Protein identification using mass spectrometric information

In an effort to gain an understanding of the value of the information in different mass spectrometric measurements for protein identification, the genome of Saccharomyces cerevisiae was studied in silico. We calculate how constraining the knowledge of the mass of a proteolytic peptide is as a function of mass and mass accuracy. We also assess the value for protein identification of additional information concerning a proteolytic peptide, including the presence or absence of a given amino acid, the number of exchangeable hydrogens, the N-terminal sequence, and the masses of mass spectrometrically produced fragment ions. Knowledge of the relative value of these different constraints is useful in the design of efficient protein identification experiments. Finally, we describe a software tool, PepFrag, for searching protein and DNA sequence databases that can use different types of mass spectrometric information to restrict the search.