Genome-wide metabolomics, proteomics and data integration: from molecule to organism
Wolfram Weckwerth1
1Dept. Mol. Systems Biology, University of Vienna
In recent years genomics has been extended to functional genomics. Towards the characterization of organisms or species on the genome level, changes on the metabolite and protein level have been shown to be essential to assign functions to genes and to describe the dynamic molecular phenotype. Gas chromatography and liquid chromatography coupled to mass spectrometry (GC/MS and LC/MS) are well suited for the fast and comprehensive analysis of ultracomplex metabolite samples. For the integration of metabolite profiles with quantitative protein profiles the shotgun proteomics approach using LC/MS and label-free quantification of unique proteins in a complex protein digest is described as well a targeted absolute quantification using internal stable-isotope-labelled peptide standards. Multivariate statistics are applied to examine sample pattern recognition and biomarker identification in systems biology. The integration of the data reveals multiple biomarkers giving evidence for an increase of information in such holistic approaches. With computational simulation of metabolic networks and experimental measurements, it can be demonstrated that biochemical regulation is reflected by metabolite network dynamics measured in a metabolomics/proteomics approach. Examples in are presented to substantiate the applicability of the integrative approach.
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