Metabolite measurement: Pitfalls to avoid and practices to follow

Wenyun Lu, Xiaoyang Su, Matthias S. Klein, Ian A. Lewis, Oliver Fiehn, Joshua D. Rabinowitz

Research output: Contribution to journalReview articlepeer-review

303 Scopus citations


Metabolites are the small biological molecules involved in energy conversion and biosynthesis. Studying metabolism is inherently challenging due to metabolites' reactivity, structural diversity, and broad concentration range. Herein, we review the common pitfalls encountered in metabolomics and provide concrete guidelines for obtaining accurate metabolite measurements, focusing on water-soluble primary metabolites. We show how seemingly straightforward sample preparation methods can introduce systematic errors (e.g., owing to interconversion among metabolites) and how proper selection of quenching solvent (e.g., acidic acetonitrile:methanol:water) can mitigate such problems. We discuss the specific strengths, pitfalls, and best practices for each common analytical platform: Liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and enzyme assays. Together this information provides a pragmatic knowledge base for carrying out biologically informative metabolite measurements.

Original languageEnglish (US)
Pages (from-to)277-304
Number of pages28
JournalAnnual review of biochemistry
StatePublished - Jun 20 2017

All Science Journal Classification (ASJC) codes

  • Biochemistry


  • Accuracy
  • Mass spectroscopy
  • Metabolite extraction
  • Metabolomics
  • Metabonomics
  • Stability


Dive into the research topics of 'Metabolite measurement: Pitfalls to avoid and practices to follow'. Together they form a unique fingerprint.

Cite this