DOI: 10.18129/B9.bioc.MSnbase    

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: Release (3.6)

MSnbase provides infrastructure to manipulation, processing and visualisation 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 and Martina Fisher.

Maintainer: Laurent Gatto <lg390 at>

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


HTML R Script A short introduction to `MSnbase` development
HTML R Script Base Functions and Classes for MS-based Proteomics
HTML R Script MSnbase IO capabilities
HTML R Script MSnbase2 benchmarking
PDF   Reference Manual
Text   NEWS


biocViews DataImport, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.4.2
In Bioconductor since BioC 2.8 (R-2.13) (7 years)
License Artistic-2.0
Depends R (>= 3.1), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.11.11), BiocParallel, ProtGenerics(>= 1.9.1)
Imports plyr, IRanges, preprocessCore, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID(>= 1.5.2), digest, lattice, ggplot2, S4Vectors, XML, Rcpp
LinkingTo Rcpp
Suggests testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata(>= 1.7.1), msdata(>= 0.12.2), roxygen2, rgl, rpx, AnnotationHub, BiocStyle(>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny
Depends On Me msmsEDA, msmsTests, ProCoNA, pRoloc, pRolocdata, pRolocGUI, proteoQC, RforProteomics, synapter, xcms
Imports Me DAPAR, DAPARdata, DEP, MSnID, MSstats, MSstatsQC, Pbase, ProteomicsAnnotationHubData, RMassBank, topdownr
Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, qcmetrics, readat, rpx
Build Report  

Package Archives

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

Source Package MSnbase_2.4.2.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) MSnbase_2.4.0.tgz
Source Repository git clone
Package Short Url
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: