Plasma membrane is composed of phospholipid bilayers, membrane proteins, cholesterol, and carbohydrate moieties modified on either lipids or proteins. It occupies only about 2% of the total cell volume. The plasma membrane proteins contribute to more than a half of the plasma membrane mass. There are various types of plasma membrane proteins, including integral membrane proteins spanning through the phospholipid bilayers, integral membrane proteins forming pore complexes, proteins embedding on the inner or outer sites of the phospholipids, and peripheral membrane proteins interacting with the proteins or lipids on either sides of the plasma membrane. Studies of membrane proteomics, in general, remain problematic owing to their intrinsic properties. Despite the low abundance, a majority of the plasma membrane proteins are poorly soluble, particularly those that contain transmembrane domains.
To overcome the problem of underrepresentation of the plasma membrane proteome from tissue, cell lysates, or plasma samples, a number of techniques have been developed for improving enrichment efficiency. Traditionally, a density gradient centrifugation, such as sucrose or Nycodenz gradients, has been employed to fractionate intracellular organelles based on their density differences. Similarities in the density of organelle membranes cause difficulties with this technique because the membranes from different organelles tend to be enriched in the same density fractions. Moreover, there are various sizes and forms of plasma membrane after cell lysis, including vesicles and open sheets; therefore, they could be present in several centrifugal fractions.
A number of studies focus on enriching the cell surface proteins using chemical labeling of primary amine or sulfhydryl groups exposed on the extracellular side of the surface, followed by an affinity enrichment of the tagged-proteins. Commonly, biotin-linked reagents are used for protein derivatization, prior to affinity purification by avidin/streptavidin molecules, which is based on stable non-covalent interaction between the biotin and avidin/streptavidin. Likewise, several studies employ a similar technique to capture cell surface glycoproteins. Since glycosylation is frequently found on the plasma membrane proteins, carbohydrate moieties serve as favorable targets for biotinylation. Aldehyde groups formed by periodate-oxidation of sugars are reactive with biotin-labeled reagents, which are suitable for the downstream affinity enrichment. Another membrane purification technique, two-phase aqueous/polymer or detergent/polymer partitioning, takes advantage of higher hydrophobicity of the membrane bilayers to separate them from other compositions. The plasma membrane bilayers can be further purified by adding plasma membrane-specific affinity ligands to one of the polymer layers.