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. 2009 Jan;37(Database issue):D773-81.
doi: 10.1093/nar/gkn701. Epub 2008 Oct 23.

Human Proteinpedia: a unified discovery resource for proteomics research

Kumaran Kandasamy  1 , Shivakumar Keerthikumar, Renu Goel, Suresh Mathivanan, Nandini Patankar, Beema Shafreen, Santosh Renuse, Harsh Pawar, Y L Ramachandra, Pradip Kumar Acharya, Prathibha Ranganathan, Raghothama Chaerkady, T S Keshava Prasad, Akhilesh Pandey
Affiliations

Human Proteinpedia: a unified discovery resource for proteomics research

Kumaran Kandasamy et al. Nucleic Acids Res. 2009 Jan.

Abstract

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developed a community portal, designated as Human Proteinpedia (http://www.humanproteinpedia.org/), for sharing both unpublished and published human proteomic data through the use of a distributed annotation system designed specifically for this purpose.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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Figures

Figure 1.
Figure 1.
HPRD molecule page with 13 novel phosphorylation sites deposited in Human Proteinpedia. HPRD molecule page for vimentin is shown with a novel serine phosphorylation site that was contributed through Human Proteinpedia. Thirteen novel phosphorylation events were identified and shared using Human Proteinpedia. The panel on the middle displays description of the experiment, phosphopeptide identifications and the peptide score calculated by the respective search engine that was used. The tandem mass spectrometry (MS/MS) spectrum is linked to all of the peptides and the lower right panel shows the MS/MS spectrum of a phosphopeptide in a spectrum viewer.
Figure 2.
Figure 2.
Display of tissue expression data submitted to Human Proteinpedia. Molecule page of vimentin in HPRD is displayed with novel tissue expression sites. It is shown as expressed in B cell and is hyperlinked to the experimental description, peptide identification data, peptide score, precursor mass, charge state, sequence identifiers and their corresponding MS/MS spectrum. Processed and raw MS/MS files are linked to ProteomeCommons as indicated in the lower left panel either using the web interface or by launching the Tranche downloader. Clicking on either one of lung, ovary, spleen, tonsil or thyroid gland will hyperlink to HPA page for vimentin that is shown in the upper right panel.
Figure 3.
Figure 3.
Display of subcellular localization data for a hypothetical protein: MGC33867/KIAA2013. Molecule page of a hypothetical protein MGC33867/KIAA2013 is displayed. Lower left panel shows subcellular localization of the protein to the endoplasmic reticulum, while the right panel shows identification of the same protein to be localized in the Golgi apparatus. Fluorescence microscopy images are provided along with the experimental annotations.
See this image and copyright information in PMC

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