1H NMR signals from urine excreted protein are a source of bias in probabilistic quotient normalization

Correia, G. D. S. et al. (2022) 1H NMR signals from urine excreted protein are a source of bias in probabilistic quotient normalization. Analytical Chemistry, 94(19), pp. 6919-6923. (doi: 10.1021/acs.analchem.2c00466) (PMID:35503092) (PMCID:PMC9118196)

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Normalization to account for variation in urinary dilution is crucial for interpretation of urine metabolic profiles. Probabilistic quotient normalization (PQN) is used routinely in metabolomics but is sensitive to systematic variation shared across a large proportion of the spectral profile (>50%). Where 1H nuclear magnetic resonance (NMR) spectroscopy is employed, the presence of urinary protein can elevate the spectral baseline and substantially impact the resulting profile. Using 1H NMR profile measurements of spot urine samples collected from hospitalized COVID-19 patients in the ISARIC 4C study, we determined that PQN coefficients are significantly correlated with observed protein levels (r2 = 0.423, p < 2.2 × 10–16). This correlation was significantly reduced (r2 = 0.163, p < 2.2 × 10–16) when using a computational method for suppression of macromolecular signals known as small molecule enhancement spectroscopy (SMolESY) for proteinic baseline removal prior to PQN. These results highlight proteinuria as a common yet overlooked source of bias in 1H NMR metabolic profiling studies which can be effectively mitigated using SMolESY or other macromolecular signal suppression methods before estimation of normalization coefficients.

Item Type:Articles
Additional Information:This research is supported by grants from the National Institute for Health Research (NIHR) [award CO-CIN-01]; the Medical Research Council [grant MC_PC_19059, MC_PC_12025], the MRC UK Consortium for MetAbolic Phenotyping (MAP/UK) [grant number MR/S010483/1], and by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, in partnership with Public Health England (PHE), in collaboration with the Liverpool School of Tropical Medicine and the University of Oxford [award 200907]; NIHR HPRU in Respiratory Infections at Imperial College London with Public Health England (PHE) [award 200927]; infrastructure support was provided by the NIHR Imperial Biomedical Research Centre (BRC).
Glasgow Author(s) Enlighten ID:Ho, Dr Antonia
Authors: Correia, G. D. S., Takis, P. G., Sands, C. J., Kowalka, A. M., Tan, T., Turtle, L., Ho, A., Semple, M. G., Openshaw, P. J. M., Baillie, J. K., Takáts, Z., and Lewis, M. R.
College/School:College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
Journal Name:Analytical Chemistry
Publisher:American Chemical Society
ISSN (Online):1520-6882
Published Online:03 May 2022
Copyright Holders:Copyright © 2022 The Authors
First Published:First published in Analytical Chemistry 94(19): 6919-6923
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
310665ISARIC - Coronavirus Clinical Characterisation ConsortiumAntonia HoMedical Research Council (MRC)MC_PC_19059 - 9815274III - Centre for Virus Research