An optimized quantitative proteomics method establishes the cell type-resolved mouse brain secretome

To understand how cells communicate in the nervous system, it is essential to define their secretome, which is challenging for primary cells because of large cell numbers being required. Here, we miniaturized secretome analysis by developing the "high-performance secretome protein enrichment with click sugars" (hiSPECS) method. To demonstrate its broad utility, hiSPECSwas used to identify the secretory response of brain slices uponLPS-induced neuroinflammation and to establish the cell type-resolved mouse brain secretome resource using primary astrocytes, microglia, neurons, and oligodendrocytes. This resource allowed mapping the cellular origin ofCSFproteins and revealed that an unexpectedly high number of secreted proteinsin vitroandin vivoare proteolytically cleaved membrane protein ectodomains. Two examples are neuronally secretedADAM22 andCD200, which we identified as substrates of the Alzheimer-linked proteaseBACE1. hiSPECSand the brain secretome resource can be widely exploited to systematically study protein secretion and brain function and to identify cell type-specific biomarkers forCNSdiseases.