Application of Bioinformatics Tools in Gel-Based Proteomics

Personalized medicine is the most promising approaches in the treatment of various diseases, especially cancer. The use of appropriate biomarkers for personalized treatment has advantage over conventional therapeutics approach, as it confer maximum effectiveness with minimum side effect. Personalized treatment can be achieved by implementation of omic studies in clinical practices. Application of genomic, transcriptomic, proteomic and metabolomic studies deliver a vast amount of data that lead to the discovery of novel biomarkers for diagnostic, prognostic and therapeutic purposes. Therefore, further exploration in omic study could lead to the implementation of personalized medicine as a standard therapeutic scheme in the clinic. Proteomics is a global study of entire proteins of cell, tissue and organism in a particular condition and time point (Graves & Haystead, 2002). Proteomics is a very comprehensive discipline that includes the study of expression, function, localization, structure, modification, and protein-protein interaction (Graves & Haystead, 2002; Lim & ElenitobaJohnson, 2004). A proteomics experiment generates vast amount of data that require further analysis, and systems biology is the main approach. Systems biology is an integrative science that studies the complex behavior of biological entities at the systems level (Kitano, 2002a, 2002b). Integrating the proteomics data into systems biology language is an important approach in understanding the behavior of the complex organisms at various levels (Souchelnytskyi, 2005). In recent years, our knowledge of proteomics and system biology is growing rapidly and create an excitement in scientific community because of its potential in novel biomarker and drug discovery (Duncan & Hunsucker, 2005). Proteomics studies are highly dependent on the technology for protein separation and identification, and bioinformatics for data analysis. By protein separation techniques, gelbased and liquid chromatography (LC)-based approaches represent the primary stream in proteomics. In gel-based approach, that is, conventional 2D gel electrophoresis (2D-GE) and 2D differential gel electrophoresis (2D-DIGE), the proteins are separated by their molecular weight and isoelectric point. In LC-based approach, the proteins or peptides are separated by using high performance liquid chromatography (Aebersold & Mann, 2003; Cravatt et al., 2007). The identification and characterization of proteins or peptides by mass spectrometry are followed after separation (Kolker et al., 2006). In more recent years, antibody-based methods emerging as important approaches in proteomics. These approaches included the