From Bioconductor: MSstats

MSstats 4.2.0 (Bioconductor version : Release 3.14, R version >= 4.1)

#Type the following in R console window
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MSstats") 
library(MSstats)

The following packages are not required but are mentioned in the extensions section:

  • MSstatsTMT: detects differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
  • MSstatsPTM: detects differentially abundant PTMs in shotgun mass spectrometry-based proteomic experiments
  • MSstatsLiP:  tool for LiP peptide and protein significance analysis
  • MSstatsLOBD: assay characterization metrics (LOB and LOD)
  • MSstatsSampleSize: Simulation-based sample size estimation for classification
  • MSstatsQC: Longitudinal system suitability monitoring and quality control for proteomic experiments
BiocManager::install("MSstatsTMT")
BiocManager::install("MSstatsPTM")
BiocManager::install("MSstatsLiP")
BiocManager::install("MSstatsLOBD")
BiocManager::install("MSstatsSampleSize")
BiocManager::install("MSstatsQC")
From GitHub: MSstats

MSstats Bioconductor development version : link

install.packages("devtools") # if you have not installed "devtools" package
devtools::install_github("Vitek-Lab/MSstats")


The development version of the package MSstats is the most recent and is available here. The versioning of the main package is updated twice a year, to synchronize with the Bioconductor release.

For use via Skyline external tool

To use MSstats via a graphical user interface, as an external tool in Skyline, please see the info here. (known issues and proposed solutions)