Treatment of Over-Saturated Protein Spots in Two-Dimensional Electrophoresis Gel Images

Article type: Research Article

Authors: Serackis, Artūras | Navakauskas, Dalius

Affiliations: Department of Electronics Systems, VGTU, Naugarduko 41-413, 422, LT-03227 Vilnius, Lithuania, e-mail: arturas.serackis@el.vgtu.lt; dalius.navakauskas@el.vgtu.lt

Abstract: The paper addresses the over-saturated protein spot detection and extraction problem in two-dimensional electrophoresis gel images. The effective technique for detection and reconstruction of over-saturated protein spots is proposed. The paper presents: an algorithm of the median filter mask adaptation for initial filtering of gel image; the models of over-saturation used for gel image analysis; several models of protein spots used for reconstruction; technique of the automatic over-saturated protein spot search and reconstruction. Experimental investigation confirms that proposed search technique lets to find up to 96% of over-saturated protein spots. Moreover the proposed flexible protein spot shape models for reconstruction are faster and more accurate in comparison to the flexible diffusion model.

Keywords: two-dimensional electrophoresis, protein spot search, image processing, image reconstruction, modelling

Journal: Informatica, vol. 21, no. 3, pp. 409-424, 2010