Shifman Mark A, Li Yuli, Colangelo Christopher M, Stone Kathryn L, Wu Terence L, Cheung Kei-Hoi, Miller Perry L, Williams Kenneth R
Center for Medical Informatics, Department of Anesthesiology, Yale University, New Haven, Connecticut 06520, USA.
J Proteome Res. 2007 Oct;6(10):4019-24. doi: 10.1021/pr070325f. Epub 2007 Sep 15.
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 includes 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 Classification 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.
我们开发了一个名为耶鲁蛋白质表达数据库（YPED）的集成式可通过网络访问的软件系统，以满足对来自高通量蛋白质组学技术的大量数据进行存储、检索和综合分析的需求。YPED是一个开源系统，它将凝胶分析结果与DIGE实验中的蛋白质鉴定结果整合在一起。该系统将用DeCyder分析的DIGE凝胶斑点和图像与从选定凝胶斑点获得的质谱蛋白质鉴定结果相关联。在凝胶内进行胰蛋白酶消化后，使用AB 4700上的MALDI-TOF/TOF对感兴趣斑点中的蛋白质进行分析，或者最近在AB 4800上进行分析，并通过Mascot结合AB GPS Explorer系统进行蛋白质鉴定。除了DIGE，YPED目前还处理来自MudPIT、iTRAQ和ICAT实验的蛋白质鉴定。样本描述与不断发展的MIAPE标准兼容。来自MudPIT和ICAT分析的串联MS/MS结果通过跨蛋白质组学管道进行验证，然后存储在数据库中以供查看并与已鉴定的蛋白质进行链接。研究人员可以通过一个安全的网络界面查看、筛选和下载他们的数据，该界面包括一个包含已鉴定蛋白质的表格、样本摘要、样本描述以及DIGE样本的可点击凝胶图像。还提供了便于样本比较和查看磷酸化蛋白质的工具。带有PANTHER分类系统注释的总结报告也可用于辅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获取。
