We investigate the gas-phase structures and fragmentation chemistry of two isomeric sodium-cationized carbohydrates using combined tandem mass spectrometry, hydrogen/deuterium exchange experiments, and computational methods. Our model systems are the glucose-based disaccharide analytes cellobiose (β-d-glucopyranosyl-(1 → 4)-d-glucose) and gentiobiose (β-d-glucopyranosyl-(1 → 6)-d-glucose). These analytes show substantially different tandem mass spectra. We characterize the rate-determining barriers to both the glycosidic and structurally-informative cross-ring bond cleavages. Sodiated cellobiose produces abundant Y and B peaks. Our deuterium labelling and computational chemistry approach provides evidence for 1,6-anhydroglucose B ion structures rather than the 1,2-anhydroglucose and oxacarbenium ion structures proposed elsewhere. Unlike those earlier proposals, this finding is consistent with the experimentally observed B/Y branching ratios. In contrast to cellobiose, sodiated gentiobiose primarily fragments by cross-ring cleavage to form various A ion types. Fragmentation is facilitated by ring-opening at the reducing end which enables losses of CHO oligomers. Deuterium labelling and theory enables rationalization of these processes. Theory and experiment also support the importance of consecutive fragmentation processes at higher collision energies.