`msmu._tools._precursor_purity`

PrecursorPurityCalculator

PrecursorPurityCalculator(tolerance=20, unit_ppm=True)

A class to calculate precursor isolation purity from mzML files or MuData objects. This class can be initialized with a tolerance value and whether to use ppm for the calculation. This class is a wrapper around the OpenMS PrecursorPurity class and provides methods to calculate. pyopenms: https://pyopenms.readthedocs.io/en/latest/py-modindex.html#module-pyopenms.PrecursorPurity

Attributes:

Name	Type	Description
`tolerance`	`float`	Tolerance for precursor purity calculation.
`unit_ppm`	`bool`	Whether to use ppm for tolerance.
`mzml`	`Path \| None`	Path to the mzML file.
`exp`	`MSExperiment \| None`	OpenMS MSExperiment object loaded from the mzML file.
`exp_src`	`Path \| None`	Source path of the loaded MSExperiment.
`exp_mtime`	`float \| None`	Last modified time of the mzML file.
`lock`	`Lock`	Thread lock for thread-safe access to the MSExperiment.

from_mudata `classmethod`

from_mudata(mdata, tolerance=20.0, unit_ppm=True)

Initialize PrecursorPurityCalculator from a MuData object.

Parameters:

Name	Type	Description	Default
`mdata`	`MuData`	MuData object containing PSM data.	required
`tolerance`	`float`	Tolerance for precursor purity calculation.	`20.0`
`unit_ppm`	`bool`	Whether to use ppm for tolerance.	`True`

PurityResult

PurityResult(purity, scan_num, filename)

to_df

to_df()

Convert the PurityResult to a pandas DataFrame.

Returns:

Type	Description
`DataFrame`	pd.DataFrame: DataFrame containing purity, scan_num, and filename.

compute_precursor_purity

compute_precursor_purity(mzml_paths, tolerance=20.0, unit_ppm=True)

Calculate precursor isolation purity for all MS2 scans in the given mzML file.