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MSstats GUI for Statistical Anaylsis of Proteomics Experiments

Bioconductor version: Release (3.19)

MSstatsShiny is an R-Shiny graphical user interface (GUI) integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of experimental designs. These include data-dependedent acquisitions (DDA) which are label-free or tandem mass tag (TMT)-based, as well as DIA, SRM, and PRM acquisitions and those targeting post-translational modifications (PTMs). The application automatically saves users selections and builds an R script that recreates their analysis, supporting reproducible data analysis.

Author: Devon Kohler [aut, cre], Deril Raju [aut], Maanasa Kaza [aut], Cristina Pasi [aut], Ting Huang [aut], Mateusz Staniak [aut], Dhaval Mohandas [aut], Eduard Sabido [aut], Meena Choi [aut], Olga Vitek [aut]

Maintainer: Devon Kohler <kohler.d at>

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


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:

MSstatsPTM LabelFree Workflow HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, GUI, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, ShinyApps, Software, TwoChannel
Version 1.6.2
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2)
Imports shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly, data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics, mockery
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Suggests rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0), shinytest2
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Follow Installation instructions to use this package in your R session.

Source Package MSstatsShiny_1.6.2.tar.gz
Windows Binary
macOS Binary (x86_64) MSstatsShiny_1.6.2.tgz
macOS Binary (arm64) MSstatsShiny_1.6.2.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive