A new algorithm has been developed for extracting site-specific rate constants for hydrogen/deuterium (H/D) exchange in gas phase protonated amino acids, their clusters and peptides. The algorithm minimizes the mutual entropy or the Kullback–Leibler information divergence between the observed concentrations and the model. Electrospray ionization-mass spectrometry (ESI-MS) results from fast flow tube and Fourier transform ion cyclotron resonance (FT-ICR) experiments, respectively, were modeled. The results for protonated glycine were in excellent agreement with previous literature data. Four rate constants were found, three of them identical corresponding to the three equivalent hydrogen atoms of the protonated amine group and a fourth higher one corresponding to the single carboxyl hydrogen. New results for the proton-bound dimer of arginine demonstrated a single high site-specific rate constant and fourteen low ones. These results are in agreement with the ion–zwitterion structure of (arginine)2H+ that has a single carboxyl hydrogen atom.