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Amyloid structures accumulate and propagate through self-assembly of partially folded proteins and peptides, resulting in a range of disease states. Key to understanding amyloid disease is the characterisation of the often toxic oligomeric species formed during the early stages of fibril assembly. Electrospray ionisation- ion mobility spectrometry - mass spectrometry (ESI-IMS-MS) has emerged as a powerful tool to investigate amyloid oligomer assembly and protein conformation change. In this review we focus on the role of ESI-IMS-MS in understanding and probing conformational changes and the early stages of protein aggregation.