Data analysis of proteome pattern

Analysing 2D electrophoresis images on the level of pixels - analogous to spectral data

Investigation of proteome changes in cereal, meat and fish tissue

The proteome is expressed from the genome, influenced by environmental and processing conditions, and can be seen as the molecular link between the genome and the functional quality characteristics of the meat. In contrast to traditional biochemical methods where one protein is studied at a time, several hundred proteins can be studied simultaneously. Understanding the variations and different components of the proteome with regard to a food quality or process parameter will lead to knowledge that can be used in optimising the food quality.

One alternative for mapping the proteome in a tissue is two-dimensional gel electrophoresis 2 DE for separation of proteins, followed by identification of separated proteins by mass spectrometry (MS). Although being very informative, the gel images are complex consisting of a very high number of more or less overlapping protein spots, where the position of the protein spots may vary from one gel image to another. Furthermore, the staining intensity and background may be variable throughout the gels and from one gel to another. Thus, the process of analysing the gel images to search for the information revealed by the proteins is a critical and complex step of the process. A novel approach for analysing 2 DE images is based on alignment of the images instead of matching protein spots and analyse the aligned gel images pixel by pixel searching for changes. Variation from one gel to another even in strongly overlapping protein spots and in saturated protein spots can then be detected. The method is given the name Pixel based analysis of Multiple images for identification of Changes (PMC)


Figure 1. Plot of an envelope of overlapping proteins for two samples (upper plots) and a vectorised cross section through the red line are given for the same samples in the lower plot. Sample 1 and 2 is the samples 4370 h1 and h2, respectively, in [1].


People
Ellen Mosleth Færgestad
Kristin Hollung
Harald Grove
Harald Martens
Ragni Ofstad

Partners
Morten Beck Rye. Chemometrics and Bioinformatics Group, Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
Beata Walczak, Institute of Chemistry, Silesian University, Katowice, Poland
Frans van den Berg, University of Copenhagen, Faculty of Life Sciences, Frederiksberg, Denmark
Ulf G. Indahl, Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway.
Susanne Jacobsen, BioCentrum-DTU, Building 224, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark;
Ib Søndergaard, BioCentrum-DTU, Building 224, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark;
Flemming Jessen, Danish Institute for Fisheries Research, DTU, Building 221, DK-2800 Kgs. Lyngby, Denmark,
Bo M. Jørgensen, Danish Institute for Fisheries Research, DTU, Building 221, DK-2800 Kgs. Lyngby, Denmark


Financial support
Matforsks strategical research programme:
Biostatistics and bioinformatics
Project period: 2005-2008
Project leader: Achim Kohler
Financed by: Norwegian Agricultural Authority

Matforsks strategical research programme:
From proteome to protein functionality
Project period: 2005-2008
Project leader: Kristin Hollung
Financed by: Norwegian Agricultural Authority

Enzyme activity in pork
2006-2007
Project leader: Mahn Singh Sidhu
Project leader at Matforsk: Kristin Hollung

Stable and high food quality of wheat – improved compatibility for Norwegian production of cereals for food
2004-2008
Project leader: Bernt Hoel
Project leader at Matforsk: Ellen Mosleth Færgestad

Publications
Mosleth, E. and Uhlen, A. K., Norwegian J. Agric. Sci. 4 27-45 1990.
Grove, H., Hollung, K., Uhlen, A. K., Martens, H. and Færgestad, E. M., in: Hochstrasser, D. R., Sanchez, J.-C., Bini, L. and Pallini, V. (Eds.), 7th Sienna meeting from genome to proteome: back to the future, Proteomics Science, Sienna 2006.
Færgestad, E. M., Berg, F. v. d., M.B.Fye, H.Grove, et al., in: Hochstrasser, D. R. and Sanchez, J.-C. (Eds.), From Genome to proteome, Siena, Italy 2006, p. 192.
Færgestad, E. M., M.Rye, B.Walczak, L.Gidskehaug, et al., Proteomics 2007, submitted.
Jacobsen, S., Grove, H., Jensen, K. N., Sørensen, H. A., et al., Electrophoresis 2007, 28, 1289-1299.

Links
Biostatistics and bioinformatics
From proteome to protein functionality

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