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Deep Metabolic Profiling Assessment of Tissue Extraction Protocols for Three Model Organisms
Hagen M Gegner1, Nils Mechtel1, Elena Heidenreich1
1Metabolomics Core Technology Platform, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
Frontiers in Chemistry
|May 13, 2022
Summary
This study compared seven metabolite extraction protocols across Drosophila, mouse, and zebrafish. A 75% ethanol and methyl tertiary-butyl ether (MTBE) combination proved most reproducible for metabolic profiling in model organisms.
Area of Science:
- Metabolomics and Systems Biology
- Comparative Genomics and Proteomics
- Biochemical Analysis and Assay Development
Background:
- Metabolic profiling aids understanding of diseases like cancer, diabetes, Alzheimer's, Parkinson's, and COVID-19.
- Model organisms are crucial for studying intricate metabolic pathways in human diseases.
- Standardized conditions and sampling are vital for successful metabolomic studies in model organisms.
Purpose of the Study:
- To systematically assess and compare seven extraction protocols for optimizing metabolite extraction across different model organisms and sample types.
- To identify the most reproducible and effective extraction method for comprehensive metabolic profiling.
- To provide a data-driven tool for scientists to select optimal protocols for their specific research contexts.
Main Methods:
- A standardized metabolic profiling assay was employed, analyzing 630 metabolites.
- Seven distinct extraction protocols were compared across three model organisms: Drosophila, mouse, and zebrafish.
- Key parameters evaluated included metabolite coverage, concentration, and inter-replicate variance.
Main Results:
- A combination of 75% ethanol and methyl tertiary-butyl ether (MTBE) emerged as the most reproducible extraction protocol.
- This protocol enabled the determination of up to 530 metabolites in mouse kidney, 509 in mouse liver, 422 in zebrafish, and 388 in Drosophila.
- A core overlap of 261 metabolites was identified across the four tested matrices (mouse kidney, mouse liver, zebrafish, Drosophila).
Conclusions:
- The 75% ethanol/MTBE extraction protocol offers superior reproducibility for metabolic profiling in diverse model organisms.
- The developed dataset and the 'MetaboExtract' shiny app empower researchers to choose optimal extraction strategies.
- This work enhances the reliability and comparability of metabolomic data across different experimental setups and species.
Keywords:
LC-MS/MSMxP Quant 500drosophilaextraction protocolmetabolomicsmodel organismsmousezebrafish
