Capsules derived from the reversible assembly of calixarene tetraureas have been characterized by electrospray ionization mass spectrometry. Ion labeling was achieved through the encapsulation of ammonium ions as guest molecules. The gas-phase ion structure of the parent calixarene was determined by isotope pattern analysis, inclusion of labeled guests, and collision experiments. Competition experiments with different guest ions revealed a clear dependence of the encapsulation process on the size and shape of the guest ions. The formation of several different heterodimeric capsules, a covalently bridged capsule, and larger dumbbell-like aggregates containing two and three charged guests has been observed. The results parallel previous findings from NMR experiments in solution and thus support the validity of the MS method for characterization of these complexes in the gas phase.