Proteomics seeks to address the entire complement of protein gene products of an organism, but experimental analysis of such complex mixtures is biased against low abundance and membrane proteins. Electrospray-ionization mass spectrometry coupled with reverse-phase chromatography was used to separate and catalogue all detectable proteins in samples of photosystem II-enriched thylakoid membrane subdomains (grana) from pea and spinach. Around 90 intact mass tags were detected corresponding to approximately 40 gene products with variable post-translational covalent modifications. Provisional identity of 30 of these gene products was proposed based upon coincidence of measured mass with that calculated from genomic sequence. Analysis of isolated photosystem II complexes allowed detection and resolution of a minor population of D1 (PsbA) that was apparently palmitoylated and not detected in less purified preparations. Based upon observed ؉80-Da adducts, D1, D2 (PsbD), CP43 (PsbC), two Lhcbs, and PsbH were confirmed to be phosphorylated, and a new phosphoprotein was proposed to be the product of psbT. The appearance of a second ؉80-Da adduct on PsbH provides direct evidence for a second phosphorylation site on PsbH, complicating interpretation of its role in regulation of thylakoid membrane organization and function, including light-state transitions. Adducts of ؉32 Da, presumably arising from oxidative modification during illumination, were associated with more highly phosphorylated forms of PsbH implying a relationship between the two phenomena. Intact mass proteomics of organellar subfractions and more highly purified protein complexes provides increasingly detailed insights into functional genomics of photosynthetic membranes.
Molecular & Cellular Proteomics 1:46 -59, 2002.With many genomes completed and many more in the pipeline it is clear that the post-genomic era has arrived. Considerable attention is now being directed toward defining the function of individual gene products and the inter-relationships between them (functional genomics). Proteomics seeks to catalogue the full complement of the gene products of a cell and the effect of development, environment, and disease upon their expression. Mass spectrometry is driving proteomics, most commonly as a tool to identify proteins separated and visualized on two-dimensional gels. However, such strategies are insensitive to low abundance proteins (1, 2), proteins that are not fully represented on two-dimensional gels (for example, some classes of intrinsic membrane proteins) and to subtle changes in covalent modifications that do not appreciably alter isoelectric point or electrophoretic mobility. To address some of these shortcomings, intact mass proteomics has been proposed (3-8).The ideal analysis of any protein includes a mass spectrum of the intact molecule to define the native covalent state and its heterogeneity (3, 4). A versatile procedure has been developed for effective electrospray-ionization mass spectrometry (MS) 1 of intact intrinsic membrane prot...