The probe of intramolecular interactions in gas-phase biomolecules using the combination of proton transfer reactions, hydrogen/deuterium exchange reactions, and molecular orbital calculations is illustrated by exploring the nearest-neighbor interactions in protonated peptides. The interactions, specifically -NH2 ... H+... O=C and C=O ... H+... O=C, are investigated with peptides that model them. The compounds that include beta-Ala, beta-Ala-Gly, and Gly-beta-Ala, Ala-Gly and Gly-Ala are used to evaluate the structural and electronic factors that are involved in the protonation of the terminal amine. Similarly, N-acetylglycine and N-acetylglycine amide are used to evaluate carbonyl group interactions in the peptide backbone. The beta-alanine residue on the terminal amine is found to increase the gas-phase basicity and decrease the H/D exchange reactivity of the protonated compound relative to analogous compounds containing only alpha-amino acids. A beta-alanine residue on the C-terminus produces compounds with similar gas-phase basicity and H/D exchange behavior as those with alpha-amino acids. The gas-phase basicity and H/D exchange behavior of the acetylglycines point to stronger intramolecular hydrogen bonding in the amide derivative than in the acid. An amide carbonyl has a greater intrinsic basicity than a carboxylic carbonyl. An analysis proposed by Meot-Ner is used to separate electronic effects from structural effects in the two types of protonation sites.