Systems Biology - Methods - Proteomics

From Keaslingwiki

1 Project Description
2 People
3 Relevant Publications
4 Equipment

Project Description

The advent of systems biology ushers in a multitude of potential applications built on the foundations of genomics, proteomics and metabolomics. Each of these complementary disciplines refers to the comprehensive, high-throughput profiling of a particular class of cellular components, genes, proteins and metabolites, respectively. Like genomics before it, proteomics began with relatively small sample sets and targeted analyses, yielding, as technology progressed, to envelop the analysis of complex mixtures that represent the entire proteome for an organism, organelle or other biological sources (e.g., biofluids, tissues). Often called “shotgun proteomics”, these untargeted methods can yield high-confidence identification of many hundreds to thousands of proteins from a biological sample. To enhance the ability to detect low abundance proteins such studies require extensive sample preparation, separation and/or purification prior to mass spectrometric analysis. The strengths of mass spectrometry such as high-throughput capabilities, facile automation and rapid protein identification are well-suited for the complex mixture analysis that large scale proteomics requires. We utilize quantitative proteomics based on isotopic labeling methods (ICAT, iTRAQ) to compare the proteome of several organisms under a variety of conditions. Such comparisons produce insight into the bacterial response to environmental stresses or the incorporation of exogenous pathways.

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People

Lead Researchers:

Advisor:

Jay Keasling

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Relevant Publications

A. Mukhopadhyay, Z. He, E. J. Alm, A. P. Arkin, E. E. Baidoo, S. C. Borglin, W. Chen, T. C. Hazen, Q. He, H-Y. Holman et al. 2006 "Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach" J. Bacteriol. 188(11):4068-4078.
A. M. Redding, A. Mukhopadhyay, D. C. Joyner, T. C. Hazen, J. D. Keasling. 2006 "Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics" Brief Funct. Genomic Proteomic s 5(2):133-143.

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