The Human Urine Metabolome

By Souhaila Bouatra, Farid Aziat, R. Mandal, Anchi Guo, Michael R Wilson, Craig Knox, T. Bjorndahl, Ramanarayan Krishnamurthy, F. Saleem, Philip Liu and 9 more. PLoS ONE, 2013

1,347 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/756320aca449242b99416258eaf4dc78d9158f6d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. David S. Wishart
2. Anchi Guo
3. Craig Knox
4. Yifeng Liu
5. R. Mandal
6. Carin Li
7. Allison Pon
8. Michael Wilson

In Spectroscopy

1. David S. Wishart
2. R. Mandal
3. Carin Li
4. Jianguo Xia

Citations in the corpus

• HMDB 4.0: the human metabolome database for 2018 (2017, background): “For instance, there are now many more compound names and synonyms (a 370% increase), substantially more compounds with biofluid concentration or tissue location data (a 50% increase), more data on normal and diseased metabolite concentrations (a 72% increase), and more data on biofluid and excreta m”
• Metabolomics for Investigating Physiological and Pathophysiological Processes. (2019, background): “MS instruments are exquisitely sensitive and often require only a few microliters of fluid to perform an experiment (51, 377).”