The phenomenon of protein misfolding and aggregation has been associated with over 50 human diseases, including Parkinson’s disease (PD). While the hallmark deposits in aggregation-associated diseases are primarily composed of fibrillar species, intermediate oligomeric species that form during the aggregation process are believed to be a major cause of toxicity. Such species are relatively poorly characterised due to several challenges that render them inaccessible to most conventional techniques; oligomers are only present at extremely low concentrations in the aggregation reaction, and are additionally highly heterogeneous and often transient in nature. In this thesis, I present complementary approaches to address these difficulties. Firstly, an ensemble of stable, kinetically trapped oligomers with varying biophysical characteristics was established, enabling detailed structure-toxicity relationships to be investigated. Secondly, a method for the simultaneous single-molecule level characterisation and fractionation of oligomeric species under native conditions was established and applied to studying intermediate species in Parkinson’s disease-associated protein aggregation. Finally, I present a general approach to optimising experimental design, which maximises both the efficiency and information gain of experiments, and demonstrate its validation and application to several experimental systems.