What is PPDB? PPDB is a Plant Proteome DataBase for Arabidopsis thaliana and maize (Zea mays). Initially PPDB was dedicated to plant plastids, but has now expanded to the whole plant proteome – hence it was renamed from Plastid PDB to Plant PDB in November 2007.

Which proteins can be searched? All protein-encoding gene models in the Arabidopsis, maize and rice, as assembled respectively in http://www.arabidopsis.org/, http://www.maizesequence.org/index.html and http://rice.plantbiology.msu.edu/, supplemented with plastid and mitochondrial genomes. These are all uploaded in PPDB and are linked to each other via a BLAST alignment. Thus every predicted protein in both species can be searched for experimental and other information (even if not experimentally identified).

What information is stored in PPDB? The PPDB stores experimental data from in-house proteome and mass spectrometry analysis, curated information about protein function, protein properties and subcellular localization. Importantly, proteins are particularly curated for possible (intra) plastid location and their plastid function. Protein accessions identified in published Arabidopsis (and other Brassicacea) proteomics papers are cross-referenced to rapidly determine previous experimental identification by mass spectrometry.

Protein report pages. Each protein has a protein report page that summarizes all information for that protein stored in PPDB. A few other databases are hyperlinked for each accession to obtain additional information for this protein accession. These report pages also provide detailed information about matched mass spectrometry data and how it maps to the protein. For individual protein searches, this is the best way to obtain a comprehensive overview.

How to extract information from PPDB? The PPDB has nine search functions to extract multiple types of information (output) stored in PPDB for any accession, by simply choosing a search function and selecting the relevant ‘radio buttons’. Information can all be extracted from the PPDB for individual accessions or in batch format.

The search functions are:
Search by Accession. (TAIR accessions or ZmGI accessions).
Search with Protein name. (free text search – note this can be slow).
Search Proteome Experiments. Select sample source by species, organ, cell type or subcellular fraction.
Search Comparative Proteomics experiments. Select particular comparative proteomics experiments.
Search Subcellular Proteomes. Extract proteins based on their curated location in the cell.
Search Protein Function. Extract all proteins with a selected function.
Search Proteomics Publications. Find major proteomics publications and the protein accessions identified.
Search Post-translational Modifications. Find all proteins with the selected PTM and show the modified peptides.
Search Biochemical Pathways. Find details about (potential) proteins operating in a selected pathway. Currently only Calvin cycle.

Extractable protein information (via selection of radiobuttons):
Annotation protein name - from original source (DFCI Gene Index) or TAIR) and in-house (lab) annotation
Subcellular location - curated (in-house) and predicted
Biochemical properties and topology - denatured or native mass, pI, gravy, TMDs, cystein content
Function - Functional PFAM domains and functional classification (MapMan system)
Mass spectrometry based identification - Mowse score, # matched peptides and queries, homologues
Sample information - genotype, tissue type, cell type, organelle, suborganellar fraction
Cross-reference to other studies - proteomics papers, fluorescence labeling studies
Homologues in other species - Arabidopsis, maize, rice

Disclaimer:
When using the PPDB, please cite the following reference: Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ. (2008) PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res. 2009;37(Database issue):D969-D974. doi:10.1093/nar/gkn654

Contact:
Klaas van Wijk (kv35@cornell.edu) or Qi Sun (qisun@cornell.edu)

    
(Image courtesy of Buchanan, B., Gruissem, W. Jones, R.L. Biochemistry and Molecular Biology of Plants , Publisher - American Society of Plant Physiologists)