The Human Urine Metabolome
Publication Date
September 04, 2013
Journal
PLOS ONE
Authors
Souhaila Bouatra, Farid Aziat, Rupasri Mandal, An Chi Guo, et al
Volume
8
Issue
9
Pages
e73076
DOI
https://dx.plos.org/10.1371/journal.pone.0073076
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0073076
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24023812
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762851
Europe PMC
http://europepmc.org/abstract/MED/24023812
Web of Science
000324515600066
Scopus
84883331522
Mendeley
http://www.mendeley.com/research/human-urine-metabolome
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Mendeley | Further Information

{"title"=>"The Human Urine Metabolome", "type"=>"journal", "authors"=>[{"first_name"=>"Souhaila", "last_name"=>"Bouatra", "scopus_author_id"=>"6505648648"}, {"first_name"=>"Farid", "last_name"=>"Aziat", "scopus_author_id"=>"25958862900"}, {"first_name"=>"Rupasri", "last_name"=>"Mandal", "scopus_author_id"=>"7006113503"}, {"first_name"=>"An Chi", "last_name"=>"Guo", "scopus_author_id"=>"7101837218"}, {"first_name"=>"Michael R.", "last_name"=>"Wilson", "scopus_author_id"=>"55574207851"}, {"first_name"=>"Craig", "last_name"=>"Knox", "scopus_author_id"=>"7005915066"}, {"first_name"=>"Trent C.", "last_name"=>"Bjorndahl", "scopus_author_id"=>"6506351507"}, {"first_name"=>"Ramanarayan", "last_name"=>"Krishnamurthy", "scopus_author_id"=>"39863169800"}, {"first_name"=>"Fozia", "last_name"=>"Saleem", "scopus_author_id"=>"36665232700"}, {"first_name"=>"Philip", "last_name"=>"Liu", "scopus_author_id"=>"55844040200"}, {"first_name"=>"Zerihun T.", "last_name"=>"Dame", "scopus_author_id"=>"42661250900"}, {"first_name"=>"Jenna", "last_name"=>"Poelzer", "scopus_author_id"=>"55843771500"}, {"first_name"=>"Jessica", "last_name"=>"Huynh", "scopus_author_id"=>"55842508700"}, {"first_name"=>"Faizath S.", "last_name"=>"Yallou", "scopus_author_id"=>"55203570600"}, {"first_name"=>"Nick", "last_name"=>"Psychogios", "scopus_author_id"=>"6504083081"}, {"first_name"=>"Edison", "last_name"=>"Dong", "scopus_author_id"=>"25931935400"}, {"first_name"=>"Ralf", "last_name"=>"Bogumil", "scopus_author_id"=>"56106896500"}, {"first_name"=>"Cornelia", "last_name"=>"Roehring", "scopus_author_id"=>"55843611600"}, {"first_name"=>"David S.", "last_name"=>"Wishart", "scopus_author_id"=>"7005602630"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84883331522", "pui"=>"369736904", "sgr"=>"84883331522", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203", "pmid"=>"24023812", "doi"=>"10.1371/journal.pone.0073076"}, "id"=>"bb1f96c3-2152-3800-aaea-f9e324b422cf", "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.", "link"=>"http://www.mendeley.com/research/human-urine-metabolome", "reader_count"=>588, "reader_count_by_academic_status"=>{"Unspecified"=>24, "Professor > Associate Professor"=>19, "Librarian"=>1, "Researcher"=>127, "Student > Doctoral Student"=>36, "Student > Ph. D. Student"=>162, "Student > Postgraduate"=>21, "Student > Master"=>73, "Other"=>22, "Student > Bachelor"=>74, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>7, "Professor"=>19}, "reader_count_by_user_role"=>{"Unspecified"=>24, "Professor > Associate Professor"=>19, "Librarian"=>1, "Researcher"=>127, "Student > Doctoral Student"=>36, "Student > Ph. D. Student"=>162, "Student > Postgraduate"=>21, "Student > Master"=>73, "Other"=>22, "Student > Bachelor"=>74, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>7, "Professor"=>19}, "reader_count_by_subject_area"=>{"Unspecified"=>39, "Agricultural and Biological Sciences"=>178, "Arts and Humanities"=>1, "Philosophy"=>1, "Business, Management and Accounting"=>1, "Veterinary Science and Veterinary Medicine"=>2, "Chemical Engineering"=>2, "Chemistry"=>136, "Computer Science"=>7, "Earth and Planetary Sciences"=>4, "Engineering"=>25, "Environmental Science"=>17, "Biochemistry, Genetics and Molecular Biology"=>62, "Nursing and Health Professions"=>7, "Materials Science"=>2, "Medicine and Dentistry"=>74, "Neuroscience"=>2, "Design"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>8, "Sports and Recreations"=>4, "Physics and Astronomy"=>3, "Psychology"=>4, "Social Sciences"=>3, "Immunology and Microbiology"=>5}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>74}, "Social