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Example: PXD003881 (Label-free quant)

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"
        },
        "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"
    ]
}