Skip to main content
SpringerLink
Log in

Advances in plant proteomics—key techniques of proteome

  • Review
  • Published:
Frontiers of Biology in China

Abstract

Following the completion of genome sequencing of model plants, such as rice (Oryza sativa L.) and Arabidopsis thaliana, the era of functional plant genomics has arrived which provides a solid basis for the development of plant proteomics. We review the background and concepts of proteomics, as well as the key techniques which include: (1) separation techniques such as 2-DE (two-dimensional electrophoresis), RP-HPLC (reverse phase high performance liquid chromatography) and SELDI (surface enhanced laser desorption/ionization) protein chip; (2) mass spectrometry such as MALDI-TOF-MS (matrix assisted laser desorption/ionizationtime of flight-mass spectrometry) and ESI-MS/MS (electrospray ionization mass spectrometry/mass spectrometry); (3) Peptide sequence tags; (4) databases related to proteomics; (5) quantitative proteome; (6) TAP (tandem affinity purification) and (7) yeast two-hybrid system. In addition, the challenges and prospects of proteomics are also discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Biemann K (1990). Nomenclature for peptide fragment ions (positive ions). Meth Enzymol, 193(1): 886–887

    Article  PubMed  CAS  Google Scholar 

  • Bjellqvist B, Sanchez J C, Pasquaili C, Ravier F, Paquet N, Frutiger S, Hughes G J, Hochstrasser D F A (1993). nonlinear wide-range immobilized pH gradient for two-dimensional electrophoresis and its definition in a relevant pH scale. Electrophoresis, 14(1): 1357–1365

    Article  PubMed  CAS  Google Scholar 

  • Carr S A, Annan R S (1998). Overview of peptide and protein analysis by mass spectrometry. In:Ausubel F M, Brent R, Kingston R E, Moore D D, Seidman J G, Smith J A, and Struhl K, eds. Current Protocols in Molecular Biology. New York: John Wiley & Sons Inc.

    Google Scholar 

  • Dunn MJ (1987). Two-dimensional polyacrylamide gel electrophoresis. In:Chrambach A, Dunn M J, Radola B J, eds.Advances in Electrophoresis, VCH, Weinheim, 1–109

    Google Scholar 

  • Eng J K, McCormack A L, Yates J R (1994). An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom, 5(11): 976–989

    Article  CAS  Google Scholar 

  • Enright A J, Iliopoulos I, Kyrpides N C, Ouzounis C A (1999). Protein interaction maps for complete genomes based on gene fusion events. Nature, 402(6757): 86–90

    Article  PubMed  CAS  Google Scholar 

  • Fenn J B, Mann M, Meng C K, Wong S F, Whitehouse CM (1989). Electrospray ionization for mass spectrometry of large biomolecules. Science, 246(4926): 64–71

    Article  PubMed  CAS  Google Scholar 

  • Fields S, Song O (1989). A novel genetic system to detect proteinprotein interactions. Nature, 340(6230): 245–246

    Article  PubMed  CAS  Google Scholar 

  • Garfin D E (2003). Two-dimensional gel electrophoresis: an overview. Trends Anal Chem, 22(5): 263–272

    Article  CAS  Google Scholar 

  • Gavin A C, Bösche M, Krausel R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick J M, Michon A M, Cruciat C M, Remor M, Höfert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier M A, Copley R R, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415(6868): 141–147

    Article  PubMed  CAS  Google Scholar 

  • Görg A, Obermaier C, Boguth G, Csordas A, Diaz J J, Madjar J J (1997). Very alkaline immobilized pH gradients for two-dimensional electrophoresis of ribosomal and nuclear proteins. Electrophoresis, 18(3–4): 328–337

    Article  PubMed  Google Scholar 

  • Görg A, Postel W, Günther S (1988). The current state of twodimensional electrophoresis with immobilized pH gradients. Electrophoresis, 9(9): 531–546

    Article  PubMed  Google Scholar 

  • Henzel WJ, Billeci TM, Stults J T, Wong S C, Grimley C, Watanabe C (1993). Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence database. Proc Natl Acad Sci USA, 90(11): 5011–5015

    Article  PubMed  CAS  Google Scholar 

  • Herbert B (1999). Advances in protein solubilization for two-dimensional electrophoresis. Electrophoresis, 20(4–5): 660–663

