MassSorter is a software tool that sorts, systemizes, and analyzes data from peptide mass fingerprinting (PMF) experiments on proteins with known amino acid sequences. Several experiments can be simultaneously analyzed for sequence coverage and posttranslational modifications occurring during sample handling, induced chemical modifications, and unexpected cleavages. Experimental m/z values are compared with m/z values from an in silico digestion, taking modifications into account. Filters can be defined by users for marking autolytic protease peaks and other contaminating peaks. MassSorter functions as a database of all the detected peptides. It includes tools for visualization of the results, such as sequence coverage, accuracy plots, statistics, and 3D models.