Abstract
There is intense interest in comprehensive proteomic approaches for analyzing integral membrane proteins and lipoproteins. Key features of mass spectrometric analysis center on enriching biological material for proteins of interest, efficiently digesting them, extracting the resulting peptides, and using fractionation methods to comprehensively sample proteins or peptides by tandem mass spectrometry. However, lipid-associated proteins are generally rich in hydrophobic domains and are often low in abundance. These features, together with the associated lipid, make their mass spectrometric analysis technically challenging. In this article, we review analytical strategies for successful proteomic analysis of lipid-associated proteins.
Highlights
PROTEOMICS OF INTEGRAL MEMBRANE PROTEINSTransmembrane proteins are embedded in a lipid bilayer. The outer membrane of a cell, the plasma membrane, typically consists of 50% lipid and 50% protein by mass (w/w; molar ratio of ?50:1), but the composition varies widely, depending on the membranes function
There is intense interest in comprehensive proteomic approaches for analyzing integral membrane proteins and lipoproteins
The recent development of new ion dissociation, electron capture dissociation (ECD) [48], and electron transfer dissociation (ETD) [49, 50] methods that efficiently fragment large peptides offers new possibilities for Mass spectrometry (MS) analysis of membrane proteins that have been digested with cyanogen bromide (CNBr)
Summary
Transmembrane proteins are embedded in a lipid bilayer. The outer membrane of a cell, the plasma membrane, typically consists of 50% lipid and 50% protein by mass (w/w; molar ratio of ?50:1), but the composition varies widely, depending on the membranes function. Integral membrane proteins typically have three major domains: i) an extracellular domain or ectodomain, ii) a hydrophobic domain embedded in the membrane, the trans-membrane domain and iii) a luminal or intracellular domain. Based on their interaction(s) with the membrane, integral membrane proteins are generally classified as single pass (bitopic) or multipass (polytopic). B-Barrels are found in only a small fraction of integral membrane proteins and do not usually present major challenge for proteomic analysis [12]. A-helices, which characterize the majority of integral membrane proteins, are problematic because they are often rigid and highly hydrophobic. It is generally critical to use various enrichment strategies to prepare them for proteomic analysis [13, 14]
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