    Article  PubMed  CAS  Google Scholar 

  • Herbert B, Molloy M P, Gooley A A, Walsh B J, Bryson W G, Williams K L (1998). Improved protein solubility in two-dimensional electrophoresis using tributyl phosphine as a reducing agent. Electrophoresis, 19(5): 845–851

    Article  PubMed  CAS  Google Scholar 

  • Hunt D F, Yates J R, Shabanowitz J, Winston S, and Hauer C R (1986). Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci USA, 83(17): 6233–6237

    Article  PubMed  CAS  Google Scholar 

  • James P, Quadroni M, Carafoli E, Gonnet G (1993). Protein identification by mass profile fingerprinting. Biocheml Biophys Res Commun, 195(1): 58–64

    Article  CAS  Google Scholar 

  • James P, Quadroni M, Carafoli E, Gonnet G (1994). Protein identification in DNA database by peptide mass fingerprinting. Protein Sci, 3(8): 1347–1350

    Article  PubMed  CAS  Google Scholar 

  • Kruft V, Eubel H, Jänsch L, Werhahn W, Braun H P (2001). Proteomic approach to identify novel mitochondrial proteins in Arabidopsis. Plant Physiol, 127(12): 1694–1710

    Article  PubMed  CAS  Google Scholar 

  • Kumar A, Snyder M (2002). Protein complexes take the bait. Nature, 415(6868): 123–124

    Article  PubMed  CAS  Google Scholar 

  • Laemmli U K (1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 225(5234): 680–685

    Article  Google Scholar 

  • Li B L (1998). Functional proteomics. Biochmistry, 18(6): 1–3

    Google Scholar 

  • Li J X, Steen H, Gygi S P (2003). Protein profiling with cleavable isotope-coded affinity tag (cicat) reagents: the yeast salinity stress response. Mol Cell Proteomics, 2(11): 1198–1204

    Article  PubMed  CAS  Google Scholar 

  • Link A J (1999). 2-D proteome analysis protocols. USA: Humana Press.

    Google Scholar 

  • Ma J, Ptashne M (1987). A new class of transcriptional activators. Cell, 51(1): 113–119

    Article  PubMed  CAS  Google Scholar 

  • Mann M, Hojrup P, Roepstorff P (1993). Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mass Spectrom, 22(6): 338–345

    Article  PubMed  CAS  Google Scholar 

  • Marcotte E M, Pellegrini M, Ng H L, Rice D W, Yeates T O, Eisenberg D (1999). Detecting protein function and protein-protein interactions from genome sequences. Science, 285(5428): 751–753

    Article  PubMed  CAS  Google Scholar 

  • Mastro R, Hall M (1999). Protein delipidation and precipitation by tri-n-butylphosphate, acetone, and methanol treatment for isoelectric focusing and two-dimensional gel electrophoresis. Anal Biochem, 273(2): 313–315

    Article  PubMed  CAS  Google Scholar 

  • Millar A H, Sweetlove L J, Giegé P, Leaver C J (2001). Analysis of the Arabidopsis mitochondrial proteome. Plant Physiol, 127(12): 1711–1727

    Article  PubMed  CAS  Google Scholar 

  • Molloy MP, Herbert B, Walsh B J, Tyler MI, Traini M, Sanchez, J C (1998). Extraction of membrane proteins by differential solubilization for separation using two-dimensional electrophoresis. Electrophoresis, 19(5): 837–844

    Article  PubMed  CAS  Google Scholar 

  • Nivinskas H, Cole K D (1996). Environmentally benign staining procedure for electrophoresis gels using coomassie brilliant blue. BioTechniques, 20(3): 380–385

    PubMed  CAS  Google Scholar 

  • O’Farrell P H (1975). High resolution two-dimensional gel electrophoresis of proteins. J Biol Chem, 250(10): 4007–4021

    PubMed  CAS  Google Scholar 

  • Onnerfjord P, Ekstrom S, Bergquist J, Nilson J, Laurell T, Marko-Varga G (1999). Homogenous sample preparation for automated high throughput analysis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom, 13(5): 315–322

    Article  PubMed  CAS  Google Scholar 

  • Opiteck G J, Ramirez S M, Jorgenson J W, Moseley M A (1998). Comprehensive two-dimensional high-performance liquid chromatography for the isolation of overexpressed proteins and proteome mapping. Anal Biochem, 258(2): 349–361

