SEQUENCE PATTERNS PRODUCED BY INCOMPLETE ENZYMATIC DIGESTION OR ONE-STEP EDMAN DEGRADATION OF PEPTIDE MIXTURES AS PROBES FOR PROTEIN DATABASE SEARCHES

Mass spectrometric peptide mapping of proteins isolated by polyacrylam ide gel electrophoresis is a rapid method for identifying proteins in sequence databases. A majority of tryptic peptide maps were found to c ontain pairs of peptide ion peaks separated by the molecular weight of the lysyl or arginyl residue. These peaks originate from amino acid s equence patterns such as Lys-Lys where trypsin has cleaved C-terminals to either one of the lysines. The peptide mass and the pattern define an N- or C-terminal sequence tag. Searching sequence databases by suc h a sequence tag results in only a moderate number of matches and sign ificantly reduces the number of database matches when used in combinat ion with a peptide mass map. Two N- or C-terminal sequence tags alone unambiguously identify a protein in most cases. The technique discusse d here is simple, does not require additional measurements, and increa ses the percentage of protein samples that can be identified by their mass maps alone. N-Terminal peptide sequence tags for database searchi ng can also be generated by manual one-step Edman degradation of the u nseparated peptide mixture.