A number of strategies have successfully extended plant proteomics into the bilayer domain. Important benefits can be afforded by including a well-resolved intact protein mass spectrum alongside peptide identification experiments; recent studies of thylakoid membranes have yielded new information on the primary structure and covalent post-translational modification of many of the integral proteins. Intact mass proteomics is advancing through the development of core technologies in separations

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... d mass spectrometry, with the goal of providing comprehensive primary structure coverage that includes transmembrane domains with reliable measurements of protein abundance and turnover. To address the limitations associated with separation technologies such as 2D-gel electrophoresis, alternative systems are being investigated and 2D-liquid chromatography of thylakoid membrane proteins, using both denaturing and non-denaturing first dimensions, has been successful, extending separation space and providing intact protein solutions for electrosprayionization mass spectrometry and top-down proteomics. High-resolution conventional, and Fourier-transform, mass spectrometry is bringing increasing resolution to tandem mass spectrometry allowing for 'top-down' mass spectrometry of intact proteins. Thus the core chromatographic technologies already developed for intact mass proteomics of integral membrane proteins also allow their 'top-down' analysis. Thylakoid membrane proteins with one and two transmembrane helices have been analysed demonstrating the ability of collision-activated dissociation (CAD) to sequence through transmem-brane domains. When analysed by top-down proteomics, the small subunits of the cytochrome b 6 f complex from Arabidopsis thylakoids reveal novel post-transcriptional/ translational modifications including the presence of glutamic acid at position 2 of PetL instead of the proline residue predicted from the gene sequence.