Cell surface protein enrichment for biomarker and drug target discovery using mass spectrometry-based proteomics

Abstract Cell surface proteins play a critical role in cell-cell interactions, nutrients and metabolite transport as well as translation of extracellular signals into intracellular responses and vice versa. Due to its accessibility, the cell surfaceome represents a major biomarker and drug target resource. Importantly, ~ 70% of contemporary pharmaceuticals target cell surface proteins. Therefore, mass spectrometry (MS)-based bottom-up proteomic profiling of proteins exposed at the cell surface is increasingly used in biomarker and drug target discovery/research. However, cell surface proteins are among the most difficult to prepare and analyze. Primary obstacles are (i) poor solubility of cell surface proteins in pure aqueous buffers, (ii) high degree of heterogeneous posttranslational modifications, and (iii) exceedingly wide expression level. Therefore, enrichment of cell surface proteins prior to MS analysis is challenging and complex procedure. The purpose of this chapter is to provide an overview of common enrichment techniques for bottom-up antibody-free MS-based cell surface proteomics in search for disease biomarkers and drug targets, including Ras oncogene-driven cancers.