Mass spectrometry (MS) has evolved as an analytical technique to effectively investigate biological constituents and in particular, non-covalent protein assemblies. Specifically, ion mobility (IM) has introduced a new analytical dimension when coupled to MS, with IM differentiating ions based on their charge, size and shape. This presentation will describe our work utilising IM-MS to characterise aggregating proteins to determine the mechanism behind protein misfolding. We are interested in prefoldin and its molecular chaperone activity on amyloid-β as studies have shown fibrillation of amyloid-β to be involved in neurological degenerative diseases. Understanding the disruption of aggregation and fibrillation through chaperone activity is essential to potential prevention of amyloid diseases.  Probing the structure of bound prefoldin to amyloid-β through the soft ionization technique of nano-electrospray coupled to IM-MS permits the observation of intact non covalent bonds and consequently the molecular interaction of chaperone activity can be characterised. In addition, we have also constructed a thermo-controlled nano-electrospray source coupled to a Waters Synapt IM-MS instrument, enabling structural changes of protein complexes to be observed as the protein aggregates under heat related stress conditions. IM-MS provides direct observation of changes in conformation and binding interactions, further developing our knowledge of the mechanism behind protein misfolding and subsequent fibril formation. These types of mechanisms are important to understand as they are related to amyloid diseases.