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Targeted Annotation

This example creates a tiny target list, generates expected adduct candidates, and then annotates a peak table against those adduct hypotheses.

The important workflow is:

  1. Create a target table with molecular formulas and retention times.
  2. Select adduct definitions from emzed.adducts.
  3. Build a candidate space with emzed.targeted.solution_space.
  4. Annotate peaks with emzed.annotate.annotate_adducts.
"""Create a targeted adduct search space and annotate matching peaks."""

import emzed


def main():
    targets = emzed.Table.create_table(
        ["mf", "rt"],
        [str, emzed.RtType],
        rows=[["H2O", 10.0]],
    )
    targets.add_enumeration()

    adducts = emzed.Table.stack_tables(
        [
            emzed.adducts.M_plus_Br,
            emzed.adducts.Two_M_plus_H,
            emzed.adducts.M_plus_ACN_plus_H,
            emzed.adducts.M_minus_H,
        ]
    )
    adducts.drop_columns("id")
    adducts.add_enumeration()

    candidates = emzed.targeted.solution_space(targets, adducts, 0.99)
    peaks = candidates.extract_columns("target_id", "rt", "mz", "adduct_name")
    peaks.rename_columns(adduct_name="original_adduct_name")

    annotated = emzed.annotate.annotate_adducts(
        peaks,
        adducts,
        mz_tol=2e-5,
        rt_tol=5.0,
        explained_abundance=0.99,
    ).sort_by("adduct_cluster_id")

    print(annotated.extract_columns("mz", "rt", "adduct_name", "adduct_cluster_id"))


if __name__ == "__main__":
    main()

found 0 gaps > rt_tol in rt values

process 1 out of 1
    process 8 peaks in rt range 0.0..11.0
    build up lookup table
    look for matches
    found matches

mz           rt        adduct_name  adduct_cluster_id
MzType       RtType    str          int              
-----------  --------  -----------  -----------------
  96.929451    0.17 m  M+Br                         0
  98.927404    0.17 m  M+Br                         0
  37.028407    0.17 m  2M+H                         0
  60.044391    0.17 m  M+ACN+H                      0
  61.047746    0.17 m  M+ACN+H                      0
  61.041426    0.17 m  M+ACN+H                      0
  17.003289    0.17 m  M-H                          0