Two strings to the systems biology bow

Co-extracting the metabolome and proteome of yeast

Simon A. Schmidt, Shana S. Jacob, Seong Beom Ahn, Thusitha Rupasinghe, Jens O. Krömer, Alamgir Khan, Cristian Varela

Research output: Contribution to journalArticle

13 Citations (Scopus)


Experimental samples are valuable and can represent a significant investment in time and resources. It is highly desirable at times to obtain as much information as possible from a single sample. This is especially relevant for systems biology approaches in which several 'omics platforms are studied simultaneously. Unfortunately, each platform has a particular extraction methodology which increases sample number and sample volume requirements when multiple 'omics are analyzed. We evaluated the integration of a yeast extraction method; specifically we explored whether fractions from a single metabolite extraction could be apportioned to multiple downstream 'omics analytical platforms. In addition, we examined how variations to a chloroform/methanol yeast metabolite extraction regime influence metabolite recoveries. We show that protein suitable for proteomic analysis can be recovered from a metabolite extraction and that recovery of lipids, while reproducible, are not wholly quantitative. Higher quenching solution temperatures (-30 °C) can be used without significant leakage of intracellular metabolites when lower fermentation temperatures (20 °C) are employed. However, extended residence time in quenching solution, in combination with vigorous washing of quenched cell pellets, leads to extensive leakage of intracellular metabolites. Finally, there is minimal difference in metabolite amounts obtained when metabolite extractions are performed at 4 °C compared to extractions at -20 °C. The evaluated extraction method delivers material suitable for metabolomic and proteomic analyses from the same sample preparation.

Original languageEnglish
Pages (from-to)173-188
Number of pages16
Issue number1
Publication statusPublished - 2013


  • extraction
  • metabolome
  • sample preparation
  • proteomics
  • lipidomics

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