Practical Methods for Deuterium Exchange/Mass Spectrometry

Deuterium exchange, also called hydrogen exchange, has been used for decades in experiments aimed at elucidating structural information and investigating protein folding (1 –4 ). Deuterium exchange takes place when any acidic proton in a protein molecule exchanges for a deuteron in bulk solvent. Exchange rates for surface-exposed sites depend on factors affecting acidity, while at buried sites, rates depend on the structure and flexibility of the surrounding tertiary structure in permitting access of those protons to bulk solvent. Hydrogen exchange has been detected by 3 H incorporation on the whole-protein scale and by nuclear magnetic resonance on the single-proton scale. More recently, deuterium exchange has been interfaced with mass spectrometry (DE-MS) to study large molecules and large multimolecular complexes (5 –7 ). In these experiments, the exchange of a proton for a deuteron is measured as an increase in the mass of a proteolytically generated peptide of one atomic mass unit. More important, when deuterium exchange is analyzed by MS according to the protocol presented here, nearly all side chain hydrogens back-exchange from deuterium to protium during the analysis, so that primarily the backbone amide hydrogens are monitored.