{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "title": "HUPO-PSI Peak annotation specification",
  "description": "Annotation of an individual peak in a mass spectrum.",
  "type": "object",
  "additionalProperties": true,
  "required": ["analyte_reference", "molecule_description"],
  "properties": {
    "analyte_reference": {
      "description": "Label of analyte to which this annotation belongs",
      "oneOf": [{ "type": "integer" }, { "type": "null" }],
      "default": null
    },
    "molecule_description": {
      "description": "Description of the molecule or molecule fragment that this peak is annotated with",
      "type": "object",
      "oneOf": [
        { "$ref": "#/definitions/peptide" },
        { "$ref": "#/definitions/internal" },
        { "$ref": "#/definitions/precursor" },
        { "$ref": "#/definitions/immonium" },
        { "$ref": "#/definitions/reference" },
        { "$ref": "#/definitions/named_compound" },
        { "$ref": "#/definitions/formula" },
        { "$ref": "#/definitions/smiles" },
        { "$ref": "#/definitions/unannotated" }
      ]
    },
    "neutral_losses": {
      "description": "Any additional gains or losses of chemical groups defined by formula or by name; multiple may be specified",
      "type": "array",
      "items": {
        "type": "string"
      },
      "default": []
    },
    "isotope": {
      "description": "An isotopic peak offset from the monoisotopic peak",
      "anyOf": [{ "type": "integer"}, {
        "type": "array",
        "items": {
          "anyOf": [
            { "type": "integer" },
            { "$ref": "#/definitions/isotope_specification" }
          ]
        }
      }],
      "default": []
    },
    "adducts": {
      "description": "The charge carrier(s) for the given annotation",
      "type": "array",
      "items": {
        "type": "string"
      },
      "default": []
    },
    "charge": {
      "description": "The charge state of the ion generating this peak; this value is unsigned",
      "type": "integer",
      "minimum": 1,
      "default": 1
    },
    "mass_error": {
      "description": "Error between observed and theoretical mass",
      "oneOf": [{ "type": "null" }, { "$ref": "#/definitions/mass_error" }],
      "default": null
    },
    "confidence": {
      "description": "Number defining confidence in peak annotation",
      "oneOf": [{ "type": "number" }, { "type": "null" }],
      "default": null
    }
  },
  "definitions": {
    "series_label": {
      "description": "Type of ion being described, specifies the required molecule description keys",
      "type": "string",
      "enum": [
        "peptide",
        "internal",
        "precursor",
        "immonium",
        "reference",
        "named_compound",
        "formula",
        "smiles",
        "unannotated"
      ]
    },
    "mass_error": {
      "description": "Error between observed and theoretical mass",
      "type": "object",
      "required": ["value", "unit"],
      "properties": {
        "value": {
          "description": "Mass error value",
          "type": "number"
        },
        "unit": {
          "description": "Mass error unit",
          "type": "string",
          "enum": ["ppm", "Da"],
          "default": "Da"
        }
      }
    },
    "peptide": {
      "description": "Canonical peptide fragment ion",
      "type": "object",
      "required": ["series_label", "series", "position"],
      "additionalProperties": false,
      "properties": {
        "series_label": {
          "$ref": "#/definitions/series_label",
          "enum": ["peptide"]
        },
        "series": {
          "description": "The peptide ion series this ion belongs to",
          "type": "string",
          "enum": [
            "b",
            "y",
            "a",
            "x",
            "c",
            "z",
            "d",
            "v",
            "w",
            "da",
            "db",
            "wa",
            "wb"
          ]
        },
        "position": {
          "description": "The position from the appropriate terminal along the peptide this ion was fragmented at (starting with 1)",
          "type": "integer",
          "minimum": 1
        },
        "sequence": {
          "description": "A ProForma 2.0 formatted peptidoform sequence describing the ion, which may be useful for contaminants or de novo sequencing",
          "oneOf": [{ "type": "string" }, { "type": "null" }]
        }
      }
    },
    "internal": {
      "description": "Internal fragment ion",
      "type": "object",
      "required": ["series_label", "start_position", "end_position"],
      "additionalProperties": false,
      "properties": {
        "series_label": {
          "$ref": "#/definitions/series_label",
          "enum": ["internal"]
        },
        "start_position": {
          "description": "N-terminal amino acid residue of the fragment in the original peptide sequence (beginning with 1, counting from the N-terminus)",
          "type": "integer",
          "minimum": 1
        },
        "end_position": {
          "description": "C-terminal amino acid residue of the fragment in the original peptide sequence (beginning with 1, counting from the N-terminus)",
