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Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Bioconductor version: Release (3.19)

The package provides statistical tools for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It provides multiple functionalities, including aata visualization, protein quantification and normalization, and statistical modeling and inference. Furthermore, it is inter-operable with other data processing tools, such as Proteome Discoverer, MaxQuant, OpenMS and SpectroMine.

Author: Devon Kohler [aut, cre], Ting Huang [aut], Meena Choi [aut], Mateusz Staniak [aut], Sicheng Hao [aut], Olga Vitek [aut]

Maintainer: Devon Kohler <kohler.d at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


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:

MSstatsTMT User Guide HTML R Script
Reference Manual PDF


biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 2.12.1
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License Artistic-2.0
Depends R (>= 4.2)
Imports limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate, plotly, htmltools
System Requirements
Bug Reports!forum/msstats
See More
Suggests BiocStyle, knitr, rmarkdown, testthat
Linking To
Depends On Me
Imports Me MSstatsPTM, MSstatsShiny
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package MSstatsTMT_2.12.1.tar.gz
Windows Binary
macOS Binary (x86_64) MSstatsTMT_2.12.1.tgz
macOS Binary (arm64) MSstatsTMT_2.12.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive