The gas-phase H/D exchange reactions of arginine (R) and arginine-containing di-and tri-peptide (gly-arg (GR), arg-gly (RG), gly-gly-arg (GGR), gly-arg-gly (GRG) and arg-gly-gly (RGG)) [M ϩ H] ϩ ions with deuterated ammonia (ND 3 ) were investigated by using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR), ion mobility-mass spectrometry (IM-MS), ab initio and density functional theory-based molecular orbital calculations and molecular modeling. Three exchanges are observed for arginine and argininecontaining tri-peptide [M ϩ H] [15]. Valentine and Clemmer used ion mobility-mass spectrometry to examine the conformation dependence of H/D exchange reactions, and suggested that ion conformation has a significant effect on H/D exchange [16,17].Compared with the intensive investigations carried out on the conformational characterization of peptides and proteins using solution-phase H/D exchange reaction chemistry, the corresponding gas-phase studies are much less comprehensive. The key question regarding gas-phase H/D exchange is: does the "solvent molecule," i.e., H/D exchange reagent, sample the entire "available surface area" of the peptide/protein ion, or is H/D exchange limited by other factors? For example, are all solution phase labile hydrogen atoms exchangeable in the gas phase and are the reactivities of all exchangeable hydrogen atoms similar? Dookeran and Harrison studied the H/D exchange reactions of 18 naturally occurring amino acids and selected di-and tripeptides with ND 3 , and reported that amino acid [M ϩ H] ϩ ions containing hydroxyl, carboxyl, and amine side chains exchange all labile hydrogen atoms, whereas the side-chain hydrogen atoms of glutamine, asparagine, and histidine [M ϩ H] ϩ ions exchange less readily, and tyrosine and arginine [M ϩ H] ϩ ions do not undergo significant exchange [18]. In a separate study, Lebrilla et al. found that the carboxylic acid group of glycine and aliphatic amino acid [M ϩ H] ϩ ions (alanine, valine, leucine, isoleucine, and proline) undergo H/D exchange three to 10 times faster than the NAddress reprint requests to Dr.