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Abstract The capacity to leverage high resolution mass spectrometry (HRMS) with transient isotope labeling experiments is an untapped opportunity to derive insights on context-specific metabolism, that is difficult to assess quantitatively. Tools are needed to comprehensively mine isotopologue information in an automated, high-throughput way without errors. We describe a tool, Stable Isotope-assisted Metabolomics for Pathway Elucidation (SIMPEL), to simplify analysis and interpretation of isotope-enriched HRMS datasets. The efficacy ofSIMPELis demonstrated through examples of central carbon and lipid metabolism. In the first description, a dual-isotope labeling experiment is paired withSIMPELand isotopically nonstationary metabolic flux analysis (INST-MFA) to resolve fluxes in central metabolism that would be otherwise challenging to quantify. In the second example,SIMPELwas paired with HRMS-based lipidomics data to describe lipid metabolism based on a single labeling experiment. Available as an R package,SIMPELextends metabolomics analyses to include isotopologue signatures necessary to quantify metabolic flux.
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Isotopically nonstationary metabolic flux analysis of plants: recent progress and future opportunities
Summary Metabolic flux analysis (MFA) is a valuable tool for quantifying cellular phenotypes and to guide plant metabolic engineering. By introducing stable isotopic tracers and employing mathematical models, MFA can quantify the rates of metabolic reactions through biochemical pathways. Recent applications of isotopically nonstationary MFA (INST‐MFA) to plants have elucidated nonintuitive metabolism in leaves under optimal and stress conditions, described coupled fluxes for fast‐growing algae, and produced a synergistic multi‐organ flux map that is a first in MFA for any biological system. These insights could not be elucidated through other approaches and show the potential of INST‐MFA to correct an oversimplified understanding of plant metabolism.
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- Award ID(s):
- 1829365
- PAR ID:
- 10577059
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- New Phytologist
- Volume:
- 242
- Issue:
- 5
- ISSN:
- 0028-646X
- Format(s):
- Medium: X Size: p. 1911-1918
- Size(s):
- p. 1911-1918
- Sponsoring Org:
- National Science Foundation
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