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A statistical analysis of the effects of urease pre-treatment on the measurement of the urinary metabolome by gas chromatography–mass spectrometry

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Abstract

Urease pre-treatment of urine has been utilized since the early 1960s to remove high levels of urea from samples prior to further processing and analysis by gas chromatography–mass spectrometry (GC–MS). Aside from the obvious depletion or elimination of urea, the effect, if any, of urease pre-treatment on the urinary metabolome has not been studied in detail. Here, we report the results of three separate but related experiments that were designed to assess possible indirect effects of urease pre-treatment on the urinary metabolome as measured by GC–MS. In total, 235 GC–MS analyses were performed and over 106 identified and 200 unidentified metabolites were quantified across the three experiments. The results showed that data from urease pre-treated samples (1) had the same or lower coefficients of variance among reproducibly detected metabolites, (2) more accurately reflected quantitative differences and the expected ratios among different urine volumes, and (3) increased the number of metabolite identifications. Overall, we observed no negative consequences of urease pre-treatment. In contrast, urease pre-treatment enhanced the ability to distinguish between volume-based and biological sample types compared to no treatment. Taken together, these results show that urease pre-treatment of urine offers multiple beneficial effects that outweigh any artifacts that may be introduced to the data in urinary metabolomics analyses.

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Acknowledgments

This work was funded by NIH NIDDK Grant DP3 DK094343. Significant portions of the work were performed at the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy’s (DOE) Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL) in Richland, Washington. PNNL is a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RLO 1830.

Informed consent

All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration of 1975, as revised in 2000. Informed consent was obtained from all patients before being included in the study.

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Authors and Affiliations

  1. Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-98, Richland, WA, USA

    Bobbie-Jo Webb-Robertson, Young-Mo Kim, Erika M. Zink, Katherine A. Hallaian, Qibin Zhang, Katrina M. Waters & Thomas O. Metz

  2. J. Craig Venter Institute, Rockville, MD, USA

    Ramana Madupu

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  1. Bobbie-Jo Webb-Robertson
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  2. Young-Mo Kim
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  3. Erika M. Zink
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  4. Katherine A. Hallaian
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  5. Qibin Zhang
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  6. Ramana Madupu
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  7. Katrina M. Waters
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  8. Thomas O. Metz
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Corresponding author

Correspondence to Thomas O. Metz.

Additional information

Bobbie-Jo Webb-Robertson and Young-Mo Kim have contributed equally to this work.

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Webb-Robertson, BJ., Kim, YM., Zink, E.M. et al. A statistical analysis of the effects of urease pre-treatment on the measurement of the urinary metabolome by gas chromatography–mass spectrometry. Metabolomics 10, 897–908 (2014). https://doi.org/10.1007/s11306-014-0642-1

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