Protein expression, quantitation changes

Proteome profiling allows quantitative and global examination of the changes in protein expression in different strains or cells under different conditions. Two-dimensional gel... 

Unlike the genome the proteome is not a static but a dynamic and constantly changing entity that is cell- and tissue-specific and dependent on the environment. Because of the dynamic nature of protein expression and fimction, these properties need to be determined quantitatively in a time-dependent manner. Proteomics, the study of the proteome, involves the analysis of the complete pattern of the expressed proteins and their post-translational modifications in a cell, tissue, or body fluid. An integrated view of any living system hence requires an analysis that takes into account the spatial as well as temporal distribution of all the proteins in a cell or tissue. The analytical effort that is necessary to deliver such an integrated view is by several orders of magnitude more complicated than that of the recently finished human genome (Lander ef al. 2001 Venter et al. 2001). 

Protein expression and function under various physiological conditions can be investigated by employing 2DE techniques. Quantitative regulation of proteomics allows us to monitor quantitative changes in protein expression within a cell or tissue under different circumstances, particularly in a disease state. 

Relative protein quantitation is the basis of all types of differential proteome analyses. In the 2D-gel approach protein staining with either visible or fluorescent dyes provides a reliable and sensitive method to detect changes in protein expression or isoform abundance. In the multidimensional LC approach quantitation relies mostly on stable isotope labeling and ratios between light and heavy isotopomers are determined by MS or MS/MS at the peptide level. Labeling can be performed on the protein level by... 

More than one replica can be made from a single gel and Quantitative changes in protein expression can be measured, subject to certain limitations. 

It is therefore clear that until these alternative approaches mature into robust techniques for quantitative protein expression profiling, 2-DE will remain the separation work-horse in many proteomic investigations. This technique has the capacity to support the simultaneous analysis of the changes in expression of hundreds to thousands of proteins and as such it remains unrivalled as an open protein expression profiling approach. 

Choe, L. D Ascenzo, M. ReMn, N.R. Pappin D. Ross, R Williamson, B. Guertin, S. Pribil, R Lee, K.H. 8-Plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzeimer s disease. Proteomics 2007, 7, 3651-3660. 

Label-free quantitation is a rapid and fairly accurate approach for the survey of change in protein expression levels between two biological samples and is a promising alternative to stable isotope labeling approaches. It is a highly reproducible method that enables relative quantitation of the proteins across samples [14,15]. In a label-free quantitative approach, each sample has to be analyzed individually and sequentially by MS (unlike... 

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