The msPurity R package was originally developed to assess the contribution of the targeted precursor in a fragmentation isolation window using a metric called “precursor ion purity”. See associated paper (Lawson et al. 2017).
A number of updates have been made since the original paper and the full functionality of msPurity now includes the following:
What we call “Precursor ion purity” is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the time of the MS/MS acquisition. The calculation is similar to the “Precursor Ion Fraction”" (PIF) metric described by (Michalski, Cox, and Mann 2011) for proteomics with the exception that purity here is interpolated at the recorded point of MS/MS acquisition using bordering full-scan spectra. Additionally, low abundance ions that are remove that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the contributing ions.
There are 3 main classes used in msPurity
Given a vector of LC-MS/MS or DIMS/MS mzML file paths the precursor ion purity of each MS/MS scan can be calculated and stored in the purityA S4 class object where a dataframe of the purity results can be accessed using the appropriate slot (
The calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window and is performed before and after the MS/MS scan of interest and interpolated at the recorded time of the MS/MS acquisition. See below