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Updated: Jun 29, 2026

mRNA Interactome Capture from Plant Protoplasts
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mRNA Interactome Capture from Plant Protoplasts

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PPDB, the Plant Proteomics Database at Cornell.

Qi Sun1, Boris Zybailov, Wojciech Majeran

  • 1Computation Biology Service Unit, Cornell Theory Center, Cornell University, Ithaca, NY 14853, USA.

Nucleic Acids Research
|October 4, 2008
PubMed
Summary

The Plant Proteomics Database (PPDB) now offers enhanced data integration for Arabidopsis and maize (Zea mays) proteomic research. It includes experimental protein identification, subcellular localization, and post-translational modifications, aiding plant science discovery.

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Area of Science:

  • Plant biology
  • Proteomics
  • Bioinformatics

Background:

  • The Plant Proteomics Database (PPDB) has served as a key resource since 2004.
  • Existing resources lacked comprehensive integration of experimental proteomic data for major crop species like maize (Zea mays) and model plants like Arabidopsis.

Purpose of the Study:

  • To enhance the Plant Proteomics Database (PPDB) with integrated experimental proteomic data for Arabidopsis and maize.
  • To improve data accessibility and enable advanced searching of protein identification, localization, and modifications.

Main Methods:

  • Utilized in-house mass spectrometry (MS) for experimental proteome identification across various plant samples.
  • Integrated over 80 published Arabidopsis proteome datasets and performed BLAST alignments for cross-species comparisons.

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Last Updated: Jun 29, 2026

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  • Manually curated subcellular localization data, with a focus on plastid proteins, and incorporated post-translational modification information.

    • Main Results:

    • Identified over 5000 protein accessions in both maize and Arabidopsis.
    • Stored and linked more than 80 published Arabidopsis proteome datasets to specific loci.
    • Manually assigned subcellular locations for over 1500 Arabidopsis proteins, emphasizing plastid proteins.
    • Added searchable features for post-translational modifications, proteotypic peptides, and spectral counts.

    Conclusions:

    • The enhanced PPDB provides a comprehensive, integrated resource for plant proteomics research.
    • New features facilitate detailed analysis of protein identification, localization, and modifications in maize and Arabidopsis.
    • PPDB supports further discovery in plant biology through accessible, curated experimental data.