We have published a methods paper describing the biochemical tools that we have developed over the years and use routinely in the lab to isolate synapses and sub-synaptic protein complexes for proteomic characterisation:
Rita Reig-Viader and Àlex Bayés. Quantitative In-Depth profiling of the Postsynaptic Density Proteome to Understand the Molecular Mechanisms Governing Synaptic Physiology and Pathology. Current Proteomic Approaches Applied to Brain Function. 2017 Human Press, Springer Protocols. ISBN 978-1-4939-7119-0.