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

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: Development (3.20)

MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

Author: Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker, Lieven Clement and Pascal Maas.

Maintainer: Laurent Gatto <laurent.gatto at>

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


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:

A short introduction to `MSnbase` development HTML R Script
Base Functions and Classes for MS-based Proteomics HTML R Script
MSnbase benchmarking HTML R Script
MSnbase IO capabilities HTML R Script
MSnbase: centroiding of profile-mode MS data HTML R Script
Reference Manual PDF


biocViews DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.31.1
In Bioconductor since BioC 2.8 (R-2.13) (13.5 years)
License Artistic-2.0
Depends R (>= 3.5), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.29.3), S4Vectors, ProtGenerics(>= 1.29.1)
Imports MsCoreUtils, PSMatch, BiocParallel, IRanges(>= 2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID(>= 1.5.2), digest, lattice, ggplot2, scales, MASS, Rcpp
System Requirements
Bug Reports
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Suggests testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata(>= 1.7.1), msdata(>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle(>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny, magrittr, SummarizedExperiment
Linking To Rcpp
Depends On Me bandle, msmsEDA, msmsTests, pRoloc, pRolocGUI, qPLEXanalyzer, synapter, DAPARdata, pRolocdata, RforProteomics
Imports Me CluMSID, DAPAR, DEP, MSnID, MSstatsQC, peakPantheR, PrInCE, ptairMS, RMassBank, squallms, topdownr, xcms, qPLEXdata
Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, msPurity, msqrob2, proDA, qcmetrics, wpm, msdata, enviGCMS, LCMSQA, pmd, RAMClustR
Links To Me
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Package Archives

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

Source Package MSnbase_2.31.1.tar.gz
Windows Binary
macOS Binary (x86_64) MSnbase_2.31.1.tgz
macOS Binary (arm64) MSnbase_2.31.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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