Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
Proteomics. 2011 Aug;11(16):3380-9. doi: 10.1002/pmic.201100071.
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.
二维差异凝胶电泳（2-D DIGE）可用于可靠地定量全局蛋白质丰度变化。蛋白质丰度变化的显著性阈值取决于实验变异（生物学和技术）。本研究使用模型生物“Aromatoleum aromaticum”EbN1 和 Phaeobacter gallaeciensis DSM 17395，估计了环境细菌 2-D DIGE 分析中固有的生物学、技术和总变异性。从重复培养物中分析了两种细菌的可溶性蛋白质组。对于 EbN1 和 DSM 17395 菌株，CV 分别揭示了低于 19%和 15%的总变异性、12%和 7%的平均技术变异性以及 18%和 17%的平均生物学变异性。方差的多变量分析证实，在大多数情况下，生物学变异性超过技术变异性是显著的。为了可视化变异性，使用多维尺度技术绘制了复杂的蛋白质数据。此外，不同处理组（不同底物条件）的比较表明，组内的变异性明显小于处理引起的差异。
