Precursor isolation purity

Precursor isolation purity (PIP) is a metric that quantifies the proportion of the target precursor ion signal relative to the total signal within the isolation window during MS/MS acquisition. High PIP values indicate that the isolated precursor is relatively free from co-isolated contaminants, which is crucial for accurate quantification, especially in isobaric labeling experiments like TMT.

In msmu, PIP is calculated using the compute_precursor_isolation_purity() function, which uses pyopenms (Röst et al., 2014) to analyze MS1 spectra and determine the purity of each precursor ion.

mdata = mm.tl.compute_precursor_isolation_purity(
    mdata,
    mzml_paths=["/path/to/mzml/files"],  # path to mzML files
    tolerance=20,                        # mass tolerance
    unit_ppm=True                        # mass tolerance in ppm
    )

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.