A targeted metabolomic protocol for short-chain fatty acids and branched-chain amino acids

Xiaojiao Zheng, Yunping Qiu, Wei Zhong, Sarah Baxter, Mingming Su, Qiong Li, Guoxiang Xie, Brandon M. Ore, Shanlei Qiao, Melanie D. Spencer, Steven H. Zeisel, Zhanxiang Zhou, Aihua Zhao, Wei Jia

Research output: Contribution to journalArticlepeer-review

170 Scopus citations


Research in obesity and metabolic disorders that involve intestinal microbiota demands reliable methods for the precise measurement of the short-chain fatty acids (SCFAs) and branched-chain amino acids (BCAAs) concentration. Here, we report a rapid method of simultaneously determining SCFAs and BCAAs in biological samples using propyl chloroformate (PCF) derivatization followed by gas chromatography-mass spectrometry (GC-MS) analysis. A one-step derivatization using 100 μL of PCF in a reaction system of water, propanol, and pyridine (v/v/v = 8:3:2) at pH 8 provided the optimal derivatization efficiency. The best extraction efficiency of the derivatized products was achieved by a two-step extraction with hexane. The method exhibited good derivatization efficiency and recovery for a wide range of concentrations with a low limit of detection for each compound. The relative standard deviations of all targeted compounds showed good intra- and inter-day (within 7 days) precision (<10 %), and good stability (<20 %) within 4 days at room temperature (23-25 °C), or 7 days when stored at -20 °C. We applied our method to measure SCFA and BCAA levels in fecal samples from rats administrated with different diet. Both univariate and multivariate statistical analysis of the concentrations of these targeted metabolites could differentiate three groups with ethanol intervention and different oils in diet. This method was also successfully employed to determine SCFA and BCAA in the feces, plasma and urine from normal humans, providing important baseline information of the concentrations of these metabolites. This novel metabolic profile study has great potential for translational research.

Original languageEnglish (US)
Pages (from-to)818-827
Number of pages10
Issue number4
StatePublished - Aug 2013
Externally publishedYes


  • Biological samples
  • Branched-chain amino acids
  • Gas chromatography-mass spectrometry
  • Propyl chloroformate
  • Short-chain fatty acids
  • Targeted metabolomics

ASJC Scopus subject areas

  • Endocrinology, Diabetes and Metabolism
  • Biochemistry
  • Clinical Biochemistry


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