# JUMP search parameter file (Version: 1.13.1, Date: 05/01/2020) search_engine = JUMP # use JUMP or SEQUEST for database search # Database settings database_name = /home/user/database/human_ft_mc2_c0_TMTpro.fasta.mdx # use .fasta.mdx for JUMP and .fasta.hdr for SEQUEST pit_file = /home/user/database/human_ft_mc2_c0_TMTpro.pit # protein inference table (pit) for grouping proteins/genes peptide_tolerance = 6 # precursor mass (MH+) tolerance, default = 6 ppm after mass correction peptide_tolerance_units = 2 # 1 = Da; 2 = ppm # Preprocessing parameters first_scan_extraction = 5000 # the first scan number for search last_scan_extraction = 6000 # the last scan number for search, use a large number (e.g. 10E6) for full scans isolation_window = 1 # +/- (isolation_window)/2 based on MS2 isolation window (e.g. 1.6 m/z) isolation_window_offset = 0.2 # +/- isolation_window_offset based on MS2 isolation window offset (e.g. 0.25 m/z) isolation_window_variation = 0.2 # +/- isolation_window_variation based on MS2 isolation window offset (e.g. 0.25 m/z) interscanppm = 15 # mass tolerance for interscan precursor identification intrascanppm = 10 # mass tolerance for intrascan isotopic decharging max_num_ppi = 0 # 0 = disable; 1-0 = max precursor ions selected for mixed MS2 search percentage_ppi = 50 # 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 and +3) ppi_charge_1 = 1 # 0 = discard MS1 with charge +1; 1 = enable original charge +1 mass_correction = 2 # 0 = no correction, 1 = MS1-based, 2 = MS1/2-based, 3 = manual correction prec_window = 3 # 0 = disable; 1-10 (Da) = mz windows for removing precursor ions MS2_deisotope = 1 # 0 = disable; 1 = enable ppm = 10 # mass tolerance for MS2 decharging and deisotoping charge12_ppm = 15 # mass tolerance for merging different charged ions with the same mass ms2_consolidation = 10 # maximal number of peaks retained within each 100-Da window TMT_data = 1 # 0 = disable; 1 = enable # Tagging tag_generation = 1 # 0 = disable; 1 = enable to generate tags tag_tolerance = 10 # mass tolerance for measuring peak distance for generating tags tag_tolerance_unit = 2 # 1 = Da; 2 = ppm tag_select_method = comb_p # tag ranking: comb_p, hyper_p or 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 = 15 # mass tolerance for MS2 ion matching frag_mass_tolerance_unit = 2 # 1 = Da; 2 = ppm ion_losses_MS2 = 0 0 0 0 # 0 = disable; 1 = enable neutral loss of H2O, HPO3, H3PO4 and NH3, respectively ion_losses_MS1 = 0 # 0 = disable; 1 = use precursor ion phosphate neutral loss to estimate #S/T phosphorylation ion_scoring = 1 # 1 = scoring product ions simultaneously; 2 = scoring ion series and charge states separately matching_method = hyper_p # PSM scoring: comb_p, hyper_p, rank_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 = 50 # max tags used for search unless the total number of tags is smaller than this defined value number_of_selected_result = 5 # maximal tentative PSMs in .spout ranked by Jscore number_of_detailed_result = 5 # maximal tentative PSMs in .spout ranked by pattern matching score second_search = 1 # 0 = disable; 1 = enable; for PSMs with FDR>0, perform the another round of search # by relaxing monoisotopic mass by including M-2, M-1, M, M+1, M+2 # Dynamic Modifications: SEQUEST requires no new database; but JUMP requires new database # 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 # TMT6-10: 229.1629321; TMT2: 225.1558327; TMT0: 224.1524779 dynamic_M = 15.99492 # add each dynamic modification by one line, starting with dynamic_aa # dynamic_C = 57.02146 # add additional dynamic modification by line, starting with dynamic_aa # Parameters for creating database (should match with the selected 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 max_modif_num = 3 # maximal modifications allowed for each peptide # Static Modification add_Nterm_peptide = 229.162932 # TMT modification or other amine labeling add_Cterm_peptide = 0.0000 add_A_Alanine = 0.0000 add_B_avg_NandD = 0.0000 add_C_Cysteine = 0.0000 # Cys alkylation add_D_Aspartic_Acid = 0.0000 add_E_Glutamic_Acid = 0.0000 add_F_Phenylalanine = 0.0000 add_G_Glycine = 0.0000 add_H_Histidine = 0.0000 add_I_Isoleucine = 0.0000 add_J_user_amino_acid = 0.0000 add_K_Lysine = 229.162932 # TMT modification or other amine labeling add_L_Leucine = 0.0000 add_M_Methionine = 0.0000 add_N_Asparagine = 0.0000 add_O_Ornithine = 0.0000 add_P_Proline = 0.0000 add_Q_Glutamine = 0.0000 add_R_Arginine = 0.0000 add_S_Serine = 0.0000 add_T_Threonine = 0.0000 add_U_user_amino_acid = 0.0000 add_V_Valine = 0.0000 add_W_Tryptophan = 0.0000 add_X_LorI = 0.0000 add_Y_Tyrosine = 0.0000 add_Z_avg_QandE = 0.0000 # Other parameters simulation = 0 # 0 = disable; 1 = enable; this function used for testing the target-decoy strategy sim_MS1 = 1000 # ppm addition for MS1 decoys sim_MS2 = 5 # Da window for randomized MS2 peaks temp_file_removal = 1 # 0 = disable (keep temporary files); 1 = enable (remove temporary files)