The increasing complexity of self-assembled supramolecules generates the need for analytical techniques that can accurately elucidate their structures. Here, we explore the ability of tandem mass spectrometry to deliver structural information on a series of self-sorted crown ether/ammonium pseudorotaxanes. Of these intertwined molecules, different charge states are accessible and the effects of Coulomb interactions on the fragmentation pattern can be examined. Three different cases can be distinguished: (1) one or more counterions are present in the complex and compete with the crown for binding to the ammonium ion. This destabilizes the supramolecular bond. (2) In multiply charged complexes, charge repulsion significantly alters the fragmentation behavior as compared with singly charged ions. (3) If guest and host are both charged, the supramolecular bond becomes very weak. The different charge states provide different pieces of information about the supramolecules under study. Although singly charged complexes provide data on the building block connectivity, the doubly charged analogs are more reliable with respect to complex stoichiometry. As there are several factors which may cause differences in the gas phase and solution behavior of supramolecules (the presence and absence of solvation, changes in the strength of non-covalent interactions upon ionization), it is important to establish well understood correlations between the complexes' gas-phase behavior and their solution structures. A more detailed understanding will help to characterize the structures of even more complex supramolecular architectures by mass spectrometry.