`msmu.tl.compute_precursor_isolation_purity`

Calculate precursor isolation purity for PSMs in the given MuData object and mzML file.

Parameters:

Name	Type	Description	Default
`mdata`	`MuData`	`MuData` object containing PSM data.	required
`mzml_paths`	`str \| Path \| list`	Full path(s) to the mzML file.	required
`tolerance`	`float`	Tolerance for precursor purity calculation. Default is `20`.	`20.0`
`unit_ppm`	`bool`	Whether to use ppm for tolerance. Default is `True`.	`True`

Returns:

Type	Description
`MuData`	`md.MuData`: `MuData` object containing purity results.

Notes

Requires psm.var columns filename and scan_num and matching local mzML files. Returns a copy with scores in psm.var["purity"]; the input is unchanged. pyopenms (Röst et al., 2014) is loaded at execution time. For standalone results and plotting, see compute_precursor_isolation_purity_from_mzml.

Examples:

import msmu as mm
mdata = mm.tl.compute_precursor_isolation_purity(mdata, ["sample.mzML"])

References

Röst, H. L., Schmitt, U., Aebersold, R., and Malmström, L. pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics 14(1), 74–77 (2014). https://doi.org/10.1002/pmic.201300246.