The R/Bioconductor PSMatch package models peptide-protein relations in proteomics data, suggesting effective analysis methods.
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 fragments and, in conjunction with the Spectra package,annotate and visualise MS2 scans.
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Deflandre et al. (2025) studied this question.
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