Geometric algorithms for the analysis of 2D-electrophoresis gels

Alon Efrat, Frank Hoffmann, Klaus Kriegel, Christof Schultz, Carola Wenk

Research output: Contribution to journalArticle

39 Scopus citations

Abstract

In proteomics, two-dimensional gel electrophoresis (2-DE) is a separation technique for proteins. The resulting protein spots can be identified either by using picking robots and subsequent mass spectrometry or by visual cross inspection of a new gel image with an already analyzed master gel. Difficulties especially arise from inherent noise and irregular geometric distortions in 2-DE images. Aiming at the automated analysis of large series of 2-DE images, or at the even more difficult interlaboratory gel comparisons, the bottleneck is to solve the two most basic algorithmic problems with high quality: Identifying protein spots and computing a matching between two images. For the development of the analysis software CAROl at Freie Universitát Berlin, we have reconsidered these two problems and obtained new solutions which rely on methods from computational geometry. Their novelties are: 1. Spot detection is also possible for complex regions formed by several "merged" (usually saturated) spots; 2. User-defined landmarks are not necessary for the matching. Furthermore, images for comparison are allowed to represent different parts of the entire protein pattern, which only partially "overlap." The implementation is done in a client server architecture to allow queries via the internet. We also discuss and point at related theoretical questions in computational geometry.

Original languageEnglish (US)
Pages (from-to)299-315
Number of pages17
JournalJournal of Computational Biology
Volume9
Issue number2
DOIs
StatePublished - Jan 1 2002

Keywords

  • Approximation algorithms
  • Delaunay triangulation
  • Gel matching
  • Spot detection
  • Two-dimensional gel electrophoresis

ASJC Scopus subject areas

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

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