PSMatch is a simple package to load, process and analyse PSMs (Peptide-Spectrum Matches). The following references are a good way to get started with the package:
PSMto read and filter peptide-spectrum matches.
To install the package from Bioconductor, make sure you have the
BiocManager package, available from CRAN, and then run
Code in this package is partly composed of functions ported from
MSnbase with the goal to (1) make them more general and (2) integrate them with the R for Mass Spectrometry infrastructure.