Proteomics complex biological proteomes

Wu, C. C. MacCoss, M. J. Shotgun proteomics tools for the analysis of complex biological systems. Curr. Opin. Mol. Ther. 2002, 4, 242-250. 

D-polyacrylamide gel electrophoresis) maps of protein mixtures is discussed. 2D PAGE is considered the classical and principal tool for protein separation—prior to mass spectrometry—to achieve the main goal of proteomics, that is, a comprehensive identification and quantification of every protein present in a complex biological sample that would allow analysis of an entire intact proteome (Wilkins et al., 1997 Righetti et al., 2001 Hamdan and Righetti, 2005). 

Yates III, J. R. (2003). Reproducibility of quantitative proteomic analyses of complex biological mixtures by multidimensional protein identification technology. Anal. Chem. 75, 5054-5061. Washburn, M. P., Wolters, D.,... 

Proteomics and Genomics— Technologies for Global Oversight of Complex Biological Systems... 

No current analytical strategy is capable of fully resolving complex biological samples. For this reason, orthogonal separation techniques are often combined to maximize peptide separation before the mass spectrometric analysis. The aim is to reduce as much as possible the number of coeluting peptides introduced into the MS at any given time, so as to maximize peptide identification and proteome coverage. 

Shotgun proteomics is the method of choice to obtain comprehensive prote-ome coverage from complex biological samples. Despite its high-throughput... 

Qualitative and quantitative comparison of proteomes under different conditions can now help to further unravel complex biological processes. This is due to drastic improvements in massively parallel protein separation, identification and characterization as well as in bioinformatics. 

The goal of this chapter is to detail the need for such activity-based methods, and to describe the development and application of ABPP by highlighting several studies that have established the utility of this chemical proteomic method as a powerful strategy for the discovery and functional analysis of complex biological proteomes, as well as their individual constituents. 

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