Many proteomic experiments require selective labeling of either N- or C-termini of proteins and recovery of terminal peptides. Although N-termini can be selectively labeled, selective labeling of protein C-termini has not been possible due to the difficulty in discriminating between the carboxyl group on the C-terminus versus that on aspartate and glutamate residues. Here we describe the first simple proteomic approach for positive selection of protein C-termini, Profiling Protein C-Termini by Enzymatic Labeling (ProC-TEL). ProC-TEL uses carboxypeptidase Y and other readily available reagents to selectively add an affinity tag to protein C-termini and to capture C-terminal peptides from complex cell lysates for mass spectrometry (MS) identification. Using ProC-TEL, we identify novel C-terminal processing and internal proteolytic cleavage events. These results indicate that ProC-TEL provides a straightforward approach for profiling C-terminal peptides and identifying protein processing in complex biological samples.