Modification and flanking amino acid information absent from final output (pout) file

Dear Concern,

I'm running MS-GF+ms2rescore, and as the title suggests, the final .pout file doesn't have flanking amino acid or modification information in the peptide column.

This is the config file I'm using:

    "$schema": "./config_schema.json",
    "general":{
        "pipeline":"infer",
        "feature_sets":[["searchengine", "ms2pip", "rt"]],
        "run_percolator":true,
        "id_decoy_pattern": "XXX_",
        "num_cpu":12,
        "config_file":null,
        "tmp_path":"path/to/tmp/",
        "mgf_path":null,
        "output_filename":"path/to/output",
        "log_level": "info",
        "plotting": false
    },
    "ms2pip": {
        "model": "HCD",
        "frag_error": 0.02,
        "modifications": [
            {"name":"Acetyl", "unimod_accession":1, "mass_shift":42.010565, "amino_acid":null, "n_term":true, "c_term": false},
            {"name":"Carbamidomethyl", "unimod_accession":4, "mass_shift":57.021464, "amino_acid":"C", "n_term":false, "c_term": false},
            {"name":"Deamidated", "unimod_accession":7, "mass_shift":0.984016, "amino_acid":"N", "n_term":false, "c_term": false},
            {"name":"PhosphoS", "unimod_accession":21, "mass_shift":79.966331, "amino_acid":"S", "n_term":false, "c_term": false},
            {"name":"PhosphoT", "unimod_accession":21, "mass_shift":79.966331, "amino_acid":"T", "n_term":false, "c_term": false},
            {"name":"PhosphoY", "unimod_accession":21, "mass_shift":79.966331, "amino_acid":"Y", "n_term":false, "c_term": false},
            {"name":"Pyro-carbamidomethyl", "unimod_accession":26, "mass_shift":39.994915, "amino_acid":"C", "n_term":false, "c_term": false},
            {"name":"Glu->pyro-Glu", "unimod_accession":27, "mass_shift":-18.010565, "amino_acid":"E", "n_term":true, "c_term": false},
            {"name":"Gln->pyro-Glu", "unimod_accession":28, "mass_shift":-17.026549, "amino_acid":"Q", "n_term":true, "c_term": false},
            {"name":"Oxidation", "unimod_accession":35, "mass_shift":15.994915, "amino_acid":"M", "n_term":false, "c_term": false},
            {"name":"iTRAQ", "unimod_accession":214, "mass_shift":144.102063, "amino_acid":null, "n_term":true, "c_term": false},
            {"name":"Ammonia-loss", "unimod_accession":385, "mass_shift":-17.026549, "amino_acid":"C", "n_term":true, "c_term": false},
            {"name":"TMT6plexN", "unimod_accession":737, "mass_shift":229.162932, "amino_acid":"N", "n_term":false, "c_term": false},
            {"name":"TMT6plex", "unimod_accession":737, "mass_shift":229.162932, "amino_acid":null, "n_term":true, "c_term": false},
            {"name":"Amidated", "unimod_accession": 2, "mass_shift": -0.984016, "amino_acid":null, "n_term": false, "c_term": true}
        ]
    },
    "maxquant_to_rescore": {
        "mgf_title_pattern": "TITLE=.*scan=([0-9]+).*$",
        "modification_mapping":{
            "ox":"Oxidation",
            "cm":"Carbamidomethyl"
        },
        "fixed_modifications":{
            "C":"Carbamidomethyl"
        }
    },
    "percolator": {}
}

I'm running these on a pair of mzid and mgf files, as mentioned in the documentation. When I run MS-GF+, I specify carbamidomethylation of C as fixed modification and oxidation of M as variable modification.

I'd be grateful for your help in this regard. Even short of an actual fix, if you can suggest a way to extract this information from the generated files, that would be great.

Thanks again and very best regards, Hassan

compomics / ms2rescore

Modification and flanking amino acid information absent from final output (pout) file #92