Example: PXD001468 (Open-Search)
The following configuration file is an example of running a chimeric open-search on a single high-res MS/MS file.
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": 1500.0,
"peptide_min_mass": 500.0,
"peptide_max_mass": 5000.0,
"ion_kinds": [
"b",
"y"
],
"min_ion_index": 2,
"max_variable_mods": 2,
"static_mods": {
"C": 57.0214
},
"variable_mods": {
"M": 15.9949
},
"decoy_tag": "rev_",
"generate_decoys": true,
"fasta": "human_contam.fasta"
},
"precursor_tol": {
"da": [
-500,
100
]
},
"fragment_tol": {
"ppm": [
-10,
10
]
},
"deisotope": true,
"chimera": true,
"min_peaks": 15,
"max_peaks": 250,
"min_matched_peaks": 4,
"max_fragment_charge": 1,
"report_psms": 2,
"predict_rt": true,
"mzml_paths": [
"PXD001468/b1906_293T_proteinID_01A_QE3_122212.mzML.gz"
]
}