The Human Urine Metabolome

Abstract

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.

Magnetic Resonance Spectroscopy: Principles and Techniques: Lessons for Clinicians

“…These include gender, age, BMI, diet, stress, medications, smoking, exercise, fasting and consumption of alcohol 24 h prior to collection. 36,37 Attempts to Figure 5 Multiple variables are generated from metabolic profiling studies.…”

“…36 Some studies have specifically identified confounding factors that influence the 1 H NMR spectrum, a few of which are emphasised include trimethylamine Noxide (TMAO) production, which is highly influenced by diet. TMAO is higher in meat eaters than vegetarians and higher in fish eaters than meat eaters 39 ; the consumption of meat can significantly increase the metabolite 1-methylhistidine 36 ; mannitol is a sugar alcohol in urine that can be explained by the consumption of foods such as apples, pineapples, asparagus and carrots; increased dietary intake of creatinine or a protein-rich diet can increase daily creatinine excretion; urinary samples from East Asian and Western populations has significantly different metabolite excretion patterns. 36,39 Additionally, males have a higher skeletal mass than females; thus different urinary levels of creatinine may be present in women samples.…”

“…36,39 Additionally, males have a higher skeletal mass than females; thus different urinary levels of creatinine may be present in women samples. 36 …”

Metabolic profiles of placenta in preeclampsia using HR-MAS MRS metabolomics

“…66 Small changes in genes or protein activity can have large consequences in metabolite concentrations. 65 At the same time, metabolites may have regulatory e ects on gene or protein expression.…”

Characterisation of the metabolome of ocular tissues and post-mortem changes in the rat retina

“…1 The total complement of metabolites in a biological system is defined as the metabolome; its composition is both sample-and time-dependent. 2,3 As metabolites are the end product of biological pathways, the metabolome is a sensitive measure of disease phenotype and a dynamic indicator of genetic, environmental or disease-specific perturbations. 1,4,5 Metabolomics is increasingly being applied as a tool in eye research.…”