{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,2]],"date-time":"2024-08-02T18:29:14Z","timestamp":1722623354431},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Metabolite databases provide a unique window into metabolome research allowing the most commonly searched biomarkers to be catalogued. Omic scale metabolite profiling, or metabolomics, is finding increased utility in biomarker discovery largely driven by improvements in analytical technologies and the concurrent developments in bioinformatics. However, the successful translation of biomarkers into clinical or biologically relevant indicators is limited.<\/jats:p>\n               <jats:p>Results: With the aim of improving the discovery of translatable metabolite biomarkers, we present search analytics for over one million METLIN metabolite database queries. The most common metabolites found in METLIN were cross-correlated against XCMS Online, the widely used cloud-based data processing and pathway analysis platform. Analysis of the METLIN and XCMS common metabolite data has two primary implications: these metabolites, might indicate a conserved metabolic response to stressors and, this data may be used to gauge the relative uniqueness of potential biomarkers.<\/jats:p>\n               <jats:p>Availability and implementation. METLIN can be accessed by logging on to: https:\/\/metlin.scripps.edu<\/jats:p>\n               <jats:p>Contact: \u00a0siuzdak@scripps.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv475","type":"journal-article","created":{"date-parts":[[2015,8,15]],"date-time":"2015-08-15T01:29:49Z","timestamp":1439602189000},"page":"3721-3724","source":"Crossref","is-referenced-by-count":7,"title":["Determining conserved metabolic biomarkers from a million database queries"],"prefix":"10.1093","volume":"31","author":[{"given":"Michael E.","family":"Kurczy","sequence":"first","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julijana","family":"Ivanisevic","sequence":"additional","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caroline H.","family":"Johnson","sequence":"additional","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Winnie","family":"Uritboonthai","sequence":"additional","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linh","family":"Hoang","sequence":"additional","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingliang","family":"Fang","sequence":"additional","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Hicks","sequence":"additional","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony","family":"Aldebot","sequence":"additional","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Duane","family":"Rinehart","sequence":"additional","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lisa J.","family":"Mellander","sequence":"additional","affiliation":[{"name":"2 Department of Physics, University of California San Diego, La Jolla, CA 92093, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ralf","family":"Tautenhahn","sequence":"additional","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gary J.","family":"Patti","sequence":"additional","affiliation":[{"name":"3 Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA,"},{"name":"4 Departments of Genetics and Medicine, Washington University School of Medicine, St. Louis, MO 63130, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mary E.","family":"Spilker","sequence":"additional","affiliation":[{"name":"5 Pfizer Worldwide Research and Development, San Diego, CA 92121, USA and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"H. Paul","family":"Benton","sequence":"additional","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gary","family":"Siuzdak","sequence":"additional","affiliation":[{"name":"1 Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA,"},{"name":"6 Departments of Chemistry, Molecular and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,8,13]]},"reference":[{"key":"2023020202410857400_btv475-B1","doi-asserted-by":"crossref","first-page":"925S","DOI":"10.1093\/jn\/133.3.925S","article-title":"Biomarkers of fat and fatty acid intake","volume":"133","author":"Arab","year":"2003","journal-title":"J. Nutr."},{"key":"2023020202410857400_btv475-B2","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.chroma.2006.05.019","article-title":"Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry","volume":"1125","author":"Bajad","year":"2006","journal-title":"J. Chromatogr. A"},{"key":"2023020202410857400_btv475-B3","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/s00216-011-5308-5","article-title":"Hydrophilic interaction liquid chromatography (HILIC)-a powerful separation technique","volume":"402","author":"Buszewski","year":"2012","journal-title":"Anal. Bioanal. Chem."},{"key":"2023020202410857400_btv475-B4","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1371\/journal.pone.0122963","article-title":"Association between an Internet-based measure of area racism and black mortality","volume":"10","author":"Chae","year":"2015","journal-title":"PLoS ONE"},{"key":"2023020202410857400_btv475-B5","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1038\/nrd2825","article-title":"OUTLOOK The microeconomics of personalized medicine: today's challenge and tomorrow's promise","volume":"8","author":"Davis","year":"2009","journal-title":"Nat. Rev. Drug Discov."},{"key":"2023020202410857400_btv475-B6","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1878-5085-4-7","article-title":"Pitfalls and limitations in translation from biomarker discovery to clinical utility in predictive and personalised medicine","volume":"4","author":"Drucker","year":"2013","journal-title":"EPMA J."},{"key":"2023020202410857400_btv475-B7","doi-asserted-by":"crossref","first-page":"U1012","DOI":"10.1038\/nature07634","article-title":"Detecting influenza epidemics using search engine query data","volume":"457","author":"Ginsberg","year":"2009","journal-title":"Nature"},{"key":"2023020202410857400_btv475-B8","doi-asserted-by":"crossref","first-page":"6931","DOI":"10.1021\/ac500734c","article-title":"Interactive XCMS online: simplifying advanced metabolomic data processing and subsequent statistical analyses","volume":"86","author":"Gowda","year":"2014","journal-title":"Anal. Chem."