The pathogenesis of neurodegenerative diseases such as Parkinson’s disease and amyotrophic lateral sclerosis is believed to be caused by the aggregation of non-native proteins. One such protein that is prone to aggregation is α-synuclein, an intrinsically disordered protein which forms toxic amyloid fibrils implicated in Parkinson’s disease. The formation of amyloid fibrils is preceded by the recruitment of misfolding monomers to form soluble oligomers, which are thought to be a major toxic component in cells, in part through damage of lipid membranes. However, very little structural and dynamic information is known about these oligomers in terms of toxicity and their interaction with lipids. The ability of native mass spectrometry, supplemented with other biophysical techniques, to analyse heterogeneous populations and resolve structural/dynamic interactions provides an ideal means to study large, heterogeneous complexes such as oligomeric α-synuclein and model membrane systems of varying lipid compositions. We have also shown that the lipid composition affects the kinetics of seeded and non-seeded fibril formation, increasing both the rate and degree of fibrillation. In addition, sing ion mobility and chemical cross-linking mass spectrometry, we have identified and isolated small α-synuclein oligomers ranging from dimers to hexamers for further structural and functional characterization. Finally, the ability of small molecules (polyphenols and flavonoids) to inhibit fibrillation was also assessed in vitro, demonstrating that flavonoids significantly inhibit α-synuclein fibril elongation and decrease the exposed hydrophobicity of these fibrils. These studies demonstrate the influence that the lipidome plays in modulating aggregation pathways and the pathogenesis of protein misfolding diseases.