MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

Bioinformatics. 2014 Sep 1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305. Epub 2014 May 2.


MSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows and data-dependent, targeted and data-independent spectral acquisition. It takes as input identified and quantified spectral peaks, and outputs a list of differentially abundant peptides or proteins, or summaries of peptide or protein relative abundance. MSstats relies on a flexible family of linear mixed models.

Availability and implementation: The code, the documentation and example datasets are available open-source at under the Artistic-2.0 license. The package can be downloaded from or from Bioconductor and used in an R command line workflow. The package can also be accessed as an external tool in Skyline (Broudy et al., 2014) and used via graphical user interface.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Data Interpretation, Statistical
  • Mass Spectrometry / methods*
  • Peptides / analysis
  • Peptides / chemistry
  • Proteins / analysis
  • Proteins / chemistry
  • Proteomics / methods*
  • Software*


  • Peptides
  • Proteins