Bioinformatics

Pixel-based analysis of multiple images for the identification of changes: A novel approach applied to unravel proteome patters of 2-D electrophoresis gel images

  1. Ellen Mosleth Færgestad Dr.1,2,*,
  2. Morten Rye3,
  3. Beata Walczak4,
  4. Lars Gidskehaug3,
  5. Jens Petter Wold1,
  6. Harald Grove1,2,
  7. Xiaohong Jia1,2,
  8. Kristin Hollung1,
  9. Ulf G. Indahl2,
  10. Frank Westad1,
  11. Frans van den Berg5,
  12. Harald Martens1,2,5,6

Article first published online: 28 AUG 2007

DOI: 10.1002/pmic.200601026

Issue

PROTEOMICS

PROTEOMICS

Volume 7, Issue 19, pages 3450–3461, No. 19 October 2007

Additional Information

How to Cite

Færgestad, E. M., Rye, M., Walczak, B., Gidskehaug, L., Wold, J. P., Grove, H., Jia, X., Hollung, K., Indahl, U. G., Westad, F., van den Berg, F. and Martens, H. (2007), Pixel-based analysis of multiple images for the identification of changes: A novel approach applied to unravel proteome patters of 2-D electrophoresis gel images. PROTEOMICS, 7: 3450–3461. doi: 10.1002/pmic.200601026

Author Information

  1. 1

    Matforsk AS, Norwegian Food Research Institute, Ås, Norway

  2. 2

    Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway

  3. 3

    Chemometrics and Bioinformatics Group, Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway

  4. 4

    Institute of Chemistry, Silesian University, Katowice, Poland

  5. 5

    University of Copenhagen, Faculty of Life Sciences, Frederiksberg, Denmark

  6. 6

    CIGENE, Center for Integrated Genetics, Ås, Norway

*Matforsk AS, Norwegian Food Research Institute, Osloveien 1, N-1430 Ås, Norway Fax: +47-64970333

Publication History

  1. Issue published online: 1 OCT 2007
  2. Article first published online: 28 AUG 2007
  3. Manuscript Received: 31 OCT 2006
Corrected by:

Erratum: Pixel-based analysis of multiple images for the identification of changes: A novel approach applied to unravel proteome patters of 2-D electrophoresis gel images

Vol. 7, Issue 24, 4613, Article first published online: 10 DEC 2007

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Keywords:

  • Bioinformatics;
  • Chemometrics;
  • Two-dimensional electrophoresis

Abstract

A novel approach for revealing patterns of proteome variation among series of 2-DE gel images is presented. The approach utilises image alignment to ensure that each pixel represents the same information across all gels. Gel images are normalised, and background corrected, followed by unfolding of the images to 1-D pixel vectors and analysing pixel vectors by multivariate data modelling. Information resulting from the data analysis is refolded back to the image domain for visualisation and interpretation. The method is rapid and suitable for automatic routines applied after the gel alignment. The approach is compared with spot volume analysis to illustrate how this approach can solve persistent problems like mismatch of protein spots, erroneous missing values and failure to detect variation in overlapping proteins. The method may also detect variation in the border area of saturated proteins. The approach is given the name pixel-based analysis of multiple images for the identification of changes (PMC). The method can be used for multiple images in general. Effects of pretreatment of the images are discussed.

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