Plant Plasma Membrane Proteomics: Challenges and Possibilities

Plasma membrane proteins are challenging to study due to their hydrophobicity and low abundance. Extraction of plasma membranes from plants is complicated by the rigid plant cell wall. The most commonly used method to enrich for plant plasma membranes is the aqueous-polymer two-phase system. Many gel-based separation techniques have been used in plasma membrane proteomics studies including one-dimensional SDS-PAGE, classical two-dimensional electrophoresis based on isoelectric focussing and SDS-PAGE, double SDS-PAGE, Blue Native-PAGE and 16-BAC-PAGE. Some of the difficulties associated with gel-based separation of hydrophobic proteins can be bypassed by the use of gel-free approaches which involve in-solution separation of proteins or liquid chromatography-based separation of peptides. Mass spectrometry is subsequently used for identification of proteins. An overview is presented of the most commonly used methods for analysis of plant plasma membrane proteomes, their strengths and weaknesses.