{
  "project_parameters": {
    "i2MassChroQ_VERSION": {
      "category": 1,
      "value": "1.0.18"
    },
    "cvparam_SpectraDataFileFormat": {
      "category": 5,
      "value": "MS:1000544"
    },
    "cvparam_SpectraDataSpectrumIDFormat": {
      "category": 5,
      "value": "MS:1000824"
    },
    "AnalysisSoftware_name": {
      "category": 2,
      "value": "X!Tandem"
    }
  },
  "masschroq_methods": {
    "alignment_method": {
      "ms1_smoothing": 15,
      "ms2_smoothing": 5,
      "ms2_tendency": 10
    },
    "quantification_method": {
      "match_between_run": true,
      "isotope_minimum_ratio": 0.9,
      "extraction": {
        "rt_range": 300,
        "integration": "max",
        "precision": {
          "unit": "ppm",
          "up": 10,
          "down": 10
        }
      },
      "prefilter": {},
      "detection": {
        "type": "zivy",
        "meanfilter": 1,
        "minmax": 3,
        "maxmin": 2,
        "threshold_on_max": 5000,
        "threshold_on_min": 3000
      }
    }
  },

  "identification_data": {
    "msrun_list": {
      "msrunb19": {
        "file": "/gorgone/pappso/data_extraction_pappso/mzXML/20120906_balliau_extract_1_B08_teal-5.mzXML"
      }
    },
    "protein_list": {
      "prota1a1": {
        "description": "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR",
        "sequence": "SLTNDWEDHLAVK"
      }
    },

    "peptide_list": {
      "pepa1a1": {
        "proforma": "SLTNDWEDHLAVK",
        "proteins": ["prota1a1"],
        "mods": "free text",
        "label_list": { "light": { "proforma": "SLTNDWEDHLAVK" } }
      }
    },

    "msrunpeptide_list": {
      "msruna1": {
        "peptide_obs": {
          "pepa1a1": [
            {
              "scan_index": 2345,
              "label": "light",
              "precursor": {
                "charge": 2,
                "mz": 2456.45,
                "intensity": 4580,
                "rt": 345.67
              }
            }
          ]
        }
      }
    }
  },

  "actions": {
    "group_list": { "g1": ["msruna1", "msruna2", "msruna3"] },
    "align_group": {
      "g1": {
        "alignment_reference": "msruna1"
      }
    },
    "quantify_all": true
  }
}
