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Example: PXD001468 (Open-Search)

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"
        },
        "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"
    ]
}