Ion-mobility mass spectrometry is emerging as a powerful tool for studying the structures of less established protein assemblies. The method provides simultaneous measurement of the mass and size of intact protein assemblies, providing information not only on the subunit composition and network of interactions but also on the overall topology and shape of protein complexes. However, how the experimental parameters affect the measured collision cross-sections remains elusive. Here, we present an extensive systematic study on a range of proteins and protein complexes with differing sizes, structures, and oligomerization states. Our results indicate that the experimental parameters, T-wave height and velocity, influence the determined collision cross-section independently and in opposite directions. Increasing the T-wave height leads to compaction of the protein structures, while higher T-wave velocities lead to their expansion. These different effects are attributed to differences in energy transmission and dissipation rates. Moreover, by analyzing proteins in their native and denatured states, we could identify the lower and upper boundaries of the collision cross-section, which reflect the "maximally packed" and "ultimately unfolded" states. Together, our results provide grounds for selecting optimal experimental parameters that will enable preservation of the nativelike conformation, providing structural information on uncharacterized protein assemblies.