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The state of the art in the analysis of two-dimensional gel electrophoresis images.

Berth M, Moser FM, Kolbe M, Bernhardt J - Appl. Microbiol. Biotechnol. (2007)

Bottom Line: Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments.Challenges for analysis software as well as good practices are highlighted.We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field.

View Article: PubMed Central - PubMed

Affiliation: DECODON GmbH, Rathenau-Strasse 49a, 17489 Greifswald, Germany.

ABSTRACT
Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments. Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments. We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results. Challenges for analysis software as well as good practices are highlighted. We emphasize image warping and related methods that are able to overcome the difficulties that are due to varying migration positions of spots between gels. Spot detection, quantitation, normalization, and the creation of expression profiles are described in detail. The recent development of consensus spot patterns and complete expression profiles enables one to take full advantage of statistical methods for expression analysis that are well established for the analysis of DNA microarray experiments. We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field.

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Analysis work flow of a 2-D-gel-based proteomics experiment in Delta2D. 1 Sample preparation; 2 2-D gel electrophoresis; 3 2-D gels are stained/detected and digitized; 4 spot positions are aligned across gel images by warping; 5 a proteome map/fusion gel image is generated by combining the images using a union fusion; 6 the union fusion image serves as basis for constructing the consensus spot pattern for the whole experiment; 7 the consensus spot pattern is transferred to all images and subsequently remodeled; 8 expression profiles are extracted and analyzed to find relevant proteins
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Fig1: Analysis work flow of a 2-D-gel-based proteomics experiment in Delta2D. 1 Sample preparation; 2 2-D gel electrophoresis; 3 2-D gels are stained/detected and digitized; 4 spot positions are aligned across gel images by warping; 5 a proteome map/fusion gel image is generated by combining the images using a union fusion; 6 the union fusion image serves as basis for constructing the consensus spot pattern for the whole experiment; 7 the consensus spot pattern is transferred to all images and subsequently remodeled; 8 expression profiles are extracted and analyzed to find relevant proteins

Mentions: The typical workflow of a 2-D-gel-based proteomics analysis using the “image warping first” approach and consensus spot patterns can be described as follows (Fig. 1):


The state of the art in the analysis of two-dimensional gel electrophoresis images.

Berth M, Moser FM, Kolbe M, Bernhardt J - Appl. Microbiol. Biotechnol. (2007)

Analysis work flow of a 2-D-gel-based proteomics experiment in Delta2D. 1 Sample preparation; 2 2-D gel electrophoresis; 3 2-D gels are stained/detected and digitized; 4 spot positions are aligned across gel images by warping; 5 a proteome map/fusion gel image is generated by combining the images using a union fusion; 6 the union fusion image serves as basis for constructing the consensus spot pattern for the whole experiment; 7 the consensus spot pattern is transferred to all images and subsequently remodeled; 8 expression profiles are extracted and analyzed to find relevant proteins
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2279157&req=5

Fig1: Analysis work flow of a 2-D-gel-based proteomics experiment in Delta2D. 1 Sample preparation; 2 2-D gel electrophoresis; 3 2-D gels are stained/detected and digitized; 4 spot positions are aligned across gel images by warping; 5 a proteome map/fusion gel image is generated by combining the images using a union fusion; 6 the union fusion image serves as basis for constructing the consensus spot pattern for the whole experiment; 7 the consensus spot pattern is transferred to all images and subsequently remodeled; 8 expression profiles are extracted and analyzed to find relevant proteins
Mentions: The typical workflow of a 2-D-gel-based proteomics analysis using the “image warping first” approach and consensus spot patterns can be described as follows (Fig. 1):

Bottom Line: Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments.Challenges for analysis software as well as good practices are highlighted.We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field.

View Article: PubMed Central - PubMed

Affiliation: DECODON GmbH, Rathenau-Strasse 49a, 17489 Greifswald, Germany.

ABSTRACT
Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments. Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments. We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results. Challenges for analysis software as well as good practices are highlighted. We emphasize image warping and related methods that are able to overcome the difficulties that are due to varying migration positions of spots between gels. Spot detection, quantitation, normalization, and the creation of expression profiles are described in detail. The recent development of consensus spot patterns and complete expression profiles enables one to take full advantage of statistical methods for expression analysis that are well established for the analysis of DNA microarray experiments. We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field.

Show MeSH
Related in: MedlinePlus