A Robust Identification of the Protein Standard’s Bands in Two-Dimensional Electrophoresis Gel Images

Arturas Serackis, Dalius Matuzevicius, Dalius Navakauskas, Eldar Sabanovic, Andrius Katkevičius, Darius Plonis

Abstract


The aim of investigation, presented in this paper was to develop a software-based assistant for protein analysis workflow. The prior characterization of the unknown protein in two-dimensional electrophoresis gel images is performed accordingly to the molecular weight and isoelectric point of each protein spot estimated from the gel image before further sequence analysis by mass spectrometry. Paper presents a method for automatic and robust identification of the protein standard’s band in two-dimensional gel image. In addition, method introduces the identification of positions of the markers, prepared by using pre-selected proteins with known molecular mass. The robustness of the method was achieved by using special validation rules in proposed original algorithms. In addition, a self-organizing map based decision support algorithm, which takes Gabor coefficients as image features and searches for the differences in preselected vertical image bars. The experimental investigation proved the good performance of the new algorithms included into proposed method. The detection of the protein standard markers works without modification of algorithm parameters on two-dimensional gel images received using different staining and destaining procedures, which results different average levels of intensity in the images.

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Developed by Institute of Industrial Electronics and Electrical Engineering of RIGA TECHNICAL UNIVERSITY