In 1994, however, an alternative approach was proposed: reconstructing the peptide sequence by comparing the observed MS2 spectrum to peptides from a given database. In this procedure, a database of proteins is digested in silico into peptides by using enzymatic cleavage rules. For each observed spectrum, all database peptides with masses close to the precursor mass associated with the spectrum are considered "candidate peptides." Here, the threshold for "close" masses depends on the precision with which the mass spectrometer measures the precursor mass. The key to the database search is a score function that evaluates how well the observed spectrum matches the peptide. This score function typically involves creating a theoretical spectrum on the basis of the peptide's amino acid sequence. This approach, pioneered by