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The original protocol of two-dimensional electrophoresis with immobilized pH gradient (IPG-Dalt; Gorg et al., Electrophoresis 1988, 9, 531-546) is updated. Merits and limits of different methods for sample solubilization, sample application (by cup-loading or ingel rehydration) with respect to the pH interval used for IPG-isoelectric focusing are critically discussed. Guidelines for running conditions of analytical and micropreparative IPG-Dalt, using wide IPGs up to pH 12 for overview patterns, or narrow IPGs for zoom-in gels for optimum resolution and detection of minor components, are stated. Results with extended separation distances as well as automated procedures are demonstrated, and a comparison between protein detection by silver staining and fluorescent dyes is given. A brief trouble shooting guide is also included.

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We present a large scale quantitation study of the membrane proteome from Halobacterium salinarum. To overcome problems generally encountered with membrane proteins, we established a membrane preparation protocol that allows the application of most proteomic techniques originally developed for soluble proteins. Proteins were quantified using two complementary approaches. For gel-based quantitation, DIGE labeling was combined with two-dimensional gel electrophoresis on an improved 16-benzyldimethyl-n-hexadecylammonium chloride/SDS system. MS-based quantitation was carried out by combining gel-free separation with the recently developed isotope-coded protein labeling technique. Good correlations between these two independent quantitation strategies were obtained. From computational analysis we conclude that labeling of free amino groups by isotopecoded protein labeling (Lys and free N termini) is better suited for membrane proteins than Cys-based labeling strategies but that quantitation of integral membrane proteins remains cumbersome compared with soluble proteins. Nevertheless we could quantify 155 membrane proteins; 101 of these had transmembrane domains. We compared two growth states that strongly affect the energy supply of the cells: aerobic versus anaerobic/phototrophic conditions. The photosynthetic protein bacteriorhodopsin is the most highly regulated protein. As expected, several other membrane proteins involved in aerobic or anaerobic energy metabolism were found to be regulated, but in total, however, the number of regulated proteins is rather small. Molecular & Cellular Proteomics 5:1543-1558, 2006.

Analysis of von Willebrand factor (vWF) multimers allows classification of the subtypes of von Willebrand disease (vWD) in human serum and platelet lysates. A novel method for multimer analysis of vWF by 2-chamber, vertical (sodium dodecyl sulfate), agarose gel electrophoresis, designed for comparing discontinuous high- and low-resolving gels for plasma and platelets, followed by Western blotting and high-sensitivity fluorescence detection (HSFD) of cyanine (Cy)5-labeled vWF multimers is presented. HSFD shows that this method has high discriminatory power for visualization and densitometric analysis of platelets and plasma vWF multimers in various types of vWD and allows rapid classification of vWD types, to separate types 2A and 2B. The described procedures of vWF multimer analysis with high-sensitivity Cy5 fluorescence detection and direct comparison of high- and low-resolving gels for screening and detection of the complete range of high- and low-molecular vWF multimers is efficient and useful for screening, detecting, and classifying vWD subtypes and makes this method diagnostically and clinically relevant.