Sciences"=>{"Social Sciences"=>3}, "Sports and Recreations"=>{"Sports and Recreations"=>4}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Psychology"=>{"Psychology"=>4}, "Unspecified"=>{"Unspecified"=>39}, "Environmental Science"=>{"Environmental Science"=>17}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>8}, "Chemical Engineering"=>{"Chemical Engineering"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Design"=>{"Design"=>1}, "Engineering"=>{"Engineering"=>25}, "Chemistry"=>{"Chemistry"=>136}, "Neuroscience"=>{"Neuroscience"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>4}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>5}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>178}, "Computer Science"=>{"Computer Science"=>7}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>62}, "Philosophy"=>{"Philosophy"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"United States"=>6, "Japan"=>1, "United Kingdom"=>7, "Switzerland"=>2, "Spain"=>5, "Costa Rica"=>1, "India"=>1, "Canada"=>3, "Sweden"=>2, "China"=>2, "Denmark"=>2, "Poland"=>2, "Brazil"=>1, "Mexico"=>1, "South Africa"=>2, "Chile"=>1, "Australia"=>1, "France"=>1, "Germany"=>3, "Estonia"=>1}, "group_count"=>24}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1190582"], "description"=>"<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>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "hmdb", "spectral", "retention", "nist", "indices", "volatile", "compounds", "urine"], "article_id"=>788478, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.t005", "stats"=>{"downloads"=>6, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_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_/788478", "title"=>"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.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190579"], "description"=>"*<p>Concentration of metabolite (Mean±SD) is expressed by µM. aa: diacyl; ae: acyl-alkyl.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "amino", "biogenic", "phosphatidylcholines", "sphingomyelins", "urine"], "article_id"=>788475, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.t007", "stats"=>{"downloads"=>7, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concentrations_of_acylcarnitines_amino_acids_biogenic_amines_lysophosphatidylcholines_phosphatidylcholines_and_sphingomyelins_in_human_urine_by_combined_DFI_LC_MS_MS_BIOCRATES_kit_/788475", "title"=>"Concentrations of acylcarnitines, amino acids, biogenic amines, lysophosphatidylcholines, phosphatidylcholines and sphingomyelins in human urine by combined DFI/LC-MS/MS (BIOCRATES kit).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190593"], "description"=>"<p>Concentrations of ions (µmol/mmol creatinine) as determined by ICP-MS.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "ions"], "article_id"=>788489, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.t008", "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concentrations_of_ions_181_mol_mmol_creatinine_as_determined_by_ICP_MS_/788489", "title"=>"Concentrations of ions (µmol/mmol creatinine) as determined by ICP-MS.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190592"], "description"=>"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>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "isoflavones", "thiols"], "article_id"=>788488, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.t009", "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concentrations_of_isoflavones_and_thiols_as_determined_by_HPLC_/788488", "title"=>"Concentrations of isoflavones and thiols as determined by HPLC.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190573"], "description"=>"<p>Numbers indicate the following metabolites (quantified compounds): 1: pyruvic acid; 2: L-lactic acid; 3: alpha-hydroxyisobutyric acid; 4: glycolic acid; 5: levulinic acid; 6∶3-hydroxyisovaleric acid; 7∶2-hydroxy-2-methylbutyric acid; 8: hydroxypropionic acid; 9∶2-methyl-3-hydroxybutyric acid; 10: malonic acid; 11∶3-hydroxyisovaleric acid; 12: methylmalonic acid; 13∶2-ethylhydracrylic acid; 14: benzoic acid; 15: phosphoric acid; 16: ethylmalonic acid; 17: succinic acid; 18: methylsuccinic acid; 19∶4-deoxythreonic acid; 20∶5-hydroxyhexanoic acid; 21: citraconic acid; 22: glutaric acid; 23: m-chlorobenzoic