Plant proteome analysis by mass spectrometry: principles, problems, pitfalls and recent developments

• Published in: Phytochemistry Vol. 65; no. 11; pp. 1449 - 1485
• Main Authors: Newton, Russell P., Brenton, A.Gareth, Smith, Chris J., Dudley, Edward
• Format: Book Review Journal Article
• Language: English
• Published: England Elsevier Ltd 01.06.2004
• Subjects: chemical analysis; chloroplasts; electrospray tandem mass spectrometry; literature reviews; mass spectrometry; Mass Spectrometry - instrumentation; Mass Spectrometry - methods; Mass Spectrometry - trends; matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry; mitochondria; Models, Molecular; organelles; plant extracts; plant proteins; Plant Proteins - analysis; Plants - genetics; Plants - metabolism; polyacrylamide gel electrophoresis; post-translational modification; protein-protein interactions; proteome; Proteome - analysis; proteomics; Proteomics - methods; Spectrometry, Mass, Electrospray Ionization; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
• ISSN: 0031-9422; 1873-3700
• DOI: 10.1016/j.phytochem.2004.04.015

Basic strategy from extraction through fractionation and purification to mass spectrometric analysis is discussed and some plant proteomic applications are reviewed, as are imminent future developments in relevant mass spectrometric instrumentation. The genome of several species has now been elucidated; these genomes indicate the proteomic potential of the cell. While identification of genomes has been, and continues to be, a technically and intellectually demanding process, the identification of the proteome contains inherently greater difficulties. The proteome of each living cell is dynamic, altering in response to the individual cell's metabolic state and reception of intracellular and extracellular signal molecules, and many of the proteins which are expressed will be post-translationally altered. Thus if the purpose of the proteome analysis is to aid the understanding of protein function and interaction, then it is identification of the proteins in their final state which is required: for this mass spectrometric identification of individual proteins, indicating site and nature of modifications, is essential. Here we review the principles of the methodologies involved in such analyses, give some indication of current achievements in plant proteomics, and indicate imminent and prospective technical developments.