possibly different than the one applied to the search. # Used to calculate NTT & NMC in pepXML output (default=1 for trypsin). # # mzXML parameters # scan_range = 0 0 # start and end scan range to search; either entry can be set independently precursor_charge = 0 0 # precursor charge range to analyze; does not override any existing charge; 0 as 1st entry ignores parameter override_charge = 0 # 0=no, 1=override precursor charge states, 2=ignore precursor charges outside precursor_charge range, 3=see online ms_level = 2 # MS level to analyze, valid are levels 2 (default) or 3 activation_method = ALL # activation method; used if activation method set; allowed ALL, CID, ECD, ETD, ETD+SA, PQD, HCD, IRMPD, SID # # misc parameters # digest_mass_range = 600.0 5000.0 # MH+ peptide mass range to analyze peptide_length_range = 5 63 # minimum and maximum peptide length to analyze (default 1 63; max length 63) num_results = 100 # number of search hits to store internally max_duplicate_proteins = 20 # maximum number of additional duplicate protein names to report for each peptide ID; -1 reports all duplicates max_fragment_charge = 3 # set maximum fragment charge state to analyze (allowed max 5) max_precursor_charge = 6 # set maximum precursor charge state to analyze (allowed max 9) nucleotide_reading_frame = 0 # 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six clip_nterm_methionine = 0 # 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine spectrum_batch_size = 15000 # max. # of spectra to search at a time; 0 to search the entire scan range in one loop decoy_prefix = DECOY_ # decoy entries are denoted by this string which is pre-pended to each protein accession equal_I_and_L = 1 # 0=treat I and L as different; 1=treat I and L as same output_suffix = # add a suffix to output base names i.e. suffix "-C" generates base-C.pep.xml from base.mzXML input mass_offsets = # one or more mass offsets to search (values substracted from deconvoluted precursor mass) precursor_NL_ions = # one or more precursor neutral loss masses, will be added to xcorr analysis # # spectral processing # minimum_peaks = 10 # required minimum number of peaks in spectrum to search (default 10) minimum_intensity = 0 # minimum intensity value to read in remove_precursor_peak = 0 # 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD), 3=phosphate neutral loss peaks remove_precursor_tolerance = 1.5 # +- Da tolerance for precursor removal clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range # # additional modifications # add_Cterm_peptide = 0.0 add_Nterm_peptide = 0.0 add_Cterm_protein = 0.0 add_Nterm_protein = 0.0 add_G_glycine = 0.0000 # added to G - avg. 57.0513, mono. 57.02146 add_A_alanine = 0.0000 # added to A - avg. 71.0779, mono. 71.03711 add_S_serine = 0.0000 # added to S - avg. 87.0773, mono. 87.03203 add_P_proline = 0.0000 # added to P - avg. 97.1152, mono. 97.05276 add_V_valine = 0.0000 # added to V - avg. 99.1311, mono. 99.06841 add_T_threonine = 0.0000 # added to T - avg. 101.1038, mono. 101.04768 add_C_cysteine = 57.021464 # added to C - avg. 103.1429, mono. 103.00918 add_L_leucine = 0.0000 # added to L - avg. 113.1576, mono. 113.08406 add_I_isoleucine = 0.0000 # added to I - avg. 113.1576, mono. 113.08406 add_N_asparagine = 0.0000 # added to N - avg. 114.1026, mono. 114.04293 add_D_aspartic_acid = 0.0000 # added to D - avg. 115.0874, mono. 115.02694 add_Q_glutamine = 0.0000 # added to Q - avg. 128.1292, mono. 128.05858 add_K_lysine = 0.0000 # added to K - avg. 128.1723, mono. 128.09496 add_E_glutamic_acid = 0.0000 # added to E - avg. 129.1140, mono. 129.04259 add_M_methionine = 0.0000 # added to M - avg. 131.1961, mono. 131.04048 add_O_ornithine = 0.0000 # added to O - avg. 132.1610, mono 132.08988 add_H_histidine = 0.0000 # added to H - avg. 137.1393, mono. 137.05891 add_F_phenylalanine = 0.0000 # added to F - avg. 147.1739, mono. 147.06841 add_U_selenocysteine = 0.0000 # added to U - avg. 150.0379, mono. 150.95363 add_R_arginine = 0.0000 # added to R - avg. 156.1857, mono. 156.10111 add_Y_tyrosine = 0.0000 # added to Y - avg. 163.0633, mono. 163.06333 add_W_tryptophan = 0.0000 # added to W - avg. 186.0793, mono. 186.07931 add_B_user_amino_acid = 0.0000 # added to B - avg. 0.0000, mono. 0.00000 add_J_user_amino_acid = 0.0000 # added to J - avg. 0.0000, mono. 0.00000 add_X_user_amino_acid = 0.0000 # added to X - avg. 0.0000, mono. 0.00000 add_Z_user_amino_acid = 0.0000 # added to Z - avg. 0.0000, mono. 0.00000 # # COMET_ENZYME_INFO _must_ be at the end of this parameters file # [COMET_ENZYME_INFO] 0. Cut_everywhere 0 - - 1. Trypsin 1 KR P 2. Trypsin/P 1 KR - 3. Lys_C 1 K P 4. Lys_N 0 K - 5. Arg_C 1 R P 6. Asp_N 0 D - 7. CNBr 1 M - 8. Glu_C 1 DE P 9. PepsinA 1 FL P 10. Chymotrypsin 1 FWYL P