title: Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review.
abstract: The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.
authors.affiliation: Imaging and Characterization Core Lab, King Abdullah University of Science and Technology, KSA, Thuwal, Saudi Arabia.
authors.forename: Abdul-Hamid
authors.initials: AH
authors.lastname: Emwas
authors.affiliation: Centro Risonanze Magnetiche - CERM, University of Florence, Florence, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Luchinat
authors.affiliation: Centro Risonanze Magnetiche - CERM, University of Florence, Florence, Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Turano
authors.affiliation: FiorGen Foundation, 50019 Sesto Fiorentino, Florence, Italy.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Tenori
authors.affiliation: Centre of Biomedical Research, Formerly known as Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Lucknow, India.
authors.forename: Raja
authors.initials: R
authors.lastname: Roy
authors.affiliation: Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK ; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD UK.
authors.forename: Reza M
authors.initials: RM
authors.lastname: Salek
authors.affiliation: School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, Australia.
authors.forename: Danielle
authors.initials: D
authors.lastname: Ryan
authors.affiliation: Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, KSA, Thuwal, Saudi Arabia.
authors.forename: Jasmeen S
authors.initials: JS
authors.lastname: Merzaban
authors.affiliation: Pharmacometabolomics Center, School of Medicine, Duke University, Durham, USA.
authors.forename: Rima
authors.initials: R
authors.lastname: Kaddurah-Daouk
authors.affiliation: Brazilian Biosciences National Laboratory, LNBio, Campinas, SP Brazil.
authors.forename: Ana Carolina
authors.initials: AC
authors.lastname: Zeri
authors.affiliation: Department of Anethesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, 850 Republican St., Seattle, WA 98109 USA.
authors.forename: G A
authors.initials: GA
authors.lastname: Nagana Gowda
authors.affiliation: Department of Anethesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, 850 Republican St., Seattle, WA 98109 USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Raftery
authors.affiliation: Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yulan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Institute of Food and Health and Conway Institute, School of Agriculture & Food Science, Dublin 4, Ireland.
authors.forename: Lorraine
authors.initials: L
authors.lastname: Brennan
authors.affiliation: Department of Computing Science, University of Alberta, Edmonton, Alberta Canada.
authors.forename: David S
authors.initials: DS
authors.lastname: Wishart
keywords: Biomarker; Diagnosis; Human diseases; Metabolites profiling; Metabolomics; Metabonomics; NMR; Recommendations ; Standardization; Urine