########################################################################################## ## Parameter file for JUMPm # ## version 1.02, Date: 04/03/2016 # ########################################################################################## labeled_data = 1 # 1 = labeled data; 0 = unlabeled data mode = 1 # 1= positive mode; -1 = negative mode labeled_ID_method = 2 # 1 = mass only; # 2= MISSILE combined with #C and #N; # 3 = MISSILE combined with #C; # 4=MISSILE combined with N# ## Database settings database = HMDB,YMDB # database type: PUBCHEM, YMDB, HMDB; use "," to combine two databases if you want to search a combined database mass_formula_database = /home/xwang4/JUMPm_database/MASS_FORMULA_DB # mass formula database structure_database = /home/xwang4/JUMPm_database/STRUCTURE_DB # structure database ## mass tolerance for matching between mono mass (C12) and formula formula_mass_tolerance_searching = 8 # mass tolerance for formula search (ppm) ## parameters for isotopic peirs c12_c13_tolerance = 4 # tolerance between C12 and C15; unit in Da c12_n15_tolerance = 4 # tolerance between C12 and C15; unit in Da tolerance_unit = 2 # 1=Da; 2=ppm relative_isotopes_intensity = 0.5 # minimal relative intensity between paired isotopes min_pair_correlation = 0.5 # minimal pairing correlation coefficient cluster_tolerance = 4 # from version 0.1.5 change ppm into cluster_tolerance (tolerance for clustering step) ## Preprocessing parameters first_scan_extraction = 0 last_scan_extraction = 5000 # the last scan used for search isolation_window = 1 # isolation window size 1= +/-0.5 mass_correction = 1 # 0 = no correction, 1 = MS1-based decharge_ppm = 3 # intrascan isotopic tolerance for decharging deisotope_ppm = 3 # intrascan isotopic tolerance for decharging ## parameters for labeling normalization loading_normalization = 0 formula_mass_tolerance_pairing = 8 # use it for the first round of search to estimate label mixing ratio ## MS2 matching 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 = 10 # scan number between MS2 and MS1 containing MS2 precursor matched MISSILE pairs ## Raw data processing data_acquisition_mode = 2 # 1 = centroid, 2 = profile for full scan and centroid for MS/MS scan ## Cluster job system cluster = 1 # 1 = cluster; 0 = single server job_management_system = SGE # SGE used by current cluster; other systems (e.g. LSF & PBS) may be used processor_number = 10 # processor number when cluster = 0 ## falsified peak mass mass_shift = 0 # Unit: ppm ##########################################################################################