MSQuant is a tool for quantitative proteomics/mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change. MSQuant’s main purpose is to make quantitation of proteins and peptides possible in the area of mass spectrometry/proteomics (science/analytical chemistry/molecular biology). E.g. an experiment where one heavy isotope-labelled sample from treated cells is compared to unlabelled, untreated cells to give quantitative answers about cellular processees.