# Parameter file for jump sequest, JUMP version 1.17, Date: 12/12/2013 search_engine = JUMP # JUMP or SEQUEST # Database settings database_name = /home/users/JUMP_database/human_ft_mc2_c57.fasta.mdx # use .fasta.hdr database peptide_tolerance = 15 # precursor mass (MH+) tolerance peptide_tolerance_units = 2 # 1 = Da; 2 = PPM; # Preprocessing parameters first_scan_extraction = 0 # the first scan used for search last_scan_extraction = 120000 # the last scan used for search isolation_window = 0.8 # +/- isolation_window interscanppm = 30 # tolerance for interscan precursor identification intrascanppm = 30 # intrascan isotopic tolerance for decharging max_num_ppi = 6 # 0 = disable; 1-9 = max precursor ions selected for mixed MS2 search percentage_ppi = 0 # minimal percentage of precursor peak intensity (ppi) when max_num_ppi = 0 ppi_charge_0 = 1 # 0 = discard uncharged MS1 (charge 0); 1 = manual charge assignment (+2,+3) ppi_charge_1 = 1 # 0 = discard MS1 with charge +1; 1 = enable original charge +1 prec_window = 0 # 0 = disable; 1-10 (Da) = mz window for removing precursor ions MS2_deisotope = 1 # 0 = disable; 1 = enable ppm = 30 # isotopic tolerance for MS2 decharging and deisotoping charge12_ppm = 60 # mass tolerance for merging different charged ions with the same mass ms2_consolidation = 10 # maximal number of peaks retained within each 100-Da window # Tagging tag_generation = 1 # generating tag for sequest; 0 = disable; 1 = enable; tag_tolerance = 30 # mass tolerance for tagging tag_tolerance_unit = 2 # 1 = Da; 2 = PPM; tag_select_method = comb_p # tag ranking: comb_p, hyper_p, rank_p # Database Searching ion_series = 1 1 0 0 0 0 0 1 0 # a, b, c, d, v, w, x, y, and z ions respectively frag_mass_tolerance = 30 # mass tolerance for matching frag_mass_tolerance_unit = 2 # 1 = Da; 2 = PPM; matching_method = comb_p # PSM scoring: hyper_p tag_search_method = 2 # 1 = exit when found; 2 = exhaustive search using tags defined by max_number_tag_for_search max_number_tags_for_search = 150 # If this number larger than the total number of tag, the total number of tag will be used number_of_selected_result = 5 # maximal tentative PSMs in .spout ranked by Jscore number_of_detailed_result = 50 # maximal tentative PSMs in .spout ranked by pattern matching score # Dynamic Modification # C: 57.02146 carbamidomethylation or 71.0371 acrylamide # STY: 79.96633; M: 15.99492; GG: 114.04293 # SILAC K:4.02511, 6.02013, 8.01420; SILAC R:6.02013, 10.00827 dynamic_M = 15.99492 # add each dynamic modification by one line, starting with dynamic_aa #dynamic_C = 57.02146 # add each dynamic modification by one line, starting with dynamic_aa # parameters for creating database enzyme_info = Tryptic KR P # LysC K ; ArgC R ; GluC DE ; digestion = full # full or partial max_mis_cleavage = 2 # maximal miscleavage sites allowed for each peptide min_peptide_mass = 400.0000 # minimal mass of peptide database max_peptide_mass = 6000.0000 # maximal mass of peptide database inclusion_decoy = 0 # 0 = skip decoys; 1 = enable decoys max_modif_num = 3 # maximal modifications allowed for each peptide # Static Modification add_Cterm_peptide = 0.0000 add_Nterm_peptide = 0.0000 add_G_Glycine = 0.0000 add_A_Alanine = 0.0000 add_S_Serine = 0.0000 add_P_Proline = 0.0000 add_V_Valine = 0.0000 add_T_Threonine = 0.0000 add_C_Cysteine = 57.02146 add_L_Leucine = 0.0000 add_I_Isoleucine = 0.0000 add_X_LorI = 0.0000 add_N_Asparagine = 0.0000 add_O_Ornithine = 0.0000 add_B_avg_NandD = 0.0000 add_D_Aspartic_Acid = 0.0000 add_Q_Glutamine = 0.0000 add_K_Lysine = 0.0000 add_Z_avg_QandE = 0.0000 add_E_Glutamic_Acid = 0.0000 add_M_Methionine = 0.0000 add_H_Histidine = 0.0000 add_F_Phenylalanine = 0.0000 add_R_Arginine = 0.0000 add_Y_Tyrosine = 0.0000 add_W_Tryptophan = 0.0000 add_J_user_amino_acid = 0.0000 add_U_user_amino_acid = 0.0000 # Simulation simulation = 0 # 0 = disable; 1 = enable; sim_MS1 = 0 # ppm addition for MS1 decoys sim_MS2 = 0 # Da window for randomized MS2 peaks