Establishment of “one-piece” large-gel 2-DE for high-resolution analysis of small amounts of sample using difference gel electrophoresis saturation labelling

Large-gel two-dimensional gel electrophoresis (2-DE) is the method of choice for high-resolution proteome analysis of complex protein mixtures. Until now, however, the advantages of large 2-DE in combination with multiplexed fluorescence dye protein labelling has been complicated by the separate handling and analysis of the second-dimension gels. Therefore, we adapted the large 2-DE procedure allowing us to run “one-piece” large 2-DE gels (40 cm × 30 cm) in the second dimension for high resolution proteome analysis. Here, we show that in combination with fluorescence dye protein saturation labelling “one-piece” large 2-DE enables analysis of small amounts of sample (3 μg protein) for high-resolution proteome analysis.