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

TLDR

MSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry‑based proteomics. Version 2.0 supports label‑free and label‑based workflows, data‑dependent, targeted and data‑independent acquisition, and uses linear mixed models to output lists of differentially abundant peptides or proteins and abundance summaries. MSstats can be accessed as an external tool in Skyline and used via a graphical user interface. Code, documentation, and example datasets are available open‑source at www.msstats.org under the Artistic‑2.0 license.

Abstract

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.The code, the documentation and example datasets are available open-source at www.msstats.org under the Artistic-2.0 license. The package can be downloaded from www.msstats.org or from Bioconductor www.bioconductor.org 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.