Updated PubMed. Ectodomain shedding is a proteolytic process that regulates level and function of membrane proteins. By quantitative protein terminomics consisting of N- and C-terminal peptide enrichment, TMT-labeling and mass spectrometry, we quantified protein termini in the cultured media across 10 human cell lines and identified cleavage sites on membrane proteins downregulated upon broad-spectrum metalloprotease inhibitor treatment.