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  "Package": "Spec2Annot",
  "Title": "Annotation of Mass Spectra",
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  "Description": "Provides a comprehensive suite of functions to efficiently\nannotate mass spectra data. Motivated by the need for rapid and\naccurate chemical identification in high-resolution mass\nspectrometry, it integrates built-in chemical databases and\nhigh-performance C++ algorithms. Users can perform\nmass-to-charge (m/Z) and retention time searches, determine\nelemental compositions of molecules using heuristic rules,\nincluding specific isotopes, and annotate MS2 spectra with\nstructural metrics using configurable chemistry rules.",
  "License": "CeCILL",
  "URL": "https://github.com/odisce/Spec2Annot",
  "BugReports": "https://github.com/odisce/Spec2Annot/issues",
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  "Repository": "https://odisce.r-universe.dev",
  "Date/Publication": "2026-09-15 15:03:52 UTC",
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  "Author": "Sylvain Dechaumet [aut, cre],\nEtienne Thevenot [ctb],\nEric Venot [rev],\nAnnelaure Damont [ctb],\nAnaïs Legrand [ctb]",
  "Maintainer": "Sylvain Dechaumet <sylvain.dechaumet@cea.fr>",
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    "add_formula_to_annot",
    "annot_to_html",
    "annotate_mz",
    "annotate_spectra",
    "brute_force_const",
    "CJ1",
    "electron_mass",
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    "find_compo_from_mass",
    "fun_generate_ions_from_mz",
    "fun_get_ion_list",
    "gen_adduct",
    "gen_formula_from_compo",
    "gen_ionlist",
    "gen_isotopes",
    "gen_losses",
    "gen_monocharge",
    "get_charge_from_compo",
    "get_dbe",
    "get_element_from_mass",
    "get_iso_from_annot",
    "get_nrule",
    "get_senior",
    "match_tables",
    "mz_calc_ion",
    "mz_from_string",
    "mz_ppm",
    "mz_range",
    "mz_vec_aggregate",
    "search_db",
    "search_db_cpp",
    "string_from_element"
  ],
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      "name": "Adduct_db",
      "title": "adduct data",
      "object": "Adduct_db",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "adduct",
        "charge",
        "mz_query"
      ],
      "rows": 5,
      "table": true,
      "tojson": true
    },
    {
      "name": "db_monocharge",
      "title": "Mono charged ions",
      "object": "db_monocharge",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "Formula",
        "charge",
        "lossL",
        "mz_query"
      ],
      "rows": 11,
      "table": true,
      "tojson": true
    },
    {
      "name": "Element",
      "title": "Periodic table as a data.table",
      "object": "Element",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "atomic_nb",
        "atomic_symb",
        "mass_nb",
        "atomic_mass",
        "isotopic_compo"
      ],
      "rows": 354,
      "table": true,
      "tojson": true
    },
    {
      "name": "ions_database",
      "title": "ions data",
      "object": "ions_database",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "Attribution",
        "exact_mass",
        "charge",
        "Type",
        "lossL",
        "ID"
      ],
      "rows": 958,
      "table": true,
      "tojson": true
    },
    {
      "name": "Isotopes_db",
      "title": "isotopes data",
      "object": "Isotopes_db",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "isotope",
        "mass",
        "abundance",
        "mass_diff"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    },
    {
      "name": "Losses_db",
      "title": "losses data",
      "object": "Losses_db",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "loss",
        "mz_query",
        "encod"
      ],
      "rows": 182,
      "table": true,
      "tojson": true
    },
    {
      "name": "spectra_full",
      "title": "Spectra example",
      "object": "spectra_full",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "mz",
        "intensity",
        "ID"
      ],
      "rows": 2484,
      "table": true,
      "tojson": true
    },
    {
      "name": "spectra_ms2",
      "title": "Spectra example",
      "object": "spectra_ms2",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "mz",
        "i"
      ],
      "rows": 29,
      "table": true,
      "tojson": true
    },
    {
      "name": "valence_db",
      "title": "Valence data",
      "object": "valence_db",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "atomic_symb",
        "valence"
      ],
      "rows": 117,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_formula_to_annot",
      "title": "Add formula to annotate_mz()",
      "topics": [
        "add_formula_to_annot"
      ]
    },
    {
      "page": "Adduct_db",
      "title": "adduct data",
      "topics": [
        "Adduct_db"
      ]
    },
    {
      "page": "annot_to_html",
      "title": "Convert annotation to html string",
      "topics": [
        "annot_to_html"
      ]
    },
    {
      "page": "annotate_mz",
      "title": "Annotate a mass spectrum",
      "topics": [
        "annotate_mz"
      ]
    },
    {
      "page": "annotate_spectra",
      "title": "Annotate a matrix and return network edges",
      "topics": [
        "annotate_spectra"
