Abstract
Two-dimensional difference gel electrophoresis (2-D DIGE) allows for reliable quantification of global protein abundance changes. The threshold of significance for protein abundance changes depends on the experimental variation (biological and technical). This study estimates biological, technical and total variation inherent to 2-D DIGE analysis of environmental bacteria, using the model organisms "Aromatoleum aromaticum" EbN1 and Phaeobacter gallaeciensis DSM 17395. Of both bacteria the soluble proteomes were analyzed from replicate cultures. For strains EbN1 and DSM 17395, respectively, CV revealed a total variation of below 19 and 15%, an average technical variation of 12 and 7%, and an average biological variation of 18 and 17%. Multivariate analysis of variance confirmed domination of biological over technical variance to be significant in most cases. To visualize variances, the complex protein data have been plotted with a multidimensional scaling technique. Furthermore, comparison of different treatment groups (different substrate conditions) demonstrated that variability within groups is significantly smaller than differences caused by treatment.
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