omicverse.metabol.annotate_peaks

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omicverse.metabol.annotate_peaks#

omicverse.metabol.annotate_peaks(mz, *, polarity='positive', ppm=10.0, custom_adducts=None, mass_db=None)[source]#

Map a list of m/z peaks to candidate KEGG compounds via adduct search.

Parameters:

  • mz (ndarray) – 1-D array of experimental m/z values.

  • polarity (str (default: 'positive')) – "positive" or "negative" — picks the adduct list. For mixed modes, pass a merged list via custom_adducts.

  • ppm (float (default: 10.0)) – Mass-matching tolerance in parts per million. 5 ppm is typical for Orbitrap; 10–20 ppm for QTOF.

  • custom_adducts (Optional[list[tuple[str, float, str]]] (default: None)) – Override the default adduct list. Each entry is (name, delta_mass, sign_str).

  • mass_db (Optional[DataFrame] (default: None)) – Compound master table with at least mw, kegg, name columns. Defaults to ov.metabol.fetch_chebi_compounds() — ~54k ChEBI 3-star compounds with monoisotopic mass and KEGG/HMDB/LIPID MAPS cross-refs. Pass your own DataFrame to restrict the search space (e.g. only lipids, or a curated clinical panel).

Returns:

One row per (m/z, adduct, candidate KEGG) match. Columns: mz (input), adduct, kegg, name, delta_ppm. Multiple candidate matches per m/z are normal.

Return type:

pd.DataFrame

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