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A High-Throughput Targeted Metabolomics Workflow for the Detection of 200 Polar Metabolites in Central Carbon Metabolism

Part of the Methods in Molecular Biology book series (MIMB,volume 1859)


Targeted metabolomics aims to analyze a set of pre-selected metabolites from biologically relevant metabolic pathways. The triple quadrupole mass spectrometry (QqQ-MS) based multiple reaction monitoring (MRM) technique is the most widely approach used for targeted metabolomics, and features high selectivity and sensitivity, good reproducibility and wide dynamic range in quantitative analysis. Here, we describe an MRM based targeted metabolomics workflow for the quantitative analysis of 200 polar metabolites in central carbon metabolic pathways, including the data acquisition method and the automated data processing procedures using our in-house R package MRMAnalyzer. The workflow described in this chapter combines a hydrophilic interaction liquid chromatography (HILIC) separation and positive/negative ion polarity switching based MS detection, and is able to acquire data from multiple types of biological samples such as bacteria, cultured mammalian cells, animal tissues and biofluids (e.g., serum and urine). Finally, the MRMAnalyzer software can automatically process the generated large-scale data set with high efficiency. We hope it is a valuable and efficient workflow for researchers to facilitate the respective biological studies using targeted metabolomics.

Key words

  • Targeted metabolomics
  • Multiple reaction monitoring
  • Central carbon metabolism
  • MRMAnalyzer

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The work was financially supported by National Natural Science Foundation of China (Grant No. 21575151) and State High-Tech Development Plan Award (the “863 program”, Grant No. 2014AA020526). Z.-J. Z. is supported by Thousand Youth Talents Program.

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Correspondence to Zheng-Jiang Zhu .

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1 Electronic Supplementary Materials

Supplementary Table 1

The general information of 200 metabolites, including metabolite name, formula, HMDB ID, METLIN ID, KEGG ID and the concentration of each metabolite in 200STD_mix. (XLSX 24 kb)

Supplementary Table 2

The in house ID, MRM transition and retention time for each defined metabolite. (CSV 19 kb)

Supplementary Table 3

The detailed MRM parameters of 200 metabolites contains metabolite name, precursor ion, product ion polarity and IDs. (CSV 14 kb)

Supplementary Table 4

The information of 10 metabolites in RTQC sample including in house ID, metabolite name, formula, precursor ion, product ion, fragmentor, CE, polarity and RT. (CSV 742 bytes)

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Cai, Y., Zhu, ZJ. (2019). A High-Throughput Targeted Metabolomics Workflow for the Detection of 200 Polar Metabolites in Central Carbon Metabolism. In: Baidoo, E. (eds) Microbial Metabolomics. Methods in Molecular Biology, vol 1859. Humana Press, New York, NY.

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8756-6

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