    Article  PubMed  CAS  Google Scholar 

  • Pappin D J C, Hojrup P, Bleasby A J (1993). Rapid identification of proteins by peptide mass fingerprinting. Curr Biol, 3(4): 327–332

    Article  PubMed  CAS  Google Scholar 

  • Peltier J B, Friso G, Kalume DE, Roepstorff P, Nilsson F, Adamska I, van Wijk K J (2000). Proteomics of the chloroplast: systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell, 12(3): 319–342

    Article  PubMed  CAS  Google Scholar 

  • Pennington S R, Dunn M J (2001). Proteomics: from Protein Squence to Function. BIOS Scientific Publishers Limited

  • Perdew G H, Schaup H W, Selivonchick D P (1983). The use of a zwitterionic detergent in two-dimensional gel electrophoresis of trout liver microsomes. Anal Biochem, 135(2): 453–455

    Article  PubMed  CAS  Google Scholar 

  • Rabilloud T, Adessi C, Giraudel A, Lunardi J (1997). Improvement of the solubilization of proteins in two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis, 18(3–4): 307–316

    Article  PubMed  CAS  Google Scholar 

  • Rabilloud T, Hubert M, Tarroux P (1986). Procedures for twodimensional electrophoresis analysis of nuclear proteins. J Chromatogr A, 351(1): 77–89.

    Article  CAS  Google Scholar 

  • Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Séraphin B (1999). A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol, 17(10): 1030–1032

    Article  CAS  Google Scholar 

  • Santoni V, Molloy M, Rabilloud T (2000). Membrane protein and proteomics: un amour impossible? Electrophoresis, 21(6): 1054–1070

    Article  PubMed  CAS  Google Scholar 

  • van Wijk K J (2001). Challenges and prospects of plant proteomics. Plant Physiol, 126(6): 501–508

    Article  PubMed  Google Scholar 

  • Wasinger V C, Cordwell S J, Cerpa-Poljak A, Yan J X, Gooley A A, Wilkins MR, Duncan MW, Harris R, Williams KL, Humphery-Smith I (1995). Progress with gene-product mapping of the mollicutes: mycoplsma genitalium. Electrophoresis, 16(1): 1090–1094

    Article  PubMed  CAS  Google Scholar 

  • Yan JX, Kett WC, Herbert BR, Gooley A A, Packer NH, Williams K L (1998). Identification and quantitation of cysteine in proteins separated by gel electrophoresis. J Chromatogr A, 813(1): 187–200

    Article  PubMed  CAS  Google Scholar 

  • Yan J X, Wait R, Berkelman, Gooley A A, Packer N H, Williams K L (2000). A modified silver staining protocol for visualization of proteins compatible with matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry. Electrophoresis, 21(17): 3666–3672

    Article  PubMed  CAS  Google Scholar 

  • Yates J R, Eng J K, McCormack A L (1995). Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal Chem, 67(18): 3202–3210

    Article  PubMed  CAS  Google Scholar 

  • Yates J R, Eng J K, McCormack A L, Schieltz D (1995). Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem, 67(8): 1426–1436

    Article  PubMed  CAS  Google Scholar 

  • Yates J R, Speicher S, Griffin P R, Hunkapiller T (1993). Peptide mass maps: a highly informative approach to protein identification. Anal Biochem, 214(2): 397–408

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Biotechnology, Hangzhou Academy of Agriculture Science, Hangzhou, 310024, China

    Songlin Ruan, Huasheng Ma, Shiheng Wang, Ya Xin, Lihua Qian & Jianxing Tong

  2. National Center for Biomedical Analysis, Beijing, 100850, China

    Jie Wang

Authors
  1. Songlin Ruan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Huasheng Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shiheng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ya Xin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lihua Qian
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jianxing Tong
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jie Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Huasheng Ma.

Additional information

__________

Translated from Heredtas (Beijing), 2006, 28(11): 1472–1486 [译自: 遗传]

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ruan, S., Ma, H., Wang, S. et al. Advances in plant proteomics—key techniques of proteome. Front. Biol. China 3, 245–258 (2008). https://doi.org/10.1007/s11515-008-0048-4

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11515-008-0048-4

Keywords

Search

Navigation