The brain is composed of many different types of neurons that form very specific connections: synapses are formed with specific cellular partners and on precise subcellular domains. It has been proposed that different combinations of molecules encode the specificity of neuronal connections, implying the existence of a “molecular synaptic code.” To test this hypothesis, we describe a new experimental strategy that allows systematic identification of the protein composition for individual synapse types. We start with mice that are genetically engineered to facilitate the purification of one type of synapse from a given neuronal population in the central nervous system, the parallel fiber/Purkinje cell synapse. The purification is performed using a combination of biochemical fractionation and affinity purification. Subsequent mass spectrometry allows us to identify approximately 60 different proteins present in the resulting sample. We have further analyzed some of the 60 proteins and show that MRCKγ, a newly identified kinase, is localized in the dendritic spines where the parallel fiber/Purkinje cell synapses are formed and that it can modulate the morphogenesis of dendritic spines. The use of this experimental strategy opens up the ability to provide insights into the underlying “molecular code” for the diverse types of synapses in the brain.