MSstats () is an open-source R-package for peptide and protein quantification in mass spectrometry-based proteomics. MSstats supports multiple data acquisition types: data-dependent acquisition (DDA) -both LFQ and label-based workflows-, data-independent acquisition (DIA) and targeted approaches. It uses a set of flexible linear mixed models to summarize the protein or peptide abundance in a single biological replicate or condition and perform the relative quantification of proteins across conditions. A simple tabular file containing the intensity of the identified peptides and proteins is needed as input. MSstats provides multiple adapters to transform the output of proteomics analysis tools like MaxQuant, Skyline or OpenMS into MSstats input format. MSstats starts from the peptide intensities obtained from the identification/quantitation tool and transforms those original intensities into normalized values using methods such as equalize median or quantiles. Remarkably, MSstats is one of the most documented and actively maintained tools for downstream analysis of proteomics data.