msPurity

msPurity is a vendor-independent R package designed for liquid chromatography (LC) and direct infusion (DI) tandem mass spectrometry (MS/MS or MS^2) in metabolomics. The tool calculates a precursor purity metric to assess the contribution of the selected precursor within an isolation window for MS^2 experiments. The metric is defined as the "intensity of a selected precursor divided by the summed intensity of the isolation window." It is interpolated at the recorded point of MS^2 acquisition using surrounding full-scan spectra. msPurity also offers options to remove isotopic peaks of the selected precursor and eliminate low abundance peaks believed to have limited contribution to the resulting MS^2 spectra. Additionally, the tool can account for the isolation efficiency of the mass spectrometer.