Two strings to the systems biology bow: co-extracting the metabolome and proteome of yeast

Schmidt, Simon A., Jacob, Shana S., Ahn, Seong Beom, Rupasinghe, Thusitha, Kroemer, Jens O., Khan, Alamgir and Varela, Cristian (2013) Two strings to the systems biology bow: co-extracting the metabolome and proteome of yeast. Metabolomics, 9 1: 173-188. doi:10.1007/s11306-012-0437-1

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Author Schmidt, Simon A.
Jacob, Shana S.
Ahn, Seong Beom
Rupasinghe, Thusitha
Kroemer, Jens O.
Khan, Alamgir
Varela, Cristian
Title Two strings to the systems biology bow: co-extracting the metabolome and proteome of yeast
Journal name Metabolomics   Check publisher's open access policy
ISSN 1573-3882
Publication date 2013-02
Year available 2012
Sub-type Article (original research)
DOI 10.1007/s11306-012-0437-1
Volume 9
Issue 1
Start page 173
End page 188
Total pages 16
Place of publication New York, NY, United States
Publisher Springer
Collection year 2013
Language eng
Abstract 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.
Keyword Extraction
Sample preparation
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Published online: 1 June 2012.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2013 Collection
Australian Institute for Bioengineering and Nanotechnology Publications
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Citation counts: TR Web of Science Citation Count  Cited 6 times in Thomson Reuters Web of Science Article | Citations
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