      ]
    },
    {
      "page": "brute_force_const",
      "title": "Group m/Z from a vector based on tolerance",
      "topics": [
        "brute_force_const"
      ]
    },
    {
      "page": "CJ1",
      "title": "Cross join of two data.table",
      "topics": [
        "CJ1"
      ]
    },
    {
      "page": "db_monocharge",
      "title": "Mono charged ions",
      "topics": [
        "db_monocharge"
      ]
    },
    {
      "page": "electron_mass",
      "title": "Return the mass of an electorn",
      "topics": [
        "electron_mass"
      ]
    },
    {
      "page": "Element",
      "title": "Periodic table as a data.table",
      "topics": [
        "Element"
      ]
    },
    {
      "page": "element_from_formula",
      "title": "Get element count from formula",
      "topics": [
        "element_from_formula"
      ]
    },
    {
      "page": "find_compo_from_mass",
      "title": "Find composition from mass",
      "topics": [
        "find_compo_from_mass"
      ]
    },
    {
      "page": "fun_generate_ions_from_mz",
      "title": "Calculate the ions database",
      "topics": [
        "fun_generate_ions_from_mz"
      ]
    },
    {
      "page": "fun_get_ion_list",
      "title": "Calculate the ions database",
      "topics": [
        "fun_get_ion_list"
      ]
    },
    {
      "page": "gen_adduct",
      "title": "Generate adduct list from mz",
      "topics": [
        "gen_adduct"
      ]
    },
    {
      "page": "gen_formula_from_compo",
      "title": "Generate formula from composition",
      "topics": [
        "gen_formula_from_compo"
      ]
    },
    {
      "page": "gen_ionlist",
      "title": "Calculate list of targetd ions from neutral mz",
      "topics": [
        "gen_ionlist"
      ]
    },
    {
      "page": "gen_isotopes",
      "title": "Function to generate isotopes from an exact mass",
      "topics": [
        "gen_isotopes"
      ]
    },
    {
      "page": "gen_losses",
      "title": "Generate losses list from mz",
      "topics": [
        "gen_losses"
      ]
    },
    {
      "page": "gen_monocharge",
      "title": "Function to generate monocharges from an exact mass",
      "topics": [
        "gen_monocharge"
      ]
    },
    {
      "page": "get_charge_from_compo",
      "title": "Get charge from composition",
      "topics": [
        "get_charge_from_compo"
      ]
    },
    {
      "page": "get_dbe",
      "title": "Calculate DBE from an elemental composition",
      "topics": [
        "get_dbe"
      ]
    },
    {
      "page": "get_element_from_mass",
      "title": "Get Element from a mass",
      "topics": [
        "get_element_from_mass"
      ]
    },
    {
      "page": "get_iso_from_annot",
      "title": "Get isotopes from annotation",
      "topics": [
        "get_iso_from_annot"
      ]
    },
    {
      "page": "get_nrule",
      "title": "Check Nitrogen rule",
      "topics": [
        "get_nrule"
      ]
    },
    {
      "page": "get_range",
      "title": "Get index in range",
      "topics": [
        "get_range"
      ]
    },
    {
      "page": "get_senior",
      "title": "Check Senior theorems",
      "topics": [
        "get_senior"
      ]
    },
    {
      "page": "ions_database",
      "title": "ions data",
      "topics": [
        "ions_database"
      ]
    },
    {
      "page": "Isotopes_db",
      "title": "isotopes data",
      "topics": [
        "Isotopes_db"
      ]
    },
    {
      "page": "Losses_db",
      "title": "losses data",
      "topics": [
        "Losses_db"
      ]
    },
    {
      "page": "match_tables",
      "title": "Match two table",
      "topics": [
        "match_tables"
      ]
    },
    {
      "page": "mz_calc_ion",
      "title": "Calculate ion mass using form",
      "topics": [
        "mz_calc_ion"
      ]
    },
    {
      "page": "mz_from_string",
      "title": "Calculate mz from a string with signs",
      "topics": [
        "mz_from_string"
      ]
    },
    {
      "page": "mz_ppm",
      "title": "Get mass deviation in ppm",
      "topics": [
        "mz_ppm"
      ]
    },
    {
      "page": "mz_range",
      "title": "Get mass range with ppm",
      "topics": [
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      "page": "mz_vec_aggregate",
      "title": "Group m/Z from a vector based on tolerance",
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      "page": "search_db",
      "title": "Search DB egaint EXP",
      "topics": [
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      ]
    },
    {
      "page": "search_db_cpp",
      "title": "Search DB egaint EXP using cpp function",
      "topics": [
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      "page": "spectra_full",
      "title": "Spectra example",
      "topics": [
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      "page": "spectra_ms2",
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      "page": "string_from_element",
      "title": "Return a string from an element table",
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      "page": "valence_db",
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      "topics": [
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      ]
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