2D Gel Analysis Software
In quantitative proteomics, these tools primarily analyze bio-markers by quantifying individual proteins, and showing the separation between one or more protein "spots" on a scanned image of a 2-DE gel. Additionally, these tools match spots between gels of similar samples to show, for example, proteomic differences between early and advanced stages of an illness. Software packages include BioNumerics 2D, Delta2D, ImageMaster, Melanie, PDQuest, Progenesis and REDFIN - among others. While this technology is widely utilized, the intelligence has not been perfected. For example, while PDQuest and Progenesis tend to agree on the quantification and analysis of well-defined well-separated protein spots, they deliver different results and analysis tendencies with less-defined less-separated spots.
Challenges for automatic software-based analysis include:
- incompletely separated (overlapping) spots (less-defined and/or separated)
- weak spots / noise (e.g., "ghost spots")
- running differences between gels (e.g., protein migrates to different positions on different gels)
- unmatched/undetected spots, leading to missing values
- mismatched spots
- errors in quantification (several distinct spots may be erroneously detected as a single spot by the software and/or parts of a spot may be excluded from quantification)
- differences in software algorithms and therefore analysis tendencies
Generated picking lists can be used for the automated in-gel digestion of protein spots, and subsequent identification of the proteins by mass spectrometry.
For an overview of the current approach for software analysis of 2DE gel images see or.
Read more about this topic: Two-dimensional Gel Electrophoresis
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