Achieving strong host–guest interactions between synthetic hosts and hydrophilic guests in solution is challenging because solvation effects overwhelm other effects. To resolve this issue, we transferred complexes of cucurbituril (CB) and monosaccharides to the gas phase and report here their intrinsic host–guest chemistry in the absence of solvation effects. It was observed that effective host–guest interactions in the gas phase mediated by ammonium cations allow the differentiation of the monosaccharide isomers in complex with CB upon vibrational excitation. The potential of the unique observation was extended to a quantitative supramolecular analytical method for the monosaccharide guests. The combination of host–guest chemistry and phase transfer presented in this study is an effective approach to overcome current limitations in supramolecular chemistry.