Protein interaction networks are becoming an increasingly important area of research within structural genomics. Here we present an ion mobility-mass spectrometry approach capable of distinguishing the overall subunit architecture of protein complexes. The approach relies on the simultaneous measurement in the gas phase of the mass and size of intact assemblies and subcomplexes. These data are then used as restraints to generate topological models of protein complexes. To test and develop our method, we have chosen two well-characterized homo-dodecameric protein complexes: ornithine carbamoyl transferase and glutamine synthetase. By forming subcomplexes related to the comparative strength of the subunit interfaces, acquiring ion mobility data, and subsequent modeling, we show that these "building blocks" retain their native interactions and do not undergo major rearrangement in either solution or gas phases. We apply this approach to study two subcomplexes of the human eukaryotic initiation factor 3, for which there is no high-resolution structure.