Data for 'PSMatch: an R/Bioconductor package to explore proteomics identification data.'

This archive stores the files used for the demonstration of the PSMatch package. The mzML file contains the observed spectra and was downloaded from the PRIDE repository PXD039419 . The .tsv file contains the identification data (PSMs) and was generated by the search engine Sage v.0.14.6. The .json file contains the search engine parameters that were used to generate the PSMs. We present the R/Bioconductor PSMatch package, that helps proteomics practitioners to load, manage and handle peptide spectrum matches. It provides functions to model peptide-protein relations, visualise these as graphs and make informed decisions about shared peptide filtering. The package also provides functions to calculate and, in conjunction with the Spectra package, annotate and visualise MS2 scans.