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Nucleic Acids Research Advance Access published online on October 23, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn701
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Human Proteinpedia: a unified discovery resource for proteomics research

Kumaran Kandasamy1,2,3, Shivakumar Keerthikumar1,2, Renu Goel1, Suresh Mathivanan1,2, Nandini Patankar1, Beema Shafreen1, Santosh Renuse1, Harsh Pawar1, Y. L. Ramachandra2, Pradip Kumar Acharya1, Prathibha Ranganathan1, Raghothama Chaerkady1,3, T. S. Keshava Prasad1 and Akhilesh Pandey3,*

1Institute of Bioinformatics, International Tech Park, Bangalore 560 066, 2Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India and 3McKusick-Nathans Institute of Genetic Medicine and the Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA

* To whom correspondence should be addressed. Tel: +410 502 6662; Fax: +410 502 7544; Email: pandey{at}jhmi.edu

Received August 16, 2008. Revised September 24, 2008. Accepted September 26, 2008.

Sharing proteomic data with the biomedical community through a unified proteomic resource, especially in the context of individual proteins, is a challenging prospect. We have developed a community portal, designated as Human Proteinpedia (http://www.humanproteinpedia.org/), for sharing both unpublished and published human proteomic data through the use of a distributed annotation system designed specifically for this purpose. This system allows laboratories to contribute and maintain protein annotations, which are also mapped to the corresponding proteins through the Human Protein Reference Database (HPRD; http://www.hprd.org/). Thus, it is possible to visualize data pertaining to experimentally validated posttranslational modifications (PTMs), protein isoforms, protein–protein interactions (PPIs), tissue expression, expression in cell lines, subcellular localization and enzyme substrates in the context of individual proteins. With enthusiastic participation of the proteomics community, the past 15 months have witnessed data contributions from more than 75 labs around the world including 2710 distinct experiments, >1.9 million peptides, >4.8 million MS/MS spectra, 150 368 protein expression annotations, 17 410 PTMs, 34 624 PPIs and 2906 subcellular localization annotations. Human Proteinpedia should serve as an integrated platform to store, integrate and disseminate such proteomic data and is inching towards evolving into a unified human proteomics resource.


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