Proteomics networking

Ward JL, Baker JM, and Beale MH (2007) Recent applications of NMR spectroscopy in plant metabolomics. FEBS J. 274 1126-1131 Weckwerth W (2007) Metabolomics methods and protocols. Humana press, Totowa, NJ Weckwerth W (2008) Integration of metabolomics and proteomics in molecular plant physiology -coping with the complexity by data-dimension-ality reduction. Physiol. Plant. 132 176-189 Weckwerth W, Wenzel K, and Fiehn O (2004) Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics 4 78-83 Wouters FS, Verveer PJ, and Bastiaens PIH (2001) Imaging biochemistry inside cells. Trends Cell Biol 11 203-211... 

Wang, P. L, and E. M. Marcotte. (2010). It s the machine that matters Predicting gene function and phenotype from protein networks. / Proteomics 73 2277-2289 Oct 10. 

Weckwerth, W., Wenzel, K., and Fiehn, O. (2004) Process for the integrated extraction identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics, 4 (1), 78-83. 

Waters KM, Shankaran H, Wiley HS, Resat H, Thrall BD. Integration of microarray and proteomics data for biological pathway analysis and network modeling of epidermal growth factor signaling in human mammary epithelial cells. Keystone Symposia, 2005. 

Zhang H,Tang X, Munske GR, et al. In vivo identification of the outer membrane protein OmcA-MtrC interaction network in Shewanella oneidensis MR-1 cells using novel hydrophobic chemical cross-linkers. J. Proteome Res. 2008 7 1712-1720. 

Guerrero C, Tagwerker C, Kaiser P, et al. An integrated mass spectrometry-based proteomic approach quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol. Cell. Proteomics. 2006 5 366-378. 

A. J. Pocklington, M. Cumiskey, J. D. Armstrong, and S. G. N. Grant. 2006, The Proteomes of Neurotransmitter Receptor Complexes from Modular Networks with Distributed Functionality Underlying Plasticity and Behaviour, www.molecularsystemsbiology.com—Article nr 2006.0023. 

W. Liebermeister and E. Klipp, Bringing metabolic networks to life Integration of kinetic, metabolic, and proteomic data. Theor. Biol. Med Modeling 3(42), (2006). 

The application of the improved MS techniques presented above with highly resolving separation methods, such as 2-D electrophoresis, capillary HPLC, and CE, resulted in the creation of a new science, proteomics63 While genomics, described by DNA databases, represents the ground stage of the cell, the study of the differential status of the cell, due to various stimuli or disease states, reflects the functional expression of protein products or proteomics. Proteomics studies are aimed at identifying the proteome, the network of proteins that define the... 

Sheehan KM, Calvert VS, Kay EW et al (2005) Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol Cell Proteomics 4 346-355... 

Proteomics includes a variety of technologies that include differential protein display on gels, protein chips, quantitation of protein amoimts, analysis of post-translational modifications, characterization of protein complexes and networks and bioinformatics. All this information in combination with genome and phenotype studies will ultimately yield a comprehensive picture of a cellular or tissue proteome (Wasinger and Corthals 2002). 

The genome of an organism provides a blue print for its structural and functional attributes. Genome functions through the synthesis, regulation, and activity of proteins. A dynamic and well balanced network of DNA-protein, RNA-protein, and protein-protein interactions (PPIs) maintain the cellular system as a complex but cohesive unit (1). Proteomics serves as a medium to unravel protein functions and ultimately to understand a living system or a disease condition (2-5). Over the years, classical genetic... 

Wolf-Yadlin, A., Hautaniemi, S., Lauffen-burger, D.A. and White, E.M. (2007) Multiple Reaction Monitoring for Robust Quantitative Proteomic Analysis of Cellular Signaling Networks. Proc Natl Acad Sci, 104, 5860-5865. 

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