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Global urinary metabolic profiling procedures using gas chromatography–mass spectrometry

Abstract

The role of urinary metabolic profiling in systems biology research is expanding. This is because of the use of this technology for clinical diagnostic and mechanistic studies and for the development of new personalized health care and molecular epidemiology (population) studies. The methodologies commonly used for metabolic profiling are NMR spectroscopy, liquid chromatography mass spectrometry (LC/MS) and gas chromatography–mass spectrometry (GC/MS). In this protocol, we describe urine collection and storage, GC/MS and data preprocessing methods, chemometric data analysis and urinary marker metabolite identification. Results obtained using GC/MS are complementary to NMR and LC/MS. Sample preparation for GC/MS analysis involves the depletion of urea via treatment with urease, protein precipitation with methanol, and trimethylsilyl derivatization. The protocol described here facilitates the metabolic profiling of 400–600 metabolites in 120 urine samples per week.

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Figure 1: Flow diagram of various stages typically involved in GC/TOFMS-based urinary metabolic profiling.
Figure 2: This figure summarizes the main steps in data preprocessing.
Figure 3: Flowchart of the main steps in data analysis.
Figure 4: An example of tight clustering of QC samples in PCA scores plot showing minimal analytical variation.
Figure 5: Screenshots of validation plots.
Figure 6: Estimated timing for metabolic profiling of 120 urine samples using GC/TOFMS.
Figure 7: A screenshot of a calibration table.

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Acknowledgements

GC/TOFMS method development was supported by the National University of Singapore (NUS) grant R-148-000-100-112 and National Medical Research Council grant R-176-000-119-213 provided to E.C.Y.C. GC/TOFMS was sponsored by the NUS grant R-279-000-249-646. P.K.K. is supported by a NUS President's Graduate fellowship.

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E.C.Y.C. and P.K.K. designed the protocol and conducted the initial study; E.C.Y.C., P.K.K. and J.K.N. wrote the manuscript; J.K.N. gave conceptual advice.

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Correspondence to Eric Chun Yong Chan.

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Chan, E., Pasikanti, K. & Nicholson, J. Global urinary metabolic profiling procedures using gas chromatography–mass spectrometry. Nat Protoc 6, 1483–1499 (2011). https://doi.org/10.1038/nprot.2011.375

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