MRMPath, a system which processes protein sequences to create theoretical masses of peptide and their peptide fragments following digestion of the protein was developed. Experimentally, these fragments are created using enzymes prior to being processed in a mass spectrometer. In MRMPath, these fragments are created theoretically. MRMPath can process protein sequences from three different sources: 1) a protein involved in a pathway; MRMPath uses a data-mining, information extraction process that identifies proteins from a comprehensive list of pathways listed in the KEGG (Kyoto Encyclopedia of Genes and Genomes) web resource; 2) a protein that is stored in the UniProt repository of proteins, EXPASY; 3) a protein or peptide supplied by the user in a text-box. MRMPath is freely available on the Internet. Only an Internet browser is needed to access and use MRMPath. The system was designed for free use, mitigating the need for platform specific computer operating systems or also for the need to download and install software. MRMPath can be accessed at http://www.uab.edu/MRMPath.