Abstract: An optimized protocol was reported with special attention focused on the wholecell protein analyses based on twodimensional gel electrophoresis (2DE) and Arabidopsis as material. The optimization included sample preparation, electrophoresis conditions, gel staining, protein spots resolution and reproducibility. The results indicate that in combination with highvoltage and longrunning time in IEF, the precipitation of proteins with ammonium acetate/methanol method will give rise to satisfactory 2DE image. The maximal detectable protein spots were estimated to be more than 1 000 under silver staining. This protocol may be applicable to other plant materials for 2DE studies. 

Key words: Arabidopsis thaliana, sample preparation, twodimensional gel electrophoresis