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Acta Biochimica et Biophysica Sinica Advance Access originally published online on March 4, 2009
Acta Biochimica et Biophysica Sinica 2009 41(4):273-279; doi:10.1093/abbs/gmp010
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© The Author 2009. Published by ABBS Editorial Office in association with Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

A platform to standardize, store, and visualize proteomics experimental data

Guangyong Zheng1,2,3,{dagger}, Hong Li1,3,4,{dagger}, Chuan Wang1,{dagger}, Quanhu Sheng1,5, Haiwei Fan3, Shaoyou Yang3, Boshu Liu3, Jianliang Dai2,3, Rong Zeng5 and Lu Xie3,*

1 Bioinformation Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
2 School of Life Sciences, Fudan University, Shanghai 200433, China
3 Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235, China
4 Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
5 Research Center for Proteome Analysis, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China

* Correspondence address. Tel: +86-21-54-06-50-16; Fax: +86-21-54-06-5-057; E-mail: xielu{at}scbit.org


  Abstract

With the development of functional genomics research, large-scale proteomics studies are now widespread, presenting significant challenges for data storage, exchange, and analysis. Here we present the Integrated Proteomics Exploring Database (IPED) as a platform for managing proteomics experimental data (both process and result data). IPED is based on the schema of the Proteome Experimental Data Repository (PEDRo), and complies with the General Proteomics Standard (GPS) drafted by the Proteomics Standards Committee of the Human Proteome Organization. In our work, we developed three components for the IPED platform: the IPED client editor, IPED server software, and IPED web interface. The client editor collects experimental data and generates an extensible markup language (XML) data file compliant with PEDRo and GPS; the server software parses the XML data file and loads information into a core database; and the web interface displays experimental results, to provide a convenient graphic representation of data. Given software convenience and data abundance, IPED is a powerful platform for data exchange and presents an important resource for the proteomics community. In its current release, IPED is available at http://www.biosino.org/iped2.

Keywords    integrated platform; general proteomics standard; XML data file; proteomics experiment

Received: September 25, 2008; Accepted: February 9, 2009

{dagger} These authors contributed equally to this work.


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