Membrane proteomics by high performance liquid chromatography-tandem mass spectrometry: Analytical approaches and challenges

Membrane proteins play diverse biologically important structural and functional roles including molecular transport, cell communication and signal transduction. The dysfunction of many are linked to deleterious human diseases and thus are of utmost importance in drug discovery. Membrane proteins comprise approximately 20-30 of all open reading frames, however they are typically under-represented in many liquid chromatography - mass spectrometry (LC-MS) proteomics experiments due to their low abundance and poor solubility. To address these analytical challenges, various membrane protein enrichment, solubilization, digestion and fractionation strategies have been employed to further improve the coverage of the membrane systems while maintaining compatibility with MS detection. This review discusses both established and emerging high-throughput gel-free analytical workflows in membrane proteomics, and the inherent advantages, disadvantages and orthogonality of the various approaches. The issues of critical importance for successful LC-MS/MS detection such as detergent selection and minimizing ion suppression in detergent-based workflows are discussed in detail. Recent studies comparing the performance of different analytical strategies are highlighted in order to provide practical insight into the choice of the most appropriate method for membrane-centric applications ranging from cell surface biomarker discovery to membrane protein interaction network mapping.