Overview of Digital Electrophoresis Analysis

Scott Medberry1, Sean Gallagher2, Butch Moomaw3

1 Agilent Technologies, Inc., Palo Alto, California, 2 UVP, Inc., Upland, California, 3 Hamamatsu Photonic Systems, Spring Branch, Texas
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 10.12
DOI:  10.1002/0471140864.ps1012s41
Online Posting Date:  September, 2005
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Abstract

Gel electrophoresis has become a ubiquitous method in molecular biology for separating biomolecules. This prominence is the result of several factors, including the robustness, speed, and potentially high throughput of the technique. The results of this method are traditionally documented using silver halide‐based photography followed by manual interpretation. While this remains an excellent method for qualitative documentation of single‐gel results, digital capture offers a number of significant advantages when documentation requires quantitation and sophisticated analysis. Digital images of gel electropherograms can be obtained rapidly using an image‐capture device, and the images can be easily manipulated using image analysis software. This overview presents reasons for digital documentation and analysis, defines some important key terms for imaging, explains the capture process and reviews the devices used for image capture, and provides an introduction to the software and methods used for one‐ and two‐dimensional digital image analysis.

Keywords: electrophoresis; imaging; software; digital analysis; quantitation

     
 
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Table of Contents

  • Reasons for Digital Documentation and Analysis
  • Key Terms for Imaging
  • Image Capture
  • Advances in CCD Technology
  • Analysis
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

   Appel, R.D., Hochstrasser, D.F., Funk, M., Vargas, J.R., Muller, A.F., and Scherrer, J.‐R. 1991. The MELANIE project: From a biopsy to automatic protein map interpretation by computer. Electrophoresis 12:722‐735.
   Garrels, J.I. 1989. The QUEST system for quantitative analysis of two‐dimensional gels. J. Biol. Chem. 264:5269‐5282.
   Glasbey, C.A. and Horgan, G.W. 1994. Image Analysis for the Biological Sciences. John Wiley & Sons, Chichester, England.
   Hamming, R.W. 1973. Numerical methods for scientists and engineers, 2nd ed. Dover Publications, New York.
   Huffman, D.A. 1952. A method for the construction of minimum‐redundancy codes. Proc. Inst. Elect. Radio Eng. 40:9‐12.
   Monardo, P.J., Boutell, T., Garrels, J.I., and Latter, G.I. 1994. A distributed system for two‐dimensional gel analysis. Comput. Appl. Biosci. 10:137‐143.
   Patton, W.F. 1995. Biologist's perspective on analytical imaging systems as applied to protein gel electrophoresis. J. Chromatogr. A. 698:55‐87.
   Plikaytis, B.D., Carlone, G.M., Edmonds, P., and Mayer, L.W. 1986. Robust estimation of standard curves for protein molecular weight and linear‐duplex DNA base‐pair number after gel electrophoresis. Anal. Biochem. 152:346‐364.
   Russ, J.C. 1995. The Image Processing Handbook. CRC Press, Boca Raton, Fla.
   Smith, J.M. and Thomas, D.J. 1990. Quantitative analysis of one‐dimensional gel electrophoresis profiles. Comput. Appl. Biosci. 6:93‐99.
   Sutherland, J.C., Lin, B., Monteleone, D.C., Mugavero, J., Sutherland, B.M., and Trunk, J. 1987. Electronic imaging system for direct and rapid quantitation of fluorescence from electrophoretic gels: Application to ethidium bromide–stained DNA. Anal. Biochem. 163:446‐457.
   Welch, T.A. 1984. A technique for high performance data compression. IEEE Computer. 17:21‐32.
Key References
   Glasbey and Horgan, 1994. See above.
  Describes general image‐processing techniques as they are applied to biological images.
   Russ, 1995. See above.
  A general reference book on digital image capture and analysis.
   Sutherland, J.C. 1993. Electronic imaging of electrophoretic gels and blots. In Advances in Electrophoresis, Vol. 6. (A. Chrambach, M.J. Dunn, and, B.J. Radola eds.) pp. 1‐41. VCH Verlagsgesellschaft mbH, Weinheim, Germany.
  Provides an overview of image capture with particular emphasis on types of capture equipment.
Internet Resources
   http://rsb.info.nih.gov/nih‐image
  NIH Image is free software that provides basic image analysis tools for the Macintosh.
   http://www.poynton.com/GammaFAQ.html
  Contains an excellent description of gamma correction in the Gamma FAQ.
   http://www‐lmmb.ncifcrf.gov/EP/table2Ddatabases.html
  A list of links to many two‐dimensional electrophoresis gel databases that are available via the Internet.
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