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A quantitative analysis of the protein composition of the synapto-axonal compartment would improve the understanding of the molecular basis of Parkinson’s disease. However, such quantitative proteomic data from diseased synapses are currently not available. The existing animal models that exist for neurodegenerative diseases only ever recapitulate parts of the pathology. In this study, we aim to understand the Parkinson’s synapse beyond alpha-synuclein and synuclein-like elements, and to find new Parkinson-relevant proteins. Our results show that neuronal pentraxin 1 (NP1) is a promising target protein involved in synapto-axonal dysfunction in PD.