The Human Urine Metabolome

Urine has long been a “favored” biofluid among metabolomics researchers. It is sterile, easy-to-obtain in large volumes, largely free from interfering proteins or lipids and chemically complex. However, this chemical complexity has also made urine a particularly difficult substrate to fully understand. As a biological waste material, urine typically contains metabolic breakdown products from a wide range of foods, drinks, drugs, environmental contaminants, endogenous waste metabolites and bacterial by-products. Many of these compounds are poorly characterized and poorly understood. In an effort to improve our understanding of this biofluid we have undertaken a comprehensive, quantitative, metabolome-wide characterization of human urine. This involved both computer-aided literature mining and comprehensive, quantitative experimental assessment/validation. The experimental portion employed NMR spectroscopy, gas chromatography mass spectrometry (GC-MS), direct flow injection mass spectrometry (DFI/LC-MS/MS), inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography (HPLC) experiments performed on multiple human urine samples. This multi-platform metabolomic analysis allowed us to identify 445 and quantify 378 unique urine metabolites or metabolite species. The different analytical platforms were able to identify (quantify) a total of: 209 (209) by NMR, 179 (85) by GC-MS, 127 (127) by DFI/LC-MS/MS, 40 (40) by ICP-MS and 10 (10) by HPLC. Our use of multiple metabolomics platforms and technologies allowed us to identify several previously unknown urine metabolites and to substantially enhance the level of metabolome coverage. It also allowed us to critically assess the relative strengths and weaknesses of different platforms or technologies. The literature review led to the identification and annotation of another 2206 urinary compounds and was used to help guide the subsequent experimental studies. An online database containing the complete set of 2651 confirmed human urine metabolite species, their structures (3079 in total), concentrations, related literature references and links to their known disease associations are freely available at http://www.urinemetabolome.ca

Bis-porphyrin tweezers: rigid or flexible linkers for better adjustment of the cavity to bidentate bases of various size

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Polypeptides with pendant porphyrins of defined sequence of chromophores: towards artificial photosynthetic systems

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HMDB 3.0--The Human Metabolome Database in 2013. Nucleic Acids Res

ABSTRACT The Human Metabolome Database (HMDB) (www. hmdb.ca) is a resource dedicated to providing scientists with the most current and comprehensive coverage of the human metabolome. Since its first release in 2007, the HMDB has been used to facilitate research for nearly 1000 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 3.0) has been significantly expanded and enhanced over the 2009 release (version

Concentrations of isoflavones and thiols as determined by HPLC.

a<p>Isoflavone metabolites measured by HPLC/UV.</p>b<p>Thiol metabolites measured by HPLC/FD.</p><p>Oc: occurrence;</p><p>NA: not available.</p

Venn diagram showing the overlap of urine metabolites detected by NMR, GC-MS, DFI/LC-MS/MS, ICP-MS, HPLC coupled to UV detection and HPLC coupled to fluorescence detection compared to the detectable urine metabolome.

<p>Venn diagram showing the overlap of urine metabolites detected by NMR, GC-MS, DFI/LC-MS/MS, ICP-MS, HPLC coupled to UV detection and HPLC coupled to fluorescence detection compared to the detectable urine metabolome.</p

Comparison of urine concentrations of 23 quantified amino acids by different assays: DFI/LC-MS/MS (BIOCRATES kit), NMR and GC-MS.

*<p>Concentration (Mean ± SD) is expressed by µM/mM creatinine. NA: not available.</p

Concentrations of metabolites in human urine as measured by GC-MS.

*<p>Concentration of metabolite (Mean ± SD) is expressed by µM. HPHPA: 3-(3-hydroxyphenyl)-3-hydroxypropanoic acid; NA: not available; NA**: not available for healthy adults.</p

Compound names, HMDB identification numbers, unique masses, mean mass spectral match quality, retention times, and NIST retention indices for volatile compounds in urine analyzed by HS-SPME-GC/MS.

<p>Compound names, HMDB identification numbers, unique masses, mean mass spectral match quality, retention times, and NIST retention indices for volatile compounds in urine analyzed by HS-SPME-GC/MS.</p