Dopamine transmission is a monoaminergic system involved in reward processing and motor control. Volume transmission is thought to be the main mechanism by which monoamines modulate effector transmission though synaptic structures are scarcely described. In the present work we aimed to unravel the cellular and molecular synaptome of single projection pathways (Zhu F, Cizeron M, Qiu Z, Benavides-Piccione R, Kopanitsa MV, Skene NG, Koniaris B, DeFelipe J, Fransén E, Komiyama NH & Grant SGN (2018) Architecture of the Mouse Brain Synaptome. Neuron 99: 781–799.e10). To that end, we established a workflow combining fluorescence tracing of the dopaminergic pathway, fluorescence activated synaptosome sorting and mass spectrometry-based proteomics. With this approach we provide the first ex-vivo model to thoroughly analyse the cellular and molecular organisation of dopaminergic synapses from mouse striatum.