Example: PXD003881 (Label-free quant)
The following configuration file is an example of running a closed-search with label-free quantification on a set of 20 runs. These runs have E. coli lysates spiked into human cell background at known amounts.
PXD001468.json
{
"database": {
"bucket_size": 8192,
"enzyme": {
"missed_cleavages": 2,
"min_len": 7,
"max_len": 50,
"cleave_at": "KR",
"restrict": "P"
},
"fragment_min_mz": 150.0,
"fragment_max_mz": 2000.0,
"peptide_min_mass": 500.0,
"peptide_max_mass": 5000.0,
"ion_kinds": [
"b",
"y"
],
"min_ion_index": 2,
"max_variable_mods": 3,
"static_mods": {
"C": 57.0215
},
"variable_mods": {
"M": 15.994
},
"decoy_tag": "rev_",
"generate_decoys": true,
"fasta": "PXD003881.fasta"
},
"quant": {
"lfq": true,
"lfq_settings": {
"peak_scoring": "Hybrid",
"integration": "Sum",
"spectral_angle": 0.6,
"ppm_tolerance": 5.0
}
},
"precursor_tol": {
"ppm": [
-20.0,
20.0
]
},
"fragment_tol": {
"ppm": [
-20.0,
20.0
]
},
"isotope_errors": [
0,
2
],
"deisotope": true,
"min_peaks": 15,
"max_peaks": 150,
"max_fragment_charge": 1,
"min_matched_peaks": 4,
"predict_rt": true,
"mzml_paths": [
"PXD003881/B03_02_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_03_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_04_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_07_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_08_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_09_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_12_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_13_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_14_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_15_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_16_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_17_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_18_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_19_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_20_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz",
"PXD003881/B03_21_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML.gz"
]
}