What is a Peptide Fragment to DO?
Introduction Peptide tandem mass spectrometry is the cornerstone of protein identification in proteomics. Recently, however, it has been shown that b ions can engage in re-arrangement processes that result in cyclic structures [1]. If these cyclic structures subsequently open up at a different bond than where they were initially formed, the resulting fragment ions no longer reflect the original amino acid sequence. The prevalence of such unwanted reactions appears to be much more important than previously acknowledged, with ~40% unidentified product ions in typical peptide collision-induced dissociation (CID) spectra. In a recent infrared (IR) spectroscopy study on CID products of the pentapeptide Leu-enkephalin we have shown that a mixture of linear and cyclic structures are formed both for b4 and a4 product ions [2]. Here, we propose to systematically characterize CID products using infrared (IR) spectroscopy and gas-phase H/D exchange, to establish trends for the cyclization chemist
