Overview of Digital Electrophoresis Analysis

Butch Moomaw1, Scott Medberry2, Sean R. Gallagher3

1 Spring Branch, Texas, 2 Redwood Shores, California, 3 UVP, LLC, Upland, California
Publication Name:  Current Protocols Essential Laboratory Techniques
Unit Number:  Unit 7.5
DOI:  10.1002/9780470089941.et0705s9
Online Posting Date:  October, 2014
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Abstract

Digital imaging is the method of choice for documentation and analysis of electrophoretic separations of protein and DNA. Digital images of gel electropherograms can be obtained rapidly using CCD‐based cameras, and the images can be easily archived and analyzed using image analysis software. This overview defines important key terms and calculations for imaging, explains the capture process, reviews the range of CCD technologies used for image capture, and provides an introduction to the software and methods used for one‐ and two‐dimensional digital image analysis. © 2014 by John Wiley & Sons, Inc.

Keywords: electrophoresis; imaging; analysis; CCD; sCMOS; 2‐D PAGE

     
 
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Table of Contents

  • Introduction
  • Reasons for Digital Documentation and Analysis
  • Key Terms for Imaging
  • Image Capture
  • Advances in CCD Technology
  • List of Typical Camera Features and Benefits
  • Analysis
  • Image Databases for Image Retrieval and Analysis
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

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.
  Janesick, J.R. 2001. Scientific charge‐coupled devices. SPIE Publications, Bellingham, Washington.
  Medberry, S., Gallagher, S., and Moomaw, B. 2004. Overview of digital electrophoresis analysis. Curr. Protoc. Mol. Biol. 66:10.5.1‐10.5.25.
  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, Florida.
  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 Comp. 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://rsbweb.nih.gov/ij/
  The main ImageJ site at the NIH, visited over 10,000,000 times to date. Contains documentation and links on ImageJ. ImageJ is free software that provides basic image analysis tools (see APPENDIX ).
  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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