Applications of Proteomics using Advanced Computer Technologies

The field of functional proteomics is built on insights into protein function made through various reductionist methods. Understanding the details of those functions in a biological system and identifying the key proteins involved necessitates the development of robust, reproducible, and high-throughput experimental methods to assess the effect of a protein on a system. Early proteomics technologies analyzed global protein levels and patterns of protein expression, including large-scale two-dimensional gel electrophoresis and liquid chromatography/mass spectrometry for global analysis. Proteomics data interpretation relies on information-rich repositories to identify the proteins in an experiment, the significance of changes, and to predict their interactions with other proteins and small molecule ligands. As the field moves to analyze increasingly complex systems, the use of computational methods for mining proteomic data will become more important. This essay presents classical, new, and emerging methods in proteomics, from isolation to mass spectrometry. The use of advanced computational methods in data processing and proteome analysis has revolutionized the field of proteomics due to the production of large datasets. Furthermore, we give a detailed classification to clearly outline the methods available and present their applications.