The development of aggregates of specific disease-associated proteins represents a common denominator for many neurodegenerative disorders. The gain of function of the aggregates is hypothesized to initiate pro-degenerative signaling pathways that cause neuronal dysfunctions and ultimately death of affected neurons. Comparing the protein interactome of the native normal functioning disease-associated protein to the interactome of the aggregated forms of the same protein may reveal disease-conducting signaling hubs of relevance to specific diseases. Here, we describe the experimental setup we used to identify specific interaction partners of soluble oligomeric α-synuclein aggregates including step-by-step protocols for preparation of antibody-conjugated Sepharose beads, purification of recombinant soluble α-synuclein oligomers, preparation of synaptosomal extracts from porcine brain, and the actual co-immunoprecipitation. Our goal is to present the reader issues for consideration before starting co-immunoprecipitation experiments and a practical overview of the technical finesses. This approach can be applied to study interaction of any purified disease-linked soluble aggregates.