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jumpm_negative.params
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jumpm_negative.params
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##########################################################################################
## Parameter file for JUMPm #
## version 1.6.6, Date: 10/05/2016 #
##########################################################################################
labeled_data = 1 # 1 = labeled data; 0 = unlabeled data
library_search = 0 # 1 = library search; only enable for unlabeled data; 0 = disable
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#
adduct = 1 # 0 = disable adduct detection; 1 = enable
## 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 = 10 # 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 = 0.1 # 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 = 10000000 # 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
## Noise filtering
signal_noise_ratio = 10 # fold of the minimum signal noise ratio
max_percentage_RT_range = 50 # threshold maximum percentage of the range of retention time of a peak
min_peak_intensity = 10000 # threshold of a peak intensity
skipping_scans = 3 # number of skipping scans during 3D formation
mass_tolerance_peak_matching = 10 # mass tolerance for peak matching during 3D formation
## parameters for labeling normalization
loading_normalization = 0
formula_mass_tolerance_pairing = 10 # use it for the first round of search to estimate label mixing ratio
## MS2 matching
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
## 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
##########################################################################################
#adduct_Cl = 34.96885271
adduct_CH2O2 = 46.00547931
#adduct_C2H4O2 = 60.02112937
#adduct_C2HF3O2 = 113.9928639