YPED: A Web-Accessible Database System for Protein Expression Analysis
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- 作者：Mark A. Shifman ; Yuli Li ; Christopher M. Colangelo ; Kathryn L. Stone ; Terence L. Wu ; Kei-Hoi Cheung ; Perry L. Miller ; Kenneth R. Williams
- 刊名：Journal of Proteome Research
- 出版年：2007
- 出版时间：October 2007
- 年：2007
- 卷：6
- 期：10
- 页码：4019 - 4024
- 全文大小：373K
- 年卷期：v.6,no.10(October 2007)
- ISSN：1535-3907
文摘
We have developed an integrated web-accessible software system called the Yale Protein ExpressionDatabase (YPED) to address the need for storage, retrieval, and integrated analysis of large amountsof data from high throughput proteomic technologies. YPED is an open source system which integratesgel analysis results with protein identifications from DIGE experiments. The system associates the DIGEgel spots and image, analyzed with DeCyder, with mass spectrometric protein identifications fromselected gel spots. Following in gel trypsin digestion, proteins in spots of interest are analyzed usingMALDI-TOF/TOF on an AB 4700 or, more recently, on an AB 4800 with protein identifications performedby Mascot in conjunction with the AB GPS Explorer system. In addition to DIGE, YPED currently handlesprotein identifications from MudPIT, iTRAQ, and ICAT experiments. Sample descriptions are compatiblewith the evolving MIAPE standards. Tandem MS/MS results from MudPIT, and ICAT analyses arevalidated with the Trans-Proteomic Pipeline and then stored in the database for viewing and linking tothe identified proteins. Researchers can view, subset, and download their data through a secure Webinterface 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 andthe viewing of phosphoproteins. A summary report with PANTHER Classification System annotationsis also available to aid in biological interpretation of the results. The source code is open-source andis available from http://yped.med.yale.edu/yped_dist.