The in silico human surfaceome

Significance Despite the fundamental importance of the surfaceome as a signaling gateway to the cellular microenvironment, it remains difficult to determine which proteoforms reside in the plasma membrane and how they interact to enable context-dependent signaling functions. We applied a machine-learning approach utilizing domain-specific features to develop the accurate surfaceome predictor SURFY and used it to define the human in silico surfaceome of 2,886 proteins. The in silico surfaceome is a public resource which can be used to filter multiomics data to uncover cellular phenotypes and surfaceome markers. By our domain-specific feature machine-learning approach, we show indirectly that the environment (extracellular, cytoplasm, or vesicle) is reflected in the biochemical properties of protein domains reaching into that environment.