DOI: 10.18129/B9.bioc.MSnbase  

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 (3.18)

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 "4.3") 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.


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biocViews DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.27.0
In Bioconductor since BioC 2.8 (R-2.13) (12 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, BiocParallel, IRanges(>= 2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID(>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS, Rcpp
LinkingTo Rcpp
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, shiny, magrittr, SummarizedExperiment
Depends On Me bandle, DAPARdata, MobilityTransformR, msmsEDA, msmsTests, pRoloc, pRolocdata, pRolocGUI, qPLEXanalyzer, RforProteomics, synapter, xcms
Imports Me cliqueMS, CluMSID, DAPAR, DEP, MSnID, MSstatsQC, peakPantheR, PrInCE, ptairMS, qPLEXdata, RMassBank, topdownr
Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, msdata, msPurity, msqrob2, proDA, qcmetrics, wpm
Links To Me
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