Loh, K.H. et al. Cell 166, 1295–1307 (2016).

Synapses, which come in excitatory and inhibitory flavors, are essential for communication between neurons. To gain insight into the differences between the types of synapses, Loh et al. developed a method to characterize the proteome of the synaptic cleft, based on an approach that they previously used to map the protein composition of organelles. They targeted horseradish peroxidase to the synaptic cleft of either glutamatergic or GABAergic synapses and then added a biotin compound, which resulted in biotinylation of resident proteins in the cleft. The biotinylated proteins could then be enriched and analyzed by mass spectrometry. Using this approach, the researchers identified 199 and 42 proteins in excitatory and inhibitory synaptic clefts, respectively, several of which they followed up on and confirmed with alternative methods.