ArticleNature communications2024
A diverse proteome is present and enzymatically active in metabolite extracts.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Biomolecular condensates can function as inherent catalysts.Molecular cell · 2026Article
- SERSome-based metabolic profiling of aqueous humor for cataract subtyping with molecule-level interpretability.Journal of nanobiotechnology · 2026Article
- Sequential Penta-Omic Extraction Method Using Single Biospecimens of Post-mortem Human Brain.bioRxiv : the preprint server for biology · 2026Article
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- Chronic High-Fat Diet Does Not Alter Overall Cancer Incidence in Trp53R270H/+ Mice.Cancer research communications · 2026Article
- Bacterial pyruvate metabolism regulates host insulin sensitivity inbioRxiv : the preprint server for biology · 2026Article
- Standardizing Methods for Shoot Metabolomics in Mycorrhizal Plants.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Dietary restriction reprograms CD8Nature metabolism · 2025Article
- A noncanonical polyamine from bacteria antagonizes host mitochondrial function.Nature communications · 2025Article
- Plant-pathogen interactions: making the case for multi-omics analysis of complex pathosystems.Stress biology · 2025Review
- Sample Preparation for Single Cell Mass Spectrometry Metabolomics Studies: Combined Cell Washing, Quenching, Drying, and Storage.Journal of visualized experiments : JoVE · 2025Article
- Glucose-dependent glycosphingolipid biosynthesis fuels CD8Cell metabolism · 2025Article
- Developing a Cell Quenching Method to Facilitate Single Cell Mass Spectrometry Metabolomics Studies.JACS Au · 2025Article
- Mitochondrial fatty acid synthesis and MECR regulate CD4+ T cell function and oxidative metabolism.Journal of immunology (Baltimore, Md. : 1950) · 2025Article
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Authors and funding
14 authors.
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Abstract
Metabolite extraction is the critical first-step in metabolomics experiments, where it is generally regarded to inactivate and remove proteins. Here, arising from efforts to improve extraction conditions for polar metabolomics, we discover a proteomic landscape of over 1000 proteins within metabolite extracts. This is a ubiquitous feature across several common extraction and sample types. By combining post-resuspension stable isotope addition and enzyme inhibitors, we demonstrate in-extract metabolite interconversions due to residual transaminase activity. We extend these findings with untargeted metabolomics where we observe extensive protein-mediated metabolite changes, including in-extract formation of glutamate dipeptide and depletion of total glutathione. Finally, we present a simple extraction workflow that integrates 3 kDa filtration for protein removal as a superior method for polar metabolomics. In this work, we uncover a previously unrecognized, protein-mediated source of observer effects in metabolomics experiments with broad-reaching implications across all research fields using metabolomics and molecular metabolism.
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