A protocol for analyzing the protein terminome of human cancer cell line culture supernatants

Characterization of protein termini is essential for understanding how the proteome is generated through biological processes such as post-translational proteolytic events. Here, we introduce a practical protocol for terminomics to achieve simple and sensitive N- and C-terminal peptide enrichment. We apply it to the terminome analysis of culture supernatants of a human cancer cell line for the purpose of identifying ectodomain shedding substrate cleavage sites with 10 μg protein per sample. For complete details on the use and execution of this protocol, please refer to Tsumagari et al. (2021).