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

Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Bioconductor version: Development (3.19)

A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.

Author: Meena Choi [aut, cre], Mateusz Staniak [aut], Tsung-Heng Tsai [aut], Ting Huang [aut], Olga Vitek [aut]

Maintainer: Meena Choi <mnchoi67 at gmail.com>

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


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:

MSstats: Protein/Peptide significance analysis HTML R Script
Reference Manual PDF


biocViews ImmunoOncology, MassSpectrometry, Normalization, Proteomics, QualityControl, Software, TimeCourse
Version 4.11.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License Artistic-2.0
Depends R (>= 4.0)
Imports MSstatsConvert, data.table, checkmate, MASS, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel, gplots, marray, stats, grDevices, graphics, methods, statmod
System Requirements
URL http://msstats.org
Bug Reports https://groups.google.com/forum/#!forum/msstats
See More
Suggests BiocStyle, knitr, rmarkdown, tinytest, covr, markdown
Linking To Rcpp, RcppArmadillo
Depends On Me
Imports Me artMS, MSstatsBig, MSstatsLiP, MSstatsPTM, MSstatsShiny, MSstatsTMT
Suggests Me
Links To Me
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Package Archives

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

Source Package MSstats_4.11.0.tar.gz
Windows Binary MSstats_4.11.0.zip
macOS Binary (x86_64) MSstats_4.11.0.tgz
macOS Binary (arm64) MSstats_4.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSstats
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSstats
Bioc Package Browser https://code.bioconductor.org/browse/MSstats/
Package Short Url https://bioconductor.org/packages/MSstats/
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