Neurons are highly polarized cells characterized by subcellular microdomains: the synapses. These compartments are specialized structures and are, for certain cellular pathways, independent from the cell body. To achieve such a functional specificity, including local mRNA translation, different molecular complexes are transported along the dendrites and locally regulated. Characterization of such a molecular diversity may help to elucidate neuronal functions as well as detect differences in neuronal dysfunctions. Here, we describe a method to specifically dissect a molecular complex according to the neuronal subcellular compartment. Specifically, the complexes are isolated by immunoprecipitation of the protein of interest from brain lysates or from purified synapses (synaptoneurosomes) and identified by mass spectrometry analysis.