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MSnbase specifications


Unique identifier OMICS_08555
Name MSnbase
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.6.4
Stability Stable
methods, gplots, testthat, SummarizedExperiment, BiocParallel, rmarkdown, AnnotationHub, shiny, magrittr, rgl, gridExtra, zoo, BiocStyle(>=2.5.19), ProtGenerics(>=1.9.1), knitr(>=1.1.0), microbenchmark, BiocGenerics(>=0.7.1), R(>=3.1), Biobase(>=2.15.2), mzR(>=2.13.6), pryr, rols, Rdisop, pRoloc, pRolocdata(>=1.7.1), msdata(>=0.19.3), roxygen2, rpx, imputeLCMD, norm
Maintained Yes




No version available



  • person_outline Laurent Gatto
  • person_outline Bernhard Y. Rerd

Publications for MSnbase

MSnbase citations


Spatial Tissue Proteomics Quantifies Inter and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC)*

PMCID: 5880102
PMID: 29363612
DOI: 10.1074/mcp.RA117.000189

[…] Both TMT and DIA data were analyzed using the same R procedures based on the MSnbase package (). Reporter ion (TMT) and peptide (DIA) intensities were log2-transformed and normalized using the vsn package (). Peptide-level data were summarized into their respective protein gro […]


Landscape of nuclear transport receptor cargo specificity

Mol Syst Biol
PMCID: 5740495
PMID: 29254951
DOI: 10.15252/msb.20177608

[…] ed. The intensity per protein of the proteinGroups.txt output of MaxQuant was used for further analysis. All comparative analyses were performed using R version 3.2.2. (R Core Team, ). The R packages MSnbase (Gatto & Lilley, ) was used for processing proteomics data, and the included package imputeLCMD was used for imputing missing values based on the definitions for missing at random (MAR) and mi […]


A draft map of the mouse pluripotent stem cell spatial proteome

Nat Commun
PMCID: 4729960
PMID: 26754106
DOI: 10.1038/ncomms9992

[…] The Bioconductor packages MSnbase and pRoloc for the R statistical programming language were used for handling of the quantitative proteomics data and the protein-localization prediction. We employed the use of the full pRoloc […]


Visualization of proteomics data using R and Bioconductor

PMCID: 4510819
PMID: 25690415
DOI: 10.1002/pmic.201400392

[…] to operate on input-specific data types (called classes) to produce custom visualizations. Using our example data stored in an MSnSet, a data container for quantitative proteomics data defined in the MSnbase package [], invoking the dedicated MAplot function produces all 15 pairwise MA plots (see the companion vignette for details). The isobar package also defines a specific MA plotting function t […]


The mzTab Data Exchange Format: Communicating Mass spectrometry based Proteomics and Metabolomics Experimental Results to a Wider Audience*

PMCID: 4189001
PMID: 24980485
DOI: 10.1074/mcp.O113.036681

[…] t will be available from version 1.4.2 onward. The converter is implemented as a plugin for the Perseus software package.mzTab read and write support has also been added to the R/Bioconductor package MSnbase (), from version 1.5.6. It can seamlessly import data stored in mzTab files, including quantitative data and metadata, into flexible object classes to subsequently apply contemporary state-of- […]


LXtoo: an integrated live Linux distribution for the bioinformatics community

BMC Res Notes
PMCID: 3461469
PMID: 22813356
DOI: 10.1186/1756-0500-5-360

[…] omparison, Chimera [] for molecular assemblies, docking and conformational ensembles, Gromacs [] for molecular dynamics, Cytoscape [] and igraph for network analysis, MeV for microarray analysis, and MSnbase [] for processing MS-based proteomics data, to name a few. LXtoo is trying to integrate software to provide analysis solutions. For instance, microarray data analysis [] and network modelling […]


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MSnbase institution(s)
Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
MSnbase funding source(s)
Supported by BBSRC Tools and Resources Development Fund (Award BB/GO24618/1) and the European Union 7th Framework Program (PRIME-XS project, grant agreement number 262067).

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