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What's the Difference? 2D DIGE Image Analysis by DeCyderTM versus SameSpotsTM.
Vanessa Schnaars1, Marvin Dörries1,2, Michael Hutchins3
1General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany.
Journal of Molecular Microbiology and Biotechnology
|November 15, 2018
Summary
Comparing two software solutions for two-dimensional difference gel electrophoresis (2D DIGE) revealed that SameSpotsTM offers faster, reproducible protein abundance analysis. Both software packages provide reliable results for quantitative proteomics, even with major abundance changes.
Area of Science:
- Proteomics
- Biochemistry
- Environmental Microbiology
Background:
- Two-dimensional difference gel electrophoresis (2D DIGE) is crucial for quantitative proteomics.
- Reproducibility and efficiency depend on replicate numbers, image acquisition, and analysis software.
- Protein abundance analysis is critically influenced by image analysis systems.
Purpose of the Study:
- To compare the performance of DeCyderTM and SameSpotsTM image analysis software for 2D DIGE.
- To evaluate the impact of different software strategies on protein spot detection and alignment.
- To assess the reproducibility and accuracy of quantitative proteomics data generated by each software.
Main Methods:
- 2D DIGE was performed on proteomes from three environmental bacteria.
- DeCyderTM and SameSpotsTM were used for image analysis with minimal user intervention.
- Protein spot detection and alignment strategies of both software were compared.
Main Results:
- SameSpotsTM enabled faster and more reproducible determination of abundance changes by analyzing proteome maps.
- Differences in raw spot volumes between software did not impact calculated abundance changes.
- Minor abundance changes were highly similar, and major changes did not affect biological interpretation.
Conclusions:
- SameSpotsTM provides efficient and reproducible quantitative proteomics analysis.
- 2D DIGE remains a valuable tool for quantitative proteomics when combined with modern imaging and analysis techniques.
- Software choice impacts analysis workflow but not the biological interpretation of significant proteomic changes.