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A stable isotope coding strategy is described for the analysis of all types of tryptic peptides, including those that areN-terminally blocked and from the C-terminus of proteins. The method exploits differential derivatization of amine and carboxylgroups generated during proteolysis as a means of coding. Carboxyl groups produced during proteolysis incorporate
18
O from H
218
O. Peptides from the C-terminus of proteins were not labeled with
18
O unless they contained a basic C-terminal amino acid. Primary amines form controls, and experimental samples were differentiallyacylated after proteolysis with either
1
H
3
- or
2
H
3
-
N
-acetoxysuccinamide. When these two types of labeling were combined, unique coding patterns were achieved for peptides arisingfrom the C-termini and blocked N-termini of proteins.