Thylakoid membrane proteomics

Proteomics seeks to monitor the global complement of proteins within a cell or organism and accompanying plasticity with respect to development and environment. The proteome is dynamic, the product of current and past gene expression, countless protein-protein interactions and selective proteolytic systems. Consequently the snapshot that a proteomic measurement yields must be integrated into proteome flux; the flow of nutrients and energy through the protein pathways that catalyze and drive life. The thylakoid membrane proteome poses many technical challenges for proteomics. Integral membrane proteins present awkward physico-chemical properties and the abundant photosynthetic machinery conceals much less abundant and no less important proteins such as channels and transporters that control the interaction of stroma and lumen. Discussed here are contrasting approaches to thylakoid proteomics; 'shotgun' techniques that provide throughput benefits by cleaving proteins into smaller more-manageable peptide chunks versus intact protein techniques that provide more detailed and accurate pictures. A two-dimensional chromatography system directly interfaced to electrospray-ionization mass spectrometry has allowed the direct visualization of large reaction-center proteins (up to 83 kDa) from both Photosystems 1 and 2 providing an attractive avenue for characterization of thylakoid membrane proteomes under different conditions because of the ability to resolve molecular heterogeneity resulting from post-translational modifications such as phosphorylation and oxidation. A high-resolution spectrum of Bacteriorhodopsin recorded to an accuracy of 8 ppm using Fourier-transform mass spectrometry demonstrates the first application of this technique to intact polytopic integral membrane proteins.