roteinProphet(TM) automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST. Importantly, it addresses two critical issues: (1) Peptides corresponding to 'single-hit' proteins (those to which no other peptides correspond) are less likely to be correct that those corresponding to 'multi-hit' proteins. (2) Many peptides are present in more than a single database protein entry.