MSstats is an R package for statistical relative quantification of proteins and peptides in global, targeted and data-independent proteomics. It handles shotgun, label-free and label-based (universal synthetic peptide-based) SRM (selected reaction monitoring), and SWATH/DIA (data independent acquisition) experiments. It can be used for experiments with complex designs (e.g. comparing more than two experimental conditions, or a time course).
Input for MSstats requires transition-level identified and quantified peaks information, including protein id, peptide id, transition id, label type (if labeling is used), condition name, biological replicate id, MS run, and intensity (quantified by either peak area or peak apex). The input tables can be exported from other software for mass spectrometer data, such as Skyline. MSstats provides functionalities for three types of analysis: (1) data processing and visualization for quality control, (2) model-based statistical analysis, in particular testing for differential protein abundance between condition and estimation of protein abundance in individual biological samples or conditions on a relative scale, and (3) model-based calculation of a sample size for a future experiment, while using the current dataset as a pilot study for variance estimation. The statistical analysis is based on a family of linear mixed-effects models. The analysis produces tables with numerical outputs, as well as visualization plots. MSstats package, example datasets with R scripts and documentation are available at http://www.msstats.org.