page_title: Two-dimensional gel electrophoresis
section_title: 2D gel analysis software
hierarchical_section_title: Two-dimensional gel electrophoresis / 2D gel analysis software
context_page_description: Two-dimensional gel electrophoresis, abbreviated as 2-DE or 2-D electrophoresis, is a form of gel electrophoresis commonly used to analyze proteins. Mixtures of proteins are separated by two properties in two dimensions on 2D gels. 2-DE was first independently introduced by O'Farrell and Klose in 1975.
context_section_description: 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 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), and 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. Mass spectrometry analysis can identify precise mass measurements along with the sequencing of peptides that range from 1000-4000 atomic mass units. 
  
  For an overview of the current approach for software analysis of 2DE gel images see or.
caption: Warping: Images of two 2D electrophoresis gels, overlaid with Delta2D. First image is colored in orange, second one colored in blue. Due to running differences, corresponding spots do not overlap.
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