Mass spectrometry (MS) has been used to study protein complexes in the gas phase since early 1990s. The speed and sensitivity that comes with MS analysis has made it integral to the fields of proteomics and structural biology. The challenge is to extend the technology and methodology to characterize the protein structure, from primary to quaternary structure, rapidly and effectively by means of MS. Tandem MS, where ions of interest are subjected to collisional activation that yields fragmentation, plays a vital role in structural characterization of biomolecules. Collision induced unfolding (CIU) is a collisional activation method in which we monitor the unfolding of protein complexes in the gas phase with the aid of ion mobility (IM) platform coupled to MS. In our group, we use both Synapt G1 and G2 traveling wave IM-MS instruments implementing CIU to study protein structure classification, protein stability, and the mechanism of unfolding in protein assemblies.