},{"key":"2023020202410857400_btv475-B9","doi-asserted-by":"crossref","first-page":"1492","DOI":"10.1126\/science.1188015","article-title":"Evidence for an alternative glycolytic pathway in rapidly proliferating cells","volume":"329","author":"Heiden","year":"2010","journal-title":"Science"},{"key":"2023020202410857400_btv475-B10","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1093\/clinchem\/17.8.802","article-title":"Metabolic profiles\u2014gas-phase methods for analysis of metabolites","volume":"17","author":"Horning","year":"1971","journal-title":"Clin. Chem."},{"key":"2023020202410857400_btv475-B11","doi-asserted-by":"crossref","first-page":"6876","DOI":"10.1021\/ac401140h","article-title":"Toward omic scale metabolite profiling: a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism","volume":"85","author":"Ivanisevic","year":"2013","journal-title":"Anal. Chem."},{"key":"2023020202410857400_btv475-B12","doi-asserted-by":"crossref","first-page":"3079","DOI":"10.1021\/ac900036d","article-title":"MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing","volume":"81","author":"Lommen","year":"2009","journal-title":"Anal. Chem."},{"key":"2023020202410857400_btv475-B13","doi-asserted-by":"crossref","first-page":"9818","DOI":"10.1021\/ac1021166","article-title":"Metabolomic analysis and visualization engine for LC-MS data","volume":"82","author":"Melamud","year":"2010","journal-title":"Anal. Chem."},{"key":"2023020202410857400_btv475-B14","doi-asserted-by":"crossref","first-page":"7604","DOI":"10.1021\/ac900954d","article-title":"X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry","volume":"81","author":"Mylonas","year":"2009","journal-title":"Anal. Chem."},{"key":"2023020202410857400_btv475-B15","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1038\/nchembio.767","article-title":"Metabolomics implicates altered sphingolipids in chronic pain of neuropathic origin","volume":"8","author":"Patti","year":"2012","journal-title":"Nat. Chem. Biol."},{"key":"2023020202410857400_btv475-B16","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/nrm3314","article-title":"Metabolomics: the apogee of the omics trilogy","volume":"13","author":"Patti","year":"2012","journal-title":"Nat. Rev. Mol. Cell. Biol."},{"key":"2023020202410857400_btv475-B17","doi-asserted-by":"crossref","first-page":"2374","DOI":"10.1073\/pnas.68.10.2374","article-title":"Quantitative analysis of urine vapor and breath by gas\u2013liquid partition chromatography","volume":"68","author":"Pauling","year":"1971","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020202410857400_btv475-B18","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1186\/1471-2105-11-395","article-title":"MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data","volume":"11","author":"Pluskal","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020202410857400_btv475-B19","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1038\/469156a","article-title":"Bring on the biomarkers","volume":"469","author":"Poste","year":"2011","journal-title":"Nature"},{"key":"2023020202410857400_btv475-B20","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1097\/01.ftd.0000179845.53213.39","article-title":"METLIN: a metabolite mass spectral database","volume":"27","author":"Smith","year":"2005","journal-title":"Ther. Drug Monitoring"},{"key":"2023020202410857400_btv475-B21","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1002\/jssc.200900803","article-title":"Hydrophilic interaction chromatography coupled to MS for metabonomic\/metabolomic studies","volume":"33","author":"Spagou","year":"2010","journal-title":"J. Sep. Sci."},{"key":"2023020202410857400_btv475-B22","doi-asserted-by":"crossref","first-page":"5035","DOI":"10.1021\/ac300698c","article-title":"XCMS online: a web-based platform to process untargeted metabolomic data","volume":"84","author":"Tautenhahn","year":"2012","journal-title":"Anal. Chem."},{"key":"2023020202410857400_btv475-B23","doi-asserted-by":"crossref","first-page":"U57","DOI":"10.1038\/nature09922","article-title":"Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease","volume":"472","author":"Wang","year":"2011","journal-title":"Nature"},{"key":"2023020202410857400_btv475-B24","doi-asserted-by":"crossref","first-page":"2856","DOI":"10.1093\/bioinformatics\/bts527","article-title":"MaConDa: a publicly accessible mass spectrometry contaminants database","volume":"28","author":"Weber","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020202410857400_btv475-B25","doi-asserted-by":"crossref","first-page":"W127","DOI":"10.1093\/nar\/gks374","article-title":"MetaboAnalyst 2.0\u2014a comprehensive server for metabolomic data analysis","volume":"40","author":"Xia","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020202410857400_btv475-B26","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1007\/s11306-012-0482-9","article-title":"Translational biomarker discovery in clinical metabolomics: an introductory tutorial","volume":"9","author":"Xia","year":"2013","journal-title":"Metabolomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/23\/3721\/49036067\/bioinformatics_31_23_3721.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/23\/3721\/49036067\/bioinformatics_31_23_3721.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:56:12Z","timestamp":1675310172000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/23\/3721\/209543"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,8,13]]},"references-count":26,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2015,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv475","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,12,1]]},"published":{"date-parts":[[2015,8,13]]}}}