The myth of automated, high-throughput two-dimensional gel analysis
The myth of automated, high-throughput two-dimensional gel analysis
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DOI：
10.1002/pmic.200700709
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发表时间：
2008-03-01
期刊：
影响因子：
3.4
通讯作者：
Gutstein, Howard B.
中科院分区：
文献类型：
--
作者：
Clark, Brittan N.;Gutstein, Howard B.
已经开发了许多软件包来处理和分析2-D凝胶图像。一些程序被吹捧为自动化的高通量解决方案。我们使用18个重复的大鼠脑蛋白提取物凝胶测试了5个市售程序。我们确定了计算机处理时间、大致的点编辑时间、校正点不匹配所需的时间以及总处理时间。我们还确定了自动检测到的点的数量，手动编辑后保留的点的数量，以及自动生成的正确匹配的百分比。我们还确定了增加重复凝胶数量对两个程序的斑点匹配效率的影响。我们发现，对于所有测试的程序，不到3%的总处理时间是自动化的。剩下的时间花在人工，主观编辑检测到的斑点和计算机生成的匹配。18个凝胶的总处理时间为22 - 84 h。自动生成的正确匹配的百分比从1%到62%不等。在实验中增加凝胶的数量会显著降低自动生成的正确匹配的百分比。我们的研究结果表明，这些2-D凝胶分析程序是不自动或快速的，也表明，匹配精度随着实验规模的增加而降低。
Many software packages have been developed to process and analyze 2-D gel images. Some programs have been touted as automated, high-throughput solutions. We tested five commercially available programs using 18 replicate gels of a rat brain protein extract. We determined computer processing time, approximate spot editing time, time required to correct spot mismatches, as well as total processing time. We also determined the number of spots automatically detected, number of spots kept after manual editing, and the percentage of automatically generated correct matches. We also determined the effect of increasing the number of replicate gels on spot matching efficiency for two of the programs. We found that for all programs tested, less than 3% of the total processing time was automated. The remainder of the time was spent in manual, subjective editing of detected spots and computer generated matches. Total processing time for 18 gels varied from 22 to 84 h. The percentage of correct matches generated automatically varied from 1 to 62%. Increasing the number of gels in an experiment dramatically reduced the percentage of automatically generated correct matches. Our results demonstrate that these 2-D gel analysis programs are not automatic or rapid, and also suggest that matching accuracy decreases as experiment size increases.