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This is the development version of PSMatch; for the stable release version, see PSMatch.

Handling and Managing Peptide Spectrum Matches

Bioconductor version: Development (3.20)

The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.

Author: Laurent Gatto [aut, cre] , Johannes Rainer [aut] , Sebastian Gibb [aut] , Samuel Wieczorek [ctb], Thomas Burger [ctb]

Maintainer: Laurent Gatto <laurent.gatto at>

Citation (from within R, enter citation("PSMatch")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

MS2 fragment ions HTML R Script
Understanding protein groups with adjacency matrices HTML R Script
Working with PSM data HTML R Script
Reference Manual PDF


biocViews Infrastructure, MassSpectrometry, Proteomics, Software
Version 1.9.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License Artistic-2.0
Depends S4Vectors
Imports utils, stats, igraph, methods, Matrix, BiocParallel, BiocGenerics, ProtGenerics(>= 1.27.1), QFeatures, MsCoreUtils
System Requirements
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Suggests msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat
Linking To
Depends On Me
Imports Me MSnbase, topdownr
Suggests Me MsDataHub
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package PSMatch_1.9.0.tar.gz
Windows Binary
macOS Binary (x86_64) PSMatch_1.9.0.tgz
macOS Binary (arm64) PSMatch_1.9.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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