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A Mechanistic Study of the H/D Exchange Reactions of Protonated Arginine and Arginine-Containing Di- and Tripeptides Yiqun Huang, Joe A. Marini, John A. McLean,* Shane E. Tichy, and David H. Russell Department of Chemistry, The Laboratory for Biological Mass Spectrometry, Texas AM University, College Station, Texas, USA 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 H] ions with deuterated ammonia (ND ) were investigated by using 3 Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR), ion mobility-mass spectrometry (IM-MS), ab initio and density functional theory-based molecular orbital calcu- lations and molecular modeling. Three exchanges are observed for arginine and arginine- containing tri-peptide [M H] ions, whereas the di-peptide [M H] ions undergo a single H/D exchange. In addition, C-terminal methylation blocks H/D exchange of arginine and the arginine-containing peptide [M H] ions, and a single H/D exchange is observed for N-terminal acetylated arginine [M H] ions. A general mechanism for H/D exchange involving a collision complex that is best described as a “solvated salt-bridge” structure is proposed. (J Am Soc Mass Spectrom 2009, 20, 2049–2057) © 2009 American Society for Mass Spectrometry ydrogen/deuterium (H/D) exchange reactions are [15]. Valentine and Clemmer used ion mobility-mass frequently used to investigate the conformation- spectrometry to examine the conformation dependence related properties of solution-phase peptides and of H/D exchange reactions, and suggested that ion H pro