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Significance Over 600 proteases work together to maintain the normal functions and homeostasis of cells in the human body. Determining protease specificity and their natural substrates is critical to understanding their biology. We present a facile, inexpensive, general, and global means to profile the natural specificity of human proteases at unprecedented depth. Using two genetically encoded substrate phage libraries, we deeply profile the substrate specificities of two important protease families, caspases involved in cell death and ADAMs family proteases that shed membrane proteins. We validated our results by recapitulating and expanding on known consensus substrates with up to 1,000-fold greater coverage.

Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries