Limits...
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.

Show MeSH

Related in: MedlinePlus

Protein amount (green) and protein synthesis (red) in a heat shock experiment of Bacillus subtilis 168. The synthesis patterns can differ dramatically between different stimuli but can be easily related using the protein amount patterns
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2279157&req=5

Fig4: Protein amount (green) and protein synthesis (red) in a heat shock experiment of Bacillus subtilis 168. The synthesis patterns can differ dramatically between different stimuli but can be easily related using the protein amount patterns

Mentions: Protein synthesis at a given point in time can be detected by using in vivo labeling with radioisotopes. Radiolabeling is perfectly suitable for the detection of changes in protein synthesis during stimulus response studies. Especially 35S radioactively labeled amino acids like methionine or cysteine or 14C-labeled compounds are applicable. After 2-D separation, the incorporated material is analyzed by phosphorimaging (Amemiya and Miyahara 1988; Johnston et al. 1990). This delivers data with a linear correlation between radioactivity and measured signal over nearly five orders of magnitude. The striking advantage of radiolabeling in stimulus/response experiments is the ability to detect fast but relatively small changes in protein quantities (Bernhardt et al. 1999; Fig. 4).Fig. 4


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)

Protein amount (green) and protein synthesis (red) in a heat shock experiment of Bacillus subtilis 168. The synthesis patterns can differ dramatically between different stimuli but can be easily related using the protein amount patterns
© Copyright Policy
Related In: Results  -  Collection

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

Fig4: Protein amount (green) and protein synthesis (red) in a heat shock experiment of Bacillus subtilis 168. The synthesis patterns can differ dramatically between different stimuli but can be easily related using the protein amount patterns
Mentions: Protein synthesis at a given point in time can be detected by using in vivo labeling with radioisotopes. Radiolabeling is perfectly suitable for the detection of changes in protein synthesis during stimulus response studies. Especially 35S radioactively labeled amino acids like methionine or cysteine or 14C-labeled compounds are applicable. After 2-D separation, the incorporated material is analyzed by phosphorimaging (Amemiya and Miyahara 1988; Johnston et al. 1990). This delivers data with a linear correlation between radioactivity and measured signal over nearly five orders of magnitude. The striking advantage of radiolabeling in stimulus/response experiments is the ability to detect fast but relatively small changes in protein quantities (Bernhardt et al. 1999; Fig. 4).Fig. 4

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