Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks

Wolfram Weckwerth, Kathrin Wenzel, Oliver Fiehn

Research output: Contribution to journalArticle

291 Scopus citations

Abstract

A novel extraction protocol is described with which metabolites, proteins and RNA are sequentially extracted from the same sample, thereby providing a convenient procedure for the analysis of replicates as well as exploiting the inherent biological variation of independent samples for multivariate data analysis. A detection of 652 metabolites, 297 proteins and clear RNA bands in a single Arabidopsis thaliana leaf sample was validated by analysis with gas chromatography coupled to a time of flight mass spectrometer for metabolites, two-dimensional liquid chromatography coupled to mass spectrometry for proteins, and Northern blot analysis for RNA. A subset of the most abundant proteins and metabolites from replicate analysis of different Arabidopsis accessions was merged to form an integrative dataset allowing both classification of different genotypes and the unbiased analysis of the hierarchical organization of proteins and metabolites within a real biochemical network.

Original languageEnglish (US)
Pages (from-to)78-83
Number of pages6
JournalProteomics
Volume4
Issue number1
DOIs
StatePublished - Jan 2004
Externally publishedYes

Keywords

  • Gas chromatography-time of flight mass spectrometer
  • Metabolomics
  • Multidimensional chromatography
  • Network topology
  • Plant systems biology
  • Transcript profiling

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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