Comparative evaluation of two two-dimensional gel electrophoresis image analysis software applications using synovial fluids from patients with joint disease
Comparative evaluation of two two-dimensional gel electrophoresis image analysis software applications using synovial fluids from patients with joint disease
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DOI：
10.1007/s00776-004-0878-0
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发表时间：
2005-01-01
影响因子：
1.7
通讯作者：
Sarkar, U
中科院分区：
文献类型：
--
作者：
Arora, PS;Yamagiwa, H;Sarkar, U
滑液（SF）的蛋白质组组成可能有助于了解关节炎的分子基础。然而.当分析通过二维凝胶电泳（2D-GE）获得的结果时，SF的高粘性和蛋白质组复杂性提出了挑战。有几种软件应用程序可用于分析2D-GE图像。尽管存在固有的优点和缺点，但使用SF或任何人类液体标本的这些应用之间没有比较。我们评估了两种常见的软件包- PDQuest和Progenesis Workstation -用于斑点检测。匹配和定量来自四名关节炎疾病患者的SF的2D-GE图像。最初，分析整个2D-凝胶图像用于斑点检测。这表明PDQuest比Progenesis更一致;然而，PDQuest似乎比Progenesis需要更多的用户干预。随后，从每个凝胶图像中选择两个小区域（良好分辨的斑点和未良好分辨的斑点），通过软件分析斑点检测、匹配、体积和分辨率。这些分析表明，与手动斑点检测（“金标准”）相比，这两种工具可以相对一致地量化分辨率良好的斑点。这两种工具提供的“3D查看器”选项可实现正确的光斑识别和匹配。这些计算机工具的优点和缺点可以为选择特定的工作站来识别关节炎的生物标志物提供指导。
The proteomic composition of synovial fluid (SF) may hold clues to understanding the molecular basis of arthritis. However. the highly viscous nature and proteomic complexity of SF present a challenge when analyzing results obtained by two-dimensional gel electrophoresis (2D-GE). Several software applications are available for analyzing 2D-GE images. Despite inherent strengths and weaknesses, no comparison between these applications has been reported using SF or any human fluid specimens. We evaluated two common software packages - PDQuest and Progenesis Workstation - for spot detection. matching, and quantitation of 2D-GE images of SF from four patients with arthritic disease. Initially, whole 2D-gel images were analyzed for spot detection. which suggested that PDQuest is more consistent than Progenesis; however, PDQuest appeared to require more user intervention than Progenesis. Subsequently, two small areas (spots well resolved and spots not well resolved) were selected from each gel image, which were analyzed by the software for spot detection, matching, volume, and resolution. These analyses suggest that both tools can quantify well-resolved spots relatively consistently when compared with manual spot detection (the "gold standard"). The "3D viewer" option offered by both tools enables correct spot identification and matching. The strengths and weaknesses of these computer tools can provide guidance in the choice of a particular workstation for identifying biomarkers of arthritis.