          "type": "integer",
          "minimum": 1
        },
        "sequence": {
          "description": "A ProForma 2.0 formatted peptidoform sequence describing the ion, which may be useful for contaminants or de novo sequencing",
          "oneOf": [{ "type": "string" }, { "type": "null" }]
        }
      }
    },
    "precursor": {
      "description": "Precursor ion",
      "type": "object",
      "required": ["series_label"],
      "additionalProperties": false,
      "properties": {
        "series_label": {
          "$ref": "#/definitions/series_label",
          "enum": ["precursor"]
        }
      }
    },
    "immonium": {
      "description": "Immonium ion",
      "type": "object",
      "required": ["series_label", "amino_acid"],
      "additionalProperties": false,
      "properties": {
        "series_label": {
          "$ref": "#/definitions/series_label",
          "enum": ["immonium"]
        },
        "amino_acid": {
          "description": "One-letter code of the amino acid represented by this immonium ion",
          "type": "string",
          "minLength": 1,
          "maxLength": 1
        },
        "modification": {
          "description": "An optional modification that may be attached to this immonium ion",
          "type": "string"
        }
      }
    },
    "reference": {
      "description": "Reference ion",
      "type": "object",
      "required": ["series_label", "reference"],
      "additionalProperties": false,
      "properties": {
        "series_label": {
          "$ref": "#/definitions/series_label",
          "enum": ["reference"]
        },
        "reference": {
          "description": "The name of a reference molecule or ion defined in a registry",
          "type": "string"
        }
      }
    },
    "named_compound": {
      "description": "named compound ion",
      "type": "object",
      "required": ["series_label", "compound_name"],
      "additionalProperties": false,
      "properties": {
        "series_label": {
          "$ref": "#/definitions/series_label",
          "enum": ["named_compound"]
        },
        "compound_name": {
          "description": "The name of the named compound ion being marked",
          "type": "string"
        }
      }
    },
    "formula": {
      "description": "Ion described by chemical formula",
      "type": "object",
      "required": ["series_label", "formula"],
      "additionalProperties": false,
      "properties": {
        "series_label": {
          "$ref": "#/definitions/series_label",
          "enum": ["formula"]
        },
        "formula": {
          "description": "The elemental formula of the ion being marked",
          "type": "string"
        }
      }
    },
    "smiles": {
      "description": "Ion described by SMILES molecular structure",
      "type": "object",
      "required": ["series_label", "smiles"],
      "additionalProperties": false,
      "properties": {
        "series_label": {
          "$ref": "#/definitions/series_label",
          "enum": ["smiles"]
        },
        "smiles": {
          "description": "The SMILES definition of the ion being marked",
          "type": "string"
        }
      }
    },
    "unannotated": {
      "description": "Unannotated ion",
      "type": "object",
      "required": ["series_label", "unannotated_label"],
      "additionalProperties": false,
      "properties": {
        "series_label": {
          "$ref": "#/definitions/series_label",
          "enum": ["unannotated"]
        },
        "unannotated_label": {
          "description": "A user-specified numeral label for an unannotated peak",
          "type": ["string", "null"]
        }
      }
    },
    "isotope_specification": {
      "description": "A defined isotopic variant of another peak",
      "type": "object",
      "required": ["isotope"],
      "additionalProperties": false,
      "properties": {
        "isotope": {
          "type": "integer",
          "description": "The number of times this isotope occurs in the chemical composition of the ion"
        },
        "variant": {
          "oneOf": [
            { "$ref": "#/definitions/element_isotopic_variant" },
            { "$ref": "#/definitions/average_isotopic_variant" },
            { "type": "null" }
          ]
        }
      }
    },
    "element_isotopic_variant": {
      "type": "object",
      "required": ["element", "nucleon_count"],
      "properties": {
        "nucleon_count": {
          "type": "integer",
          "description": "The number of nucleons this isotope differs in with respect to the monoisotopic isotopologue"
        },
        "element": {
          "type": "string",
          "description": "The name of element the isotopologue comes from"
        }
      }
    },
    "average_isotopic_variant": {
      "type": "object",
      "required": ["averaged"],
      "additionalProperties": false,
      "properties": {
        "averaged": {
          "type": "boolean",
          "description": "Whether or not the isotopic peak is defined as the \"average\" isotopomer of the known chemical composition"
        }
      }
    }
  }
}