Protein Image Alignment via Piecewise Affine Transformations

Abstract We present a new approach for aligning families of 2D gels. Instead of choosing one of the gels as reference and performing pairwise alignment, we construct an ideal gel that is representative for the entire family and obtain a set of piecewise affine transformations that optimally align each gel of the family to the ideal gel. The coefficients defining the transformations as well as the ideal landmarks are obtained as the solution of a large-scale quadratic programming problem that can be solved efficiently by interiorpoint methods. 1 Proteomics and 2-D PAGE Proteome analysis involves the separation, visualization and analysis of complex mixtures containing as many as several thousand proteins obtained from whole cells, tissues or organisms. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), first introduced by O'Farrell [9] and Klose [8] in 1975, remains a core technology for separating complex protein mixtures in the majority of proteome projects. The main g...

• Type: Journal
• Year: 2006
• Where: JCB
• Authors: Florian A. Potra, Xing Liu, Françoise Seillier-Moiseiwitsch, Anindya Roy, Yaming Hang, Mark R. Marten, Babu Raman, Carol Whisnant
• Keywords: Gels, Ideal Gel, JCB 2006, Proteins