A diverse proteome is present and enzymatically active in metabolite extracts.

Autor: House RRJ; Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, USA.; Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA.; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Soper-Hopper MT; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Vincent MP; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Ellis AE; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Capan CD; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Madaj ZB; Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA., Wolfrum E; Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA., Isaguirre CN; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Castello CD; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Johnson AB; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Escobar Galvis ML; Office of the Cores, Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA., Williams KS; Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA., Lee H; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Sheldon RD; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA. ryan.sheldon@vai.org.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2024 Jul 10; Vol. 15 (1), pp. 5796. Date of Electronic Publication: 2024 Jul 10.
DOI: 10.1038/s41467-024-50128-z
Abstrakt: 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.
(© 2024. The Author(s).)
Databáze: MEDLINE
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