The Plant Proteome Database (PPDB; http://ppdb.tc.cornell.edu), launched in 2004 (1), provides an integrated resource for experimentally identified proteins in Arabidopsis thaliana, maize (Zea mays) and rice (Oryza sativa) (2). Internal BLAST alignments link maize, rice and Arabidopsis information. Experimental identification is based on in-house mass spectrometry of cell type-specific proteomes, or specific subcellular proteomes, and total leaf proteome samples. In addition, more than 80 published Arabidopsis proteome datasets from subcellular compartments or organs are stored in PPDB and linked to each locus. 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. New features of PPDB include searchable post-translational modifications and searchable experimental proteotypic peptides and spectral count information for each identified accession based on in-house experiments. Active links to other community databases (e.g. TAIR and TIGR) are present.
  1. Friso, G., Giacomelli, L., Ytterberg, A. J., Peltier, J. B., Rudella, A., Sun, Q., and Wijk, K. J. (2004) In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database. Plant Cell 16, 478-499
  2. Sun, Q., Zybailov, B., Majeran, W., Friso, G., Olinares, P. D., and van Wijk, K. J. (2009) PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res 37, D969-974

Klaas Jan van Wijk
Department of Plant Biology, Emerson Hall
Cornell University
Ithaca NY 14853