Positional proteomics for identification of secreted proteoforms released by site-specific processing of membrane proteins

Proteolytic processing shapes cellular interactions with the environment. As a pathway of unconventional protein secretion, ectodomain shedding releases soluble proteoforms of membrane-anchored proteins. This can trigger subsequent cleavage within the membrane stub and the release of additional soluble fragments to intra-and extracellular environments. Distinct membrane-bound proteases, or sheddases, may cleave the same membrane proteins at different sites. Determination of these precise cleavage sites is important, as differently processed proteoforms may exhibit distinct physiological properties and execute antagonistic paracrine and endocrine signaling functions. Conventional quantitative proteomic approaches reliably identify shed proteoforms, but typically not their termini and are thus not able distinguish between functionally different proteoforms differing only by a few amino acids. Dedicated positional proteomics overcomes this challenge and enables proteome-wide identification of protein N- and C-termini. Here, we review positional proteomics techniques, summarize their application to ectodomain shedding and discuss current challenges and developments.