acid; 24; 3,4-dihydroxybutanoic acid; 25∶3-methylglutaconic acid; 26: adipic acid; 27: pyroglutamic acid; 28∶3-methyladipic acid; 29: sumiki’s acid; 30: o-hydroxyphenylacetic acid; 31: oxoglutaric acid; 32: pimelic acid; 33∶3-hydroxymethylglutaric acid; 34∶3-hydroxyphenylacetic acid; 35∶4-hydroxybenzoic acid; 36∶2-furoylglycine; 37: suberic acid; 38: quinolinic acid; 39: Cis/Trans-aconitic acid; 40: homovanillic acid; 41: azelaic acid; 42: hippuric acid; 43∶3,4-dihydroxybenzeneacetic acid; 44∶3-(3-hydroxyphenyl)-3-hydroxypropanoic acid (HPHPA); 45: vanillylmandelic acid; 46∶4-hydroxyphenyllactic acid; 47: indoleacetic acid; 48: palmitic acid; 49: kynurenic acid; 50∶3-hydroxyhippuric acid; 51∶3-hydroxysebacic acid; 52: Trans-ferulic acid; 53∶5-hydroxyindoleacetic acid; 54: stearic acid.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "gc-ms", "ion", "chromatogram", "acids", "extracted"], "article_id"=>788469, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.g003", "stats"=>{"downloads"=>19, "page_views"=>368, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Typical_GC_MS_total_ion_chromatogram_of_organic_acids_extracted_from_human_urine_/788469", "title"=>"Typical GC-MS total ion chromatogram of organic acids extracted from human urine.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190588"], "description"=>"<p>Historic data on metabolite characterization of human urine by different platforms.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "metabolite", "characterization", "urine"], "article_id"=>788483, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.t001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Historic_data_on_metabolite_characterization_of_human_urine_by_different_platforms_/788483", "title"=>"Historic data on metabolite characterization of human urine by different platforms.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190572"], "description"=>"<p>Numbers indicate the following metabolites (quantified compounds): 1: L-valine; 2: oxalic acid; 3∶3-hydroxyisobutyric acid; 4: L-serine; 5: glycine; 6: succinic acid; 7: glyceric acid; 8∶4-deoxythreonic acid; 9∶2,4-dihydroxybutanoic acid; 10∶3,4-dihydroxybutanoic acid; 11: adipic acid; 12: creatinine; 13: threonic acid; 14: L-phenylalanine; 15: p-hydroxyphenylacetic acid; 16: L-ornithine; 17: L-asparagine; 18: L-arabinose; 19: D-xylitol; 20: D-xylulose; 21: Cis/Trans-aconitic acid; 22: hippuric acid; 23: isocitric acid; 24: D-galactose; 25: D-glucose; 26: L- tyrosine; 27: sorbitol; 28: gluconic acid; 29: scyllitol; 30: myoinositol; 31: uric acid; 32: pseudouridine.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "ion", "chromatogram", "water-soluble", "metabolites", "extracted"], "article_id"=>788468, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.g002", "stats"=>{"downloads"=>2, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Typical_total_ion_chromatogram_of_water_soluble_metabolites_extracted_from_human_urine_/788468", "title"=>"Typical total ion chromatogram of water-soluble metabolites extracted from human urine.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190586"], "description"=>"<p>Chemical superclasses in the urine metabolome database.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "superclasses", "urine", "metabolome"], "article_id"=>788482, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.t002", "stats"=>{"downloads"=>10, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chemical_superclasses_in_the_urine_metabolome_database_/788482", "title"=>"Chemical superclasses in the urine metabolome database.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190568"], "description"=>"<p>Numbers indicates the following metabolites: 1: creatinine; 2: citric acid; 3: glycine; 4: formic acid; 5: methanol; 6: guanidoacetic acid; 7: acetic acid; 8: L-cysteine; 9: glycolic acid; 10: creatine; 11: isocitric acid; 12: hippuric acid; 13: L-glutamine; 14: L-alanine; 15: L-lysine; 16: gluconic acid; 17∶2- hydroxyglutaric acid; 18: D-glucose; 19: indoxyl sulfate; 20: trimethyl-N-oxide; 21: ethanolamine; 22: L-lactic acid; 23: taurine; 24: L-threonine; 25: dimethylamine; 26: pyroglutamic acid; 27: trigonelline; 28: sucrose; 29: trimethylamine; 30: mannitol; 31: L-serine; 32: acetone; 33: L-cystine; 34: adipic acid; 35: L-histidine; 36: L-tyrosine; 37: imidazole; 38: mandelic acid; 39: dimethylglycine; 40: Cis-aconitic acid; 41: urea; 42∶3-(3-hydroxyphenyl)-3-hydroxypropanoic acid (HPHPA); 43: phenol; 45: isobutyric acid; 46: methylsuccinic acid; 47∶3-aminoisobutyric acid; 48: L-fucose; 49: N-acetylaspartic acid; 50: N-acetylneuraminic acid; 51: acetoacetic acid; 52: Alpha-aminoadipic acid; 53: methylguanidine; 54: phenylacetylglutamine.