The efficiency and reproducibility of two-dimensional difference gel electrophoresis (2D DIGE) depends on several crucial steps: (i) adequate number of replicate gels, (ii) accurate image acquisition, and (iii) statistically confident protein abundance analysis. The latter is inherently determined by the image analysis system. Available software solutions apply different strategies for consecutive image alignment and protein spot detection. While DeCyderTM performs spot detection on single gels prior to the alignment of spot maps, SameSpotsTM completes image alignment in advance of spot detection. In this study, the performances of DeCyderTM and SameSpotsTM were compared considering all protein spots detected in 2D DIGE resolved proteomes of three different environmental bacteria with minimal user interference. Proteome map-based analysis by SameSpotsTM allows for fast and reproducible abundance change determination, avoiding time-consuming, manual spot matching. The different raw spot volumes, determined by the two software solutions, did not affect calculated abundance changes. Due to a slight factorial difference, minor abundance changes were very similar, while larger differences in the case of major abundance changes did not impact biological interpretation in the studied cases. Overall, affordable fluorescent dyes in combination with fast CCD camera-based image acquisition and user-friendly image analysis still qualify 2D DIGE as a valuable tool for quantitative proteomics.

中文翻译：

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有什么不同？DeCyderTM与SameSpotsTM进行2D DIGE图像分析。

二维差异凝胶电泳（2D DIGE）的效率和可重复性取决于几个关键步骤：（i）足够数量的复制凝胶，（ii）准确的图像采集，以及（iii）统计上可信的蛋白质丰度分析。后者由图像分析系统固有地确定。可用的软件解决方案为连续的图像对齐和蛋白质斑点检测应用了不同的策略。尽管DeCyderTM在对齐点图之前先对单个凝胶进行点检测，但SameSpotsTM会在点检测之前完成图像对齐。在这项研究中，比较了DeCyderTM和SameSpotsTM的性能，并考虑了在三种不同环境细菌的2D DIGE解析蛋白质组中检测到的所有蛋白质斑点，而用户干扰最小。通过SameSpotsTM进行的基于蛋白质组图的分析，可以快速，可重复地确定丰度变化，从而避免了耗时的手动点匹配。两种软件解决方案确定的不同原始斑点量不会影响计算出的丰度变化。由于细微的因子差异，较小的丰度变化非常相似，而较大的丰度变化的较大差异不会影响所研究案例的生物学解释。总体而言，可负担得起的荧光染料与基于CCD相机的快速图像采集和用户友好的图像分析相结合，仍然使2D DIGE成为定量蛋白质组学的宝贵工具。由两种软件确定的解决方案，均不影响计算出的丰度变化。由于细微的因子差异，较小的丰度变化非常相似，而较大的丰度变化的较大差异不会影响所研究案例的生物学解释。总体而言，可负担得起的荧光染料与基于CCD相机的快速图像采集和用户友好的图像分析相结合，仍然使2D DIGE成为定量蛋白质组学的宝贵工具。由两种软件确定的解决方案，均不影响计算出的丰度变化。由于细微的因子差异，较小的丰度变化非常相似，而对于较大的丰度变化，较大的差异不会影响所研究案例的生物学解释。总体而言，可负担得起的荧光染料与基于CCD相机的快速图像采集和用户友好的图像分析相结合，仍然使2D DIGE成为定量蛋白质组学的宝贵工具。