general-sage-ptms-full.json

{
    "database": {
        "bucket_size": 8192,
        "enzyme": {
            "missed_cleavages": 0,
            "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, 31.9898],
            "P": [15.994, 31.9898],
            "[": [42.0105, 27.9949, 43.0058, 14.01565, 28.0313, 57.0215],
            "]": [-0.9840],
            "N": [0.984],
            "Q": [0.984, -17.02654],
            "K": [27.9949, 43.0058, 14.01565, 28.0313],
            "E": [-18.01056, 52.91146],
            "D": [52.91146]
        },
        "generate_decoys": true,
        "decoy_tag": "DECOY_",
        "fasta": "Homo-sapiens-uniprot-reviewed-20240615.fasta"
    },
    "precursor_tol": {
        "ppm": [
            -20,
            20
        ]
    },
    "fragment_tol": {
        "ppm": [
            -10,
            10
        ]
    },
    "isotope_errors": [
        0,
        3
    ],
    "quant": {
        "lfq": true,
        "lfq_settings": {
            "peak_scoring": "Hybrid",
            "integration": "Sum",
            "spectral_angle": 0.6,
            "ppm_tolerance": 5.0
        }
    },
    "deisotope": true,
    "min_peaks": 15,
    "max_peaks": 300,
    "max_fragment_charge": 1,
    "min_matched_peaks": 4,
    "mzml_paths": [
        "./20150901_QEp1_LC7_PhGe_SA_Plate1E_45_6.mzML",
        "./20150618_QEp1_LC7_PhGe_SA_Plate1B_45_1.mzML",
        "./20150907_QEp1_LC7_PhGe_SA_Plate2D_52_5.mzML",
        "./20150618_QEp1_LC7_PhGe_SA_Plate1B_1_1.mzML"
    ]
}