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "500", "mhz", "spectra", "urine"], "article_id"=>788464, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.g001", "stats"=>{"downloads"=>29, "page_views"=>394, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Typical_500_MHz_1_H_NMR_spectra_of_urine_from_human_urine_/788464", "title"=>"Typical 500 MHz <sup>1</sup>H-NMR spectra of urine from human urine.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190595", "https://ndownloader.figshare.com/files/1190596", "https://ndownloader.figshare.com/files/1190597", "https://ndownloader.figshare.com/files/1190598", "https://ndownloader.figshare.com/files/1190599", "https://ndownloader.figshare.com/files/1190600"], "description"=>"<div><p>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 <a href=\"http://www.urinemetabolome.ca\" target=\"_blank\">http://www.urinemetabolome.ca</a>.</p></div>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "urine"], "article_id"=>788491, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0073076.s001", "https://dx.doi.org/10.1371/journal.pone.0073076.s002", "https://dx.doi.org/10.1371/journal.pone.0073076.s003", "https://dx.doi.org/10.1371/journal.pone.0073076.s004", "https://dx.doi.org/10.1371/journal.pone.0073076.s005", "https://dx.doi.org/10.1371/journal.pone.0073076.s006"], "stats"=>{"downloads"=>173, "page_views"=>120, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Human_Urine_Metabolome_/788491", "title"=>"The Human Urine Metabolome", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190580"], "description"=>"*<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>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "metabolites", "urine"], "article_id"=>788476, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.t006", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concentrations_of_metabolites_in_human_urine_as_measured_by_GC_MS_/788476", "title"=>"Concentrations of metabolites in human urine as measured by GC-MS.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190577"], "description"=>"<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>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "diagram", "overlap", "urine", "metabolites", "hplc", "coupled", "uv", "detection", "fluorescence", "compared", "detectable"], "article_id"=>788473, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.g005", "stats"=>{"downloads"=>16, "page_views"=>591, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_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_/788473", "title"=>"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.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190590"], "description"=>"*<p>Concentration (Mean ± SD) is expressed by µM/mM creatinine. NA: not available.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "urine", "concentrations", "23", "quantified", "amino", "acids", "nmr"], "article_id"=>788485, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.t010", "stats"=>{"downloads"=>6, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_urine_concentrations_of_23_quantified_amino_acids_by_different_assays_DFI_LC_MS_MS_BIOCRATES_kit_NMR_and_GC_MS_/788485", "title"=>"Comparison of urine concentrations of 23 quantified amino acids by different assays: DFI/LC-MS/MS (BIOCRATES kit), NMR and GC-MS.