MSstats logo


MSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. It 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.

Main website, Bioconductor, Skyline external toolGithubManuscript.


Cardinal is an R package designed for efficient analysis of mass spectrometry-based imaging experiments. The capabilities include visualization of single and composit ion images, pre-processing (normalization, smoothing, baseline reduction, peak picking, filtering and alignment), as well as traditional and novel supervised and unsupervised methods such as image segmentation (clustering), principle components analysis, and partial least squares discriminant analysis.

Main website, Bioconductor, Github, Manuscript.



Matter is an R package designed for rapid prototyping of new statistical methods when working with larger-than-memory datasets on disk. Unlike related packages bigmemory and ff, which also work with file-backed larger-than-memory datasets, matter aims to offer strict control over memory and maximum flexibility with on-disk data structures, so it can be easily adapted to domain-specific file formats, including user-customized file formats.

Bioconductor, Github, Manuscript.