############################## ## Parameter file for JUMPm ## ############################## #################################### ## Parameters for data properties ## #################################### labeled_data = 1 # 0 = unlabeled data, 1 = labeled data labeled_ID_method = 2 # 1 = mass only, 2 = MISSILE combined with #C and #N, 3 = MISSILE combined with #C, 4 = MISSILE combined with N# LC_column = HILIC # type of LC column, e.g. HILIC, C18, C4, etc. mode = -1 # 1 = positive mode, -1 = negative mode ######################################################## ## Parameters for search methods and output directory ## ######################################################## database_search = 1 # 0 = do not search a database, 1 = search a database (database should be specified) library_search = 0 # 0 = do not search a library, 1 = search a library (library should be specified) adduct = 1 # 0 = disable adduct detection, 1 = enable database = HMDB,YMDB # database type: PUBCHEM, YMDB, HMDB (use "," to combine multiple databases if you want to search a combined database) library = /home/usr/JUMPm_database/Metabolome_library.txt # path of .txt file containing library compound information output_name = test # Used for unlabeled data analysis. Prefix "align_" will be automatically added mass_formula_database = /home/usr/JUMPm_database/MASS_FORMULA_DB # mass formula database structure_database = /home/usr/JUMPm_database/STRUCTURE_DB # structure database formula_mass_tolerance_searching = 50 # mass tolerance for searching formula (ppm) ############################################### ## Whether skip the feature detection or not ## ############################################### skip_feature_detection = 0 # 0 = don't skip (i.e. perform feature detection), 1 = skip ## If you choose 'skip_feature_detection = 1', then specify absolute path(s) of feature file(s) separated by new line ## Note that .mzXML file(s) should be located in the same place where the following .feature file(s) are feature_files = /home/usr/samples/sample1.1.feature /home/usr/samples/sample2.1.feature /home/usr/samples/sample3.1.feature ####################################### ## Parameters for processing spectra ## ####################################### data_acquisition_mode = 2 # 1 = centroid, 2 = profile for full scan and centroid for MS/MS scan first_scan_extraction = 1000 # the first scan used for search last_scan_extraction = 1050 # the last scan used for search isolation_window = 1 # isolation window size 1= +/-0.5 mass_correction = 0 # 0 = no correction, 1 = MS1-based decharge_ppm = 16 # intrascan isotopic tolerance for decharging deisotope_ppm = 16 # intrascan isotopic tolerance for decharging ########################################################### ## Parameters for feature detection (for advanced users) ## ########################################################### signal_noise_ratio = 10 # fold of the minimum signal noise ratio max_percentage_RT_range = 100 # threshold maximum percentage of the range of retention time of a peak min_peak_intensity = 10000 # threshold of a peak intensity skipping_scans = 10 # number of skipping scans during 3D formation mass_tolerance_peak_matching = 3 # mass tolerance for peak matching during 3D formation ############################################# ## Parameters for isotopic pairs (labeled) ## ############################################# c12_c13_tolerance = 4 # tolerance between C12 and C15 c12_n15_tolerance = 4 # tolerance between C12 and C15 tolerance_unit = 2 # 1 = Da, 2 = ppm relative_isotopes_intensity = 0.1 # minimal relative intensity between paired isotopes min_pair_correlation = 0.5 # minimal pairing correlation coefficient cluster_tolerance = 4 # tolerance for clustering step ###################################################################### ## Parameters for feature alignment (unlabeled, for advanced users) ## ###################################################################### reference_feature = 0 # 0 = reference feature is automatically chosen, # otherwise put the absolute path of a feature file to be used as a reference tol_initial = 20 # initial m/z-tolerance for the global calibration (default = 20 ppm) sd_width = 5 # SD-width for RT- and m/z-tolerances # (when finding "matched/aligned" features, default = 5) skip_loading_bias_correction = 1 # 0 = don't skip (i.e. perform loading-bias correction/normalization), 1 = skip rescue = 1 # 1 = rescue unaligned features by loosening RT- and m/z-tolerances; 0 = no ## RT- and m/z-tolerance settings in rescueing step (possibly multiple times) rt_tolerance_unit = 1, 2 # 1 = SD-width of dynamic RT-shifts, 2 = seconds rt_tolerance_value = 10, 10 # RT-tolerance value(s) according to the above unit(s) mz_tolerance_unit = 1, 2 # 1 = SD-width of dynamic m/z-shifts, 2 = ppm mz_tolerance_value = 10, 10 # m/z-tolerance value(s) according to the above unit(s) pct_full_alignment = 100 # percentage of samples are grouped into a feature ####################################################################################### ## Parameters for processing MS2 spectra of features (unlabeled, for advanced users) ## ####################################################################################### tol_precursor = 10 # PPM tolerance for finding a MS1 peak corresponding to a feature tol_intra_ms2_consolidation = 10 # PPM tolerance for merging MS2 spectra within a run tol_inter_ms2_consolidation = 20 # PPM tolerance for merging MS2 spectra between runs ######################################### ## Parameters for matching MS2 spectra ## ######################################### fragment_method = 1 # 1 = metfrag; 2 = CFM-ID percentage_ms2_peaks = 50 # in percentage (50 = 50%); number of MS2 peaks used for matching frag_mass_tolerance = 0.01 # mass tolerance for MS2 ion matching frag_mass_tolerance_unit = 1 # 1 = Da; 2 = PPM; matched_scan_dist = 500 # scan number between MS2 and MS1 containing MS2 precursor # matched MISSILE pairs ################################### ## Parameters for cluster system ## ################################### cluster = 0 # 0 = single server, 1 = cluster job_management_system = SGE # LSF may be used ############################### ## Adducts for positive mode ## ############################### #adduct_NH3 = 17.0271024 #adduct_Na = 21.9825 #adduct_K = 37.956438 #adduct_CH3O = 32.026769 #adduct_ACN = 41.0271024 #adduct_ACNNa = 63.0090478 #adduct_2ACN = 82.0536502 ############################### ## Adducts for negative mode ## ############################### adduct_Cl = 35.97612871 adduct_HCOO = 46.0049306 adduct_CH3COO = 60.0205798 adduct_2H = -1.007825 adduct_-2H+Na = 21.9813968 adduct_-2H+K = 37.9553348 adduct_CH2O2 = 46.00547931