Proteomics as a Functional Genomics Tool

  • Ulrike Mathesius
  • Nijat Imin
  • Siria H. A. Natera
  • Barry G. Rolfe
Part of the Methods in Molecular Biology™ book series (MIMB, volume 236)


To understand the function of all the genes in an organism, one needs to know not only which genes are expressed, when, and where, but also what the protein end products are and under which conditions they accumulate in certain tissues. Proteomics aims at describing the whole protein output of the genome and complements transcriptomic and metabolomic studies. Proteomics depends on extracting, separating, visualizing, identifying, and quantifying the proteins and their interactions present in an organism or tissue at any one time. All of these stages have limitations. Therefore, it is, at present, impossible to describe the whole proteome of any organism. Plants might synthesize many thousands of proteins at one time, and the whole potentially synthesized proteome certainly exceeds the number of estimated genes for that genome. This occurs because the gene products of one gene can differ due to alternative splicing and a variety of possible posttranslational modifications. It is, therefore, essential to optimize every step towards detecting the whole proteome while realizing the limitations. We concentrate here on the most commonly used steps in high-throughput plant proteomics with the techniques we have found most reproducible and with the highest resolution and quality.

Key Words

expressed sequence tags glycosylation mass spectrometry model plants N-terminal sequencing peptide mass fingerprinting phosphorylation posttranslational modifications protein-protein interaction proteome analysis two-dimensional gel electrophoresis 


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Copyright information

© Humana Press Inc., Totowa, NJ 2003

Authors and Affiliations

  • Ulrike Mathesius
    • 1
    • 2
  • Nijat Imin
    • 1
    • 2
  • Siria H. A. Natera
    • 1
    • 2
  • Barry G. Rolfe
    • 1
    • 2
  1. 1.ARC Centre of Excellence for Integrative Legume ResearchAustralian National UniversityCanberraAustralia
  2. 2.Genomic Interactions Group, Research School of Biological SciencesAustralian National UniversityCanberraAustralia

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