An overview on enrichment methods for cell surface proteome profiling

Abstract

Cell surface proteins are essential for many important biological processes, including cell–cell interactions, signal transduction, and molecular transportation. With the characteristics of low abundance, high hydrophobicity, and high heterogeneity, it is difficult to get a comprehensive view of cell surface proteome by direct analysis. Thus, it is important to selectively enrich the cell surface proteins before liquid chromatography with mass spectrometry analysis. In recent years, a variety of enrichment methods have been developed. Based on the separation mechanism, these methods could be mainly classified into three types. The first type is based on their difference in the physicochemical property, such as size, density, charge, and hydrophobicity. The second one is based on the bimolecular affinity interaction with lectin or antibody. And the third type is based on the chemical covalent coupling to free side groups of surface‐exposed proteins or carbohydrate chains, such as primary amines, carboxyl groups, glycan side chains. In addition, metabolic labeling and enzymatic reaction‐based methods have also been employed to selectively isolate cell surface proteins. In this review, we will provide a comprehensive overview of the enrichment methods for cell surface proteome profiling.

A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics

“…Analyzing glycoproteomes from whole-cell lysate generates confounding artifacts that complicate determination of what glycoforms are biologically relevant and present on the cell surface. Several approaches have been developed to label cell-surface glycoproteins on live cells, prior to cell lysis and protein extraction ( 306 , 307 ). One variation functions similarly to the approaches above: sialic acids are oxidized on live cells via mild periodate treatment, and aldehyde-containing sialylated glycopeptides are captured on hydrazide beads.…”

Identification of Oocyst-Driven Toxoplasma gondii Infections in Humans and Animals through Stage-Specific Serology—Current Status and Future Perspectives

“…Nevertheless, an important determinant would be a complete knowledge of the surfaceome, i.e., the entirety of all proteins on the cell surface [99]. Experimental approaches for this involve specific labeling of surface proteins (e.g., via biotinylation) and their subsequent enrichment, followed by their identification by mass spectrometry [100]. A single study has reported such data for tachyzoites of T. gondii [101] (similar data for bradyzoites and sporozoites are not available).…”

Quantitative Temporal Viromics

“…PM proteins are typically of low abundance and underrepresented in proteomic samples. It is therefore necessary to selectively enrich for PM proteins prior to proteolysis and MS. Methods for this purpose include those that isolate PM proteins by utilizing their physicochemical properties (size, charge, or hydrophobicity), use bimolecular affinity interaction with a lectin or antibody, or use chemical covalent coupling to the side groups of surface exposed proteins (86). Plasma membrane profiling (PMP) involves the selective oxidation and aminooxy-biotinylation of sialylated PM glycoproteins, followed by affinity purification with high capacity streptavidin (87, 88) (Figure 2b).…”