# comment lines begin with a '#' in the first position [SEQUEST] database_name = /mnt/local/dbase/Sanger-Worm/wormpep160-ecoli-contam.fasta peptide_mass_tolerance = 3.000 create_output_files = 1 ; 0=no, 1=yes ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 fragment_ion_tolerance = 0.0 ; leave at 0.0 unless you have real poor data num_output_lines = 5 ; # peptide results to show num_description_lines = 3 ; # full protein descriptions to show for top N peptides show_fragment_ions = 0 ; 0=no, 1=yes print_duplicate_references = 1 ; 0=no, 1=yes enzyme_number = 0 xcorr_mode = 0 ; 0 regular Xcorr(default), 1 - EE, 2 - ET, 3 - TT # # Up to 3 differential searches can be performed. # Amino acids can not appear in more than one differential search parameter # diff_search_options = 0.0 X 0.0 X 0.0 X # # new parameters # max_num_differential_AA_per_mod = 0 ; max # of modified AA per diff. mod in a peptide nucleotide_reading_frame = 0 ; 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six mass_type_parent = 0 ; 0=average masses, 1=monoisotopic masses remove_precursor_peak = 1 ; 0=no, 1=yes mass_type_fragment = 1 ; 0=average masses, 1=monoisotopic masses ion_cutoff_percentage = 0.0 ; prelim. score cutoff % as a decimal number i.e. 0.30 for 30% match_peak_count = 0 ; number of auto-detected peaks to try matching (max 5) match_peak_allowed_error = 1 ; number of allowed errors in matching auto-detected peaks match_peak_tolerance = 1.0 ; mass tolerance for matching auto-detected peaks max_num_internal_cleavage_sites = 1 ; maximum value is 5; for enzyme search # partial sequence info ... overrides entries in .dta files # up to 10 partial sequences ... each must appear in peptides # analyzed in the forward or reverse directions partial_sequence = # protein mass & mass tolerance value i.e. 80000 10% # or protein min & max value i.e. 72000 88000 (0 for both = unused) protein_mass_filter = 0 0 # For sequence_header_filter, enter up to five (5) strings where any one must # be in the header of a sequence entry for that entry to be searched. # Strings are space separated and '~' substitutes for a space within a string. # Example: sequence_header_filter = human homo~sapien trypsin sequence_header_filter = add_C_terminus = 0.0000 ; added to C-terminus (peptide mass & all Y"-ions) add_N_terminus = 0.0000 ; added to N-terminus (B-ions) add_G_Glycine = 0.0000 ; added to G - avg. 57.0519, mono. 57.02146 add_A_Alanine = 0.0000 ; added to A - avg. 71.0788, mono. 71.03711 add_S_Serine = 0.0000 ; added to S - avg. 87.0782, mono. 87.02303 add_P_Proline = 0.0000 ; added to P - avg. 97.1167, mono. 97.05276 add_V_Valine = 0.0000 ; added to V - avg. 99.1326, mono. 99.06841 add_T_Threonine = 0.0000 ; added to T - avg. 101.1051, mono. 101.04768 add_C_Cysteine = 57.0000 ; added to C - avg. 103.1388, mono. 103.00919 add_L_Leucine = 0.0000 ; added to L - avg. 113.1594, mono. 113.08406 add_I_Isoleucine = 0.0000 ; added to I - avg. 113.1594, mono. 113.08406 add_X_LorI = 0.0000 ; added to X - avg. 113.1594, mono. 113.08406 add_N_Asparagine = 0.0000 ; added to N - avg. 114.1038, mono. 114.04293 add_O_Ornithine = 0.0000 ; added to O - avg. 114.1472, mono 114.07931 add_B_avg_NandD = 0.0000 ; added to B - avg. 114.5962, mono. 114.53494 add_D_Aspartic_Acid = 0.0000 ; added to D - avg. 115.0886, mono. 115.02694 add_Q_Glutamine = 0.0000 ; added to Q - avg. 128.1307, mono. 128.05858 add_K_Lysine = 0.0000 ; added to K - avg. 128.1741, mono. 128.09496 add_Z_avg_QandE = 0.0000 ; added to Z - avg. 128.6231, mono. 128.55059 add_E_Glutamic_Acid = 0.0000 ; added to E - avg. 129.1155, mono. 129.04259 add_M_Methionine = 0.0000 ; added to M - avg. 131.1926, mono. 131.04049 add_H_Histidine = 0.0000 ; added to H - avg. 137.1411, mono. 137.05891 add_F_Phenyalanine = 0.0000 ; added to F - avg. 147.1766, mono. 147.06841 add_R_Arginine = 0.0000 ; added to R - avg. 156.1875, mono. 156.10111 add_Y_Tyrosine = 0.0000 ; added to Y - avg. 163.1760, mono. 163.06333 add_W_Tryptophan = 0.0000 ; added to W - avg. 186.2132, mono. 186.07931 # # SEQUEST_ENZYME_INFO _must_ be at the end of this parameters file # [SEQUEST_ENZYME_INFO] 0. No_Enzyme 0 - - 1. Trypsin 1 KR P 2. Chymotrypsin 1 FWY P 3. Clostripain 1 R - 4. Cyanogen_Bromide 1 M - 5. IodosoBenzoate 1 W - 6. Proline_Endopept 1 P - 7. Staph_Protease 1 E - 8. Trypsin_K 1 K P 9. Trypsin_R 1 R P 10. AspN 0 D - 11. Cymotryp/Modified 1 FWYL P 12. Elastase 1 ALIV P 13. Elastase/Tryp/Chymo 1 ALIVKRWFY P