摘要：SummaryEctodomain shedding is a proteolytic process that regulates the levels and functions of membrane proteins. Dysregulated shedding is linked to severe diseases, including cancer and Alzheimer's disease. However, the exact cleavage sites of shedding substrates remain largely unknown. Here, we explore the landscape of ectodomain shedding by generating large-scale, cell-type-specific maps of shedding cleavage sites. By means of N- and C-terminal peptide enrichment and quantitative mass spectrometry, we quantified protein termini in the culture media of 10 human cell lines and identified 489 cleavage sites on 163 membrane proteins whose proteolytic terminal fragments are downregulated in the presence of a broad-spectrum metalloprotease inhibitor. A major fraction of the presented cleavage sites was identified in a cell-type-specific manner and mapped onto receptors, cell adhesion molecules, and protein kinases and phosphatases. We confidently identified 86 cleavage sites as metalloprotease substrates by means of knowledge-based scoring.Graphical abstractDisplay OmittedHighlights•Secretomes across 10 human cell lines were investigated by protein terminomics•Cell-type-specific maps of shedding cleavage sites were generated•Most of the cleavage sites were identified in a cell-type-specific manner•Knowledge-based scoring enabled prediction of responsible sheddasesMolecular Biology; Cell Biology; Omics; Proteomics
