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.