-
Notifications
You must be signed in to change notification settings - Fork 1
/
jumpm.params
125 lines (112 loc) · 6.92 KB
/
jumpm.params
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
##############################
## Parameter file for JUMPm ##
##############################
####################################
## Parameters for data properties ##
####################################
labeled_data = 0 # 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)
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)
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 = 10 # 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 = 1 # the first scan used for search
last_scan_extraction = 1000000 # 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 = 10 # intrascan isotopic tolerance for decharging
deisotope_ppm = 10 # 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 = 1 # 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