A Workflow to Perform Targeted Metabolomics at the Untargeted Scale on a Triple Quadrupole Mass Spectrometer

Michaela Schwaiger-Haber, Ethan Stancliffe, Valerie Arends, Bharat Thyagarajan, Miriam Sindelar, Gary J. Patti

Research output: Contribution to journalArticlepeer-review

26 Scopus citations

Abstract

The thousands of features commonly observed when performing untargeted metabolomics with quadrupole time-of-flight (QTOF) and Orbitrap mass spectrometers often correspond to only a few hundred unique metabolites of biological origin, which is in the range of what can be assayed in a single targeted metabolomics experiment by using a triple quadrupole (QqQ) mass spectrometer. A major benefit of performing targeted metabolomics with QqQ mass spectrometry is the affordability of the instruments relative to high-resolution QTOF and Orbitrap platforms. Optimizing targeted methods to profile hundreds of metabolites on a QqQ mass spectrometer, however, has historically been limited by the availability of authentic standards, particularly for “unknowns” that have yet to be structurally identified. Here, we report a strategy to develop multiple reaction monitoring (MRM) methods for QqQ instruments on the basis of high-resolution spectra, thereby enabling us to use data from untargeted metabolomics to design targeted experiments without the need for authentic standards. We demonstrate that using high-resolution fragmentation data alone to design MRM methods results in the same quantitative performance as when methods are optimized by measuring authentic standards on QqQ instruments, as is conventionally done. The approach was validated by showing that Orbitrap ID-X data can be used to establish MRM methods on a Thermo TSQ Altis and two Agilent QqQs for hundreds of metabolites, including unknowns, without a dependence on standards. Finally, we highlight an application where metabolite profiling was performed on an ID-X and a QqQ by using the strategy introduced here, with both data sets yielding the same result. The described approach therefore allows us to use QqQ instruments, which are often associated with targeted metabolomics, to profile knowns and unknowns at a comprehensive scale that is typical of untargeted metabolomics.

Original languageEnglish (US)
Pages (from-to)35-45
Number of pages11
JournalACS Measurement Science Au
Volume1
Issue number1
DOIs
StatePublished - Aug 18 2021

Bibliographical note

Funding Information:
The authors would like to thank Matthew Murphy, Annika Teschke, and Thomas White for help with standard and solvent preparation. This work was supported by funding from the National Institutes of Health grants U01CA235482 (G.J.P.), R35ES2028365 (G.J.P.), and U19AG063893 (B.T.). Figure 1 and Figure 4A were created with BioRender.com .

Funding Information:
The authors declare the following competing financial interest(s): The Patti laboratory has a research collaboration agreement with Thermo Fisher Scientific and receives financial support from Agilent Technologies. Acknowledgments

Publisher Copyright:
© 2021 The Authors. Published by American Chemical Society.

Keywords

  • Untargeted metabolomics
  • collision energy conversion
  • high-resolution mass spectrometry
  • targeted metabolomics
  • triple quadrupole mass spectrometry

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