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 polyacrylamide gel electrophoresis is a rapid method for identifying proteins in sequence databases. A majority of tryptic peptide maps were found to contain pairs of peptide ion peaks separated by the molecular weight of the lysyl or arginyl residue. These peaks originate from amino acid sequence 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 such a sequence tag results in only a moderate number of matches and significantly reduces the number of database matches when used in combination with a peptide mass map. Two N- or C-terminal sequence tags alone unambiguously identify a protein in most cases. The technique discussed here is simple, does not require additional measurements, and increases the percentage of protein samples that can be identified by their mass maps alone. N-Terminal peptide sequence tags for database searching can also be generated by manual one-step Edman degradation of the unseparated peptide mixture.