Amyloid β (Aβ) oligomers are thought to play an important role in the onset and progression of Alzheimer’s disease (AD). Several oligomer-binding proteins have been implicated in mechanisms leading to AD pathology. Such proteins could provide insights into the pathways involved in the disease process of AD and might reveal novel targets for disease-modifying therapy approaches. Here, we separated different native Aβ assemblies in brain homogenates of human AD post mortem tissue by density gradient centrifugation, then isolated Aβ-containing complexes by co-immunoprecipitation. Mass spectrometry of immunoprecipitated proteins with label-free quantification (LFQ) showed numerous significant changes between AD and control samples, confirming familiar binding proteins and also indicating putative new interactors.