Quantitative secretome analysis using improved secretome-protein-enrichment-with-click-sugars method (iSPECS) establishes the cell type-resolved mouse brain glyco-secretome

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To understand how cells communicate with each other, it is essential to define the cellular secretome, a collection of proteins including soluble secreted, unconventionally secreted and proteolytically-shed proteins. Quantitative methodologies to decipher the secretome are challenging, due to the requirement of large cell numbers and abundant serum proteins that interfere with the detection of low-abundant cellular secretome proteins. Here, we miniaturized secretome analysis by developing the improved secretome-protein-enrichment-with-click-sugars method (iSPECS), which identifies the glyco-secretome. We applied this method to provide a cell type-resolved mouse brain glyco-secretome resource. Our data show that a surprisingly high number of secreted proteins are generated by ectodomain shedding in a cell type-specific manner. Two examples are neuronally secreted ADAM22 and CD200, which we identified as new substrates of the Alzheimer-linked protease BACE1. Taken together, iSPECS and the brain glyco-secretome resource can be exploited for a wide range of applications to study protein secretion and shedding.