{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T04:58:51Z","timestamp":1776056331733,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,8,25]],"date-time":"2021-08-25T00:00:00Z","timestamp":1629849600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Accurate and efficient compound annotation is a long-standing challenge for LC\u2013MS-based data (e.g. untargeted metabolomics and exposomics). Substantial efforts have been devoted to overcoming this obstacle, whereas current tools are limited by the sources of spectral information used (in-house and public databases) and are not automated and streamlined. Therefore, we developed metID, an R package that combines information from all major databases for comprehensive and streamlined compound annotation. metID is a flexible, simple and powerful tool that can be installed on all platforms, allowing the compound annotation process to be fully automatic and reproducible. A detailed tutorial and a case study are provided in Supplementary Materials.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/jaspershen.github.io\/metID.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab583","type":"journal-article","created":{"date-parts":[[2021,8,25]],"date-time":"2021-08-25T09:51:26Z","timestamp":1629885086000},"page":"568-569","source":"Crossref","is-referenced-by-count":39,"title":["metID: an R package for automatable compound annotation for LC\u2212MS-based data"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9608-9964","authenticated-orcid":false,"given":"Xiaotao","family":"Shen","sequence":"first","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"}]},{"given":"Si","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"}]},{"given":"Liang","family":"Liang","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"}]},{"given":"Songjie","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"}]},{"given":"K\u00e9vin","family":"Contrepois","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"}]},{"given":"Zheng-Jiang","family":"Zhu","sequence":"additional","affiliation":[{"name":"Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai 200032, China"}]},{"given":"Michael","family":"Snyder","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine , Stanford, CA 94304, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,8,25]]},"reference":[{"key":"2023020108413540100_btab583-B1","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.copbio.2018.07.010","article-title":"Challenges, progress and promises of metabolite annotation for LC\u2013MS-based metabolomics","volume":"55","author":"Chaleckis","year":"2019","journal-title":"Curr. Opin. Biotechnol"},{"key":"2023020108413540100_btab583-B2","doi-asserted-by":"crossref","first-page":"1112","DOI":"10.1016\/j.cell.2020.04.043","article-title":"Molecular choreography of acute exercise","volume":"181","author":"Contrepois","year":"2020","journal-title":"Cell"},{"key":"2023020108413540100_btab583-B3","first-page":"109","article-title":"Analytical metabolomics and applications in health, environmental and food science","volume":"10","author":"Fraga-Corral","year":"2020","journal-title":"Crit. Rev. Anal. Chem"},{"key":"2023020108413540100_btab583-B4","doi-asserted-by":"crossref","first-page":"1516","DOI":"10.1038\/s41467-019-09550-x","article-title":"Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics","volume":"10","author":"Shen","year":"2019","journal-title":"Nat. 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Drug Discov"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab583\/40081282\/btab583.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/2\/568\/49006586\/btab583.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/2\/568\/49006586\/btab583.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T14:59:12Z","timestamp":1675263552000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/2\/568\/6357695"}},"subtitle":[],"editor":[{"given":"Olga","family":"Vitek","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,8,25]]},"references-count":7,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,1,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab583","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.05.08.443258","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,15]]},"published":{"date-parts":[[2021,8,25]]}}}