YPED: A web-accessible database system for protein expression analysis
YPED: A web-accessible database system for protein expression analysis
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DOI：
10.1021/pr070325f
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发表时间：
2007-10-01
影响因子：
4.4
通讯作者：
Williams, Kenneth R.
中科院分区：
文献类型：
--
作者：
Shifman, Mark A.;Li, Yuli;Williams, Kenneth R.
我们已经开发了一个集成的网络访问软件系统，称为耶鲁蛋白质表达数据库（YPED），以满足存储，检索和综合分析大量高通量蛋白质组学技术的数据的需要。YPED是一个开源系统，它将凝胶分析结果与DIGE实验的蛋白质鉴定相结合。该系统将用DeCyder分析的DIGE凝胶点和图像与来自所选凝胶点的质谱蛋白质鉴定相关联。在凝胶胰蛋白酶消化后，在AB 4700上或最近在AB 4800上使用MALDI-TOF/TOF分析感兴趣的点中的蛋白质，由Mascot结合AB GPS Explorer系统进行蛋白质鉴定。除了DIGE之外，YPED目前还处理MudPIT、iTRAQ和ICAT实验中的蛋白质鉴定。样品说明与不断发展的MIAPE标准兼容。来自MudPIT和ICAT分析的串联MS/MS结果使用Trans-Proteomic Pipeline进行验证，然后存储在数据库中，用于查看和链接到已识别的蛋白质。研究人员可以通过一个安全的Web界面查看，子集和下载他们的数据，该界面包括一个包含识别的蛋白质的表格，一个样本摘要，样本描述和DIGE样本的可点击凝胶图像。有工具可用于促进样品比较和磷蛋白的观察。还提供了带有PANTHER分类系统注释的总结报告，以帮助对结果进行生物学解释。源代码是开源的，可从http://yped.med.yale.edu/yped-dist获得。
We have developed an integrated web-accessible software system called the Yale Protein Expression Database (YPED) to address the need for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED is an open source system which integrates gel analysis results with protein identifications from DIGE experiments. The system associates the DIGE gel spots and image, analyzed with DeCyder, with mass spectrometric protein identifications from selected gel spots. Following in gel trypsin digestion, proteins in spots of interest are analyzed using MALDI-TOF/TOF on an AB 4700 or, more recently, on an AB 4800 with protein identifications performed by Mascot in conjunction with the AB GPS Explorer system. In addition to DIGE, YPED currently handles protein identifications from MudPIT, iTRAQ, and ICAT experiments. Sample descriptions are compatible with the evolving MIAPE standards. Tandem MS/MS results from MudPIT, and ICAT analyses are validated with the Trans-Proteomic Pipeline and then stored in the database for viewing and linking to the identified proteins. Researchers can view, subset, and download their data through a secure Web interface that indudes a table containing proteins identified, a sample summary, the sample description, and a clickable gel image for DIGE samples. Tools are available to facilitate sample comparison and the viewing of phosphoproteins. A summary report with PANTHER dassification System annotations is also available to aid in biological interpretation of the results. The source code is open-source and is available from http://yped.med.yale.edu/yped-dist.