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Nucleic Acids Research Advance Access published online on October 2, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn654
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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

PPDB, the Plant Proteomics Database at Cornell

Qi Sun1, Boris Zybailov2, Wojciech Majeran2, Giulia Friso2, Paul Dominic B. Olinares2 and Klaas J. van Wijk2,*

1Computation Biology Service Unit, Cornell Theory Center and 2Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA

*To whom correspondence should be addressed. Tel: +1 607 255 3664; Fax: +1 607 255 5407; Email: kv35{at}cornell.edu

Received August 15, 2008. Revised September 17, 2008. Accepted September 18, 2008.

The Plant Proteomics Database (PPDB; http://ppdb.tc.cornell.edu), launched in 2004, provides an integrated resource for experimentally identified proteins in Arabidopsis and maize (Zea mays). Internal BLAST alignments link maize and Arabidopsis information. Experimental identification is based on in-house mass spectrometry (MS) of cell type-specific proteomes (maize), or specific subcellular proteomes (e.g. chloroplasts, thylakoids, nucleoids) and total leaf proteome samples (maize and Arabidopsis). So far more than 5000 accessions both in maize and Arabidopsis have been identified. In addition, more than 80 published Arabidopsis proteome datasets from subcellular compartments or organs are stored in PPDB and linked to each locus. Using MS-derived information and literature, more than 1500 Arabidopsis proteins have a manually assigned subcellular location, with a strong emphasis on plastid proteins. Additional new features of PPDB include searchable posttranslational modifications and searchable experimental proteotypic peptides and spectral count information for each identified accession based on in-house experiments. Various search methods are provided to extract more than 40 data types for each accession and to extract accessions for different functional categories or curated subcellular localizations. Protein report pages for each accession provide comprehensive overviews, including predicted protein properties, with hyperlinks to the most relevant databases.


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