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190574"], "description"=>"<p>Numbers indicate the following metabolites: 1∶3-methyl sulfolane; 2∶3-hexanone; 3∶2-pentanone; 4∶1-hydroxy-2-pentanone; 5: allyl methylsulphide; 6: dimethyl disulfide; 7∶4-heptanone; 8∶1-methylcyclohexanol; 9; 2-hexanone; 10∶3,4-dimethylthiophene; 11: diallyl sulphide; 12∶5-methyl-2-hexanone; 13∶1,3-dithio cyclohexane; 14: dimethyl trisulfide; 15: phenol; 16: o-cymene; 17: p-cymene; 18: m-cymene; 19∶1,4-cineol; 20: p-cresol; 21: linalool oxide; 22: iso-menthol; 23: Alpha-p-dimethylstyrene; 24: L-menthol; 25: undecane; 26: ledene oxide (II); 27: salicylic acid methyl ester; 28: Beta-carvone; 29: piperitone; 30: o-thymol; 31: Beta-cyclocitrol; 32∶4,7-dimethyl-benzofuran; 33: cuminal: 34∶2,6,10,10 Tetramethyl-oxa-spiro-4,5-dec-6-ene; 35∶4-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2-butanone; 36∶1,2,3,4-tetrahydro-1,1,6-trimethyl naphthalene; 37: Alpha-cedrene; 38∶1,2,3,4-tetrahydro-1,5,7-trimethylnapthalene; 39∶1,2-diydro-1,1,6-trimethyl-napthalene; 40: Beta-guaiene; 41: Beta-damascenone; 42∶2,5-cyclohexadiene-1,4-dione-2,6-di-tert-butyl; 43: himachalene; 44∶4-(2,6,6-trimethylcyclohexa-1,3-dienyl)-but-3-en-2-one: 45∶1-(2,6,6-trimethyl-1-cyclohexen-1-yl)-1-penten-3-one; 46∶2,4-Bis (1,1-dimethylethyl)-phenol; 47∶1-(2,3,6-trimethyl phenyl)-3-buten-2-one; 48: L-calamenene; 49: Beta-vatirenene; 50∶1,6,7-trimethylnaphthalene; 51: azulol; 52∶3,3,5,6-tetramethyl-1-indanone.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "chromatogram", "volatile", "compounds", "pooled", "urine"], "article_id"=>788470, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.g004", "stats"=>{"downloads"=>9, "page_views"=>215, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Typical_gas_chromatogram_of_volatile_organic_compounds_VOC_from_a_pooled_human_urine_sample_/788470", "title"=>"Typical gas chromatogram of volatile organic compounds (VOC) from a pooled human urine sample.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190585"], "description"=>"*<p>Concentration of metabolite (Mean ± SD) is expressed by µM.</p>a<p>The mean daily vitamin B6 intake was well below the recommended dietary allowance for men and woman;</p>b<p>depends greatly on amount of alcohol consumed;</p>c<p>after administration of lactose;</p>d<p>after administration of 1 g of coumarin;</p>e<p>After styrene exposure; and</p>f<p>after consumption of chocolate.</p><p>NA: not available; NA**: not available for healthy adults; ADP: Adenosine-5-diphosphate; HPHPA: 3-(3-hydroxyphenyl)-3-hydroxypropanoic acid; Oc: occurrence.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "occurrence", "urine", "metabolites"], "article_id"=>788481, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.t003", "stats"=>{"downloads"=>5, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concentrations_Mean_range_and_occurrence_of_urine_metabolites_as_determined_by_NMR_/788481", "title"=>"Concentrations [Mean (range)] and % occurrence of urine metabolites as determined by NMR.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-04 02:17:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1190583"], "description"=>"a<p>Polar metabolites.</p>b<p>Targeted organic acids.</p>c<p>Targeted bile acids. HPHPA: 3-(3-hydroxyphenyl)-3-hydroxypropanoic acid.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Carbohydrate metabolism", "Metabolic pathways", "Nitrogen metabolism", "Small molecules", "Computational biology", "Biological data management", "text mining", "systems biology", "Analytical chemistry", "Chemical analysis", "Quantitative analysis", "chromatography", "Diagnostic medicine", "Clinical laboratory sciences", "urology", "metabolites", "urine", "extracts", "gc-ms", "volatile"], "article_id"=>788479, "categories"=>["Information And Computing Sciences", "Medicine", "Chemistry", "Biological Sciences"], "users"=>["Souhaila Bouatra", "Farid Aziat", "Rupasri Mandal", "An Chi Guo", "Michael R. Wilson", "Craig Knox", "Trent C. Bjorndahl", "Ramanarayan Krishnamurthy", "Fozia Saleem", "Philip Liu", "Zerihun T. Dame", "Jenna Poelzer", "Jessica Huynh", "Faizath S. Yallou", "Nick Psychogios", "Edison Dong", "Ralf Bogumil", "Cornelia Roehring", "David S. Wishart"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073076.t004", "stats"=>{"downloads"=>6, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_metabolites_identified_in_human_urine_extracts_by_GC_MS_except_volatile_compounds_/788479", "title"=>"List of metabolites identified in human urine extracts by GC-MS (except volatile compounds).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-04 02:17:41"}

PMC Usage Stats | Further Information

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Relative Metric

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