Methods for Computer Analysis and Comparison of Two-Dimensional Protein Patterns Obtained by Electrophoresis

  • Reinhold C. Mann
  • Betty K. Mansfield
  • James K. Selkirk
Part of the NATO ASI Series book series (volume 30)


Mammalian cells contain thousands of proteins each representing an important function for maintaining the homeostasis of the cell at the biochemical, genetic, or structural level. Two-dimensional gel electrophoresis is uniquely sensitive in its ability to separate these proteins in the first dimension by isoelectric focusing as a function of net charge, and in the second dimension as a function of molecular weight ([13]). The presence of a certain radioactively labeled protein in a preparation is indicated by a spot that is produced on a film. The intensity of the spot is indicative of the amount of protein. Usually several hundred, even up to a few thousand spots, i.e., proteins, can be distinguished in a gel image, which makes rigorous quantitative analysis by simple visual inspection impossible. Analysis of the voluminous information inherent in a gel image requires localization, quantitation and possibly identification of each protein. In addition, and equally importantly, it is necessary to make local and global comparisons between multiple gels that reflect potential changes in protein patterns from various disease states or after carcinogen or mutagen treatment, in order to demonstrate subtle changes that occur in the progression to the diseased state.


Projection Pursuit Simple Visual Inspection Spot Profile Projection Pursuit Method Rigorous Quantitative Analysis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. [1]
    Anderson N.L., J. Taylor, A.E. Scandora, B.P. Coulter, N.G. Anderson, “The TYCHO system for computer analysis of two-dimensional gel electrophoresis patterns,” Clin. Chem., 27, 1807–1820, (1981).Google Scholar
  2. [2]
    Anderson N.L., J. P. Hofmann, A. Gemmell, J. Taylor, “Global approaches to quantitative analysis of gene expression patterns observed by use of two-dimensional gel electrophoresis,” Clin. Chem., 30/12, 2031–2036, (1984).Google Scholar
  3. [3]
    Bossinger J., M.J. Miller, K.P. Vo, E.P. Geiduschek, N.H. Xuong, “Quantitative analysis of two-dimensional electrophoretograms,” J. Biol. Chem., 254, 7986–7998, (1979).Google Scholar
  4. [4]
    Davidson J.B., “Electronic autofluorography: principles, problems, and prospects,” in: Electrophoresis, V. Neuhoff, ed., Verlag Chemie, 235–251, (1984).Google Scholar
  5. [5]
    Friend E., W. Scher, J.G. Holland, T. Sato, “Hemoglobin synthesis in murine virus- induced leukemic cells in vitro: Stimulation of erythroid differentiation by dimethyl sulfoxide,” Proc. Natl Acad. Sci. USA, 68, 378–382, (1971).Google Scholar
  6. [6]
    Garrels J.I., “Two-dimensional gel electrophoresis and computer analysis of protein synthesized by clonal cell lines,” J. Biol Chem., 254, 7961–7979, (1979).Google Scholar
  7. [7]
    Huber P. J., “Projection pursuit,” Annals of Statistics 13:435–475, 1985.MathSciNetMATHCrossRefGoogle Scholar
  8. [8]
    Lemkin P.F., L.E. Lipkin, “GELLAB: A computer system for 2d gel electrophoresis analysis, Parts I, II, III,” Comp. Biomed. Res., 14, 272–297, 335–380, 407–446, (1981)CrossRefGoogle Scholar
  9. [9]
    Lutin W. A., C.F. Kyle, J.A. Freeman, “Quantitation of brain proteins by computer analyzed two-dimensional electrophoresis,” in: Electrophoresis 78, N. Catsimpoolas, ed., Elsevier/North Holland, Amsterdam-New York, 1979.Google Scholar
  10. [10]
    Mann R.C., B.K. Mansfield, J.K. Selkirk, “Automated analysis of digital images generated by two-dimensional gel electrophoresis,” in: Pattern Recognition in Practice II, E. S. Gelsema, L. N. Kanal (eds.), Elsevier/North Holland, Amsterdam, 1986, pp. 301–311.Google Scholar
  11. [11]
    Miller M.J., P.K. Vo, C. Nielsen, E.P. Geiduschek, N.H. Xuong “Computer analysis of two-dimensional gels: Semi-automatic matching,” Clin. Chem., 28, 867–875, (1982).Google Scholar
  12. [12]
    Miller M.J., A.D. Olson, S.S. Thorgeirsson, “Computer analysis of two-dimensional gels: automatic matching,” Electrophoresis 5., 297–303, (1984).CrossRefGoogle Scholar
  13. [13]
    O’Farrell P.H., “High resolution two-dimensional electrophoresis of proteins,” J. Biol.Chem., 250, 4007–4021, (1975).Google Scholar
  14. [14]
    Pardowitz I., H.G. Zimmer, V. Neuhoff, “Spot identification in two-dimensional patterns by a least-squares template matching,” Clin. Chem., 30, 1985–1988, (1984).Google Scholar
  15. [15]
    Ridder G., E. Von Bargen, D. Burgard, H. Pickrum, E. Williams “Quantitative analysis and pattern recognition of two-dimensional electrophoresis gels,” Clin. Chem., 30, 1919–1924, (1984).Google Scholar
  16. [16]
    Serra J., Image Analysis and Mathematical Morphology, Academic Press, London- New York, 1982.MATHGoogle Scholar
  17. [17]
    Skolnick M.M., S.R. Sternberg, J.V. Neel, “Computer programs for adapting two- dimensional gels to the study of mutation,” Clin. Chem., 28, 969–978, (1982).Google Scholar
  18. [18]
    Skolnick M.M., “Automated comparison of image similarities and differences,” PhD Thesis, University of Michigan 1984, University Microfilms International, Ann Arbor, Michigan.Google Scholar
  19. [19]
    Vo K.P., M.J. Miller, E.P. Geiduschek, C. Nielsen, A. Olson, N.H. Xuong, “Computer analysis of two-dimensional gels,” Anal.Biochem., 112, 258–271, (1981).CrossRefGoogle Scholar
  20. [20]
    Young I.T., G.L. Beckers, L. Dorst, A. Boerman, “Choosing filter parameters for non-linear image filtering,” in: Pattern Recognition in Practice II, E.S. Gelsema, L.N. Kanal (eds.), Elsevier/North Holland, Amsterdam, 1986, pp. 5–14.Google Scholar

Copyright information

© Springer-verlag Berlin Heidelberg 1987

Authors and Affiliations

  • Reinhold C. Mann
    • 1
  • Betty K. Mansfield
    • 1
  • James K. Selkirk
    • 2
  1. 1.Biology DivisionOak Ridge National LaboratoryOak RidgeUSA
  2. 2.National Toxicology ProgramNIEHSResearch Triangle ParkUSA

Personalised recommendations