{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T20:27:48Z","timestamp":1780604868904,"version":"3.54.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2017,8,14]],"date-time":"2017-08-14T00:00:00Z","timestamp":1502668800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["097821\/Z\/11\/Z and 105614\/Z\/14\/Z"],"award-info":[{"award-number":["097821\/Z\/11\/Z and 105614\/Z\/14\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The Polyomics integrated Metabolomics Pipeline (PiMP) fulfils an unmet need in metabolomics data analysis. PiMP offers automated and user-friendly analysis from mass spectrometry data acquisition to biological interpretation. Our key innovations are the Summary Page, which provides a simple overview of the experiment in the format of a scientific paper, containing the key findings of the experiment along with associated metadata; and the Metabolite Page, which provides a list of each metabolite accompanied by \u2018evidence cards\u2019, which provide a variety of criteria behind metabolite annotation including peak shapes, intensities in different sample groups and database information.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PiMP is available at http:\/\/polyomics.mvls.gla.ac.uk, and access is freely available on request. 50\u2009GB of space is allocated for data storage, with unrestricted number of samples and analyses per user. Source code is available at https:\/\/github.com\/RonanDaly\/pimp and licensed under the GPL.<\/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\/btx499","type":"journal-article","created":{"date-parts":[[2017,8,11]],"date-time":"2017-08-11T11:08:52Z","timestamp":1502449732000},"page":"4007-4009","source":"Crossref","is-referenced-by-count":55,"title":["PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data"],"prefix":"10.1093","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0493-8592","authenticated-orcid":false,"given":"Yoann","family":"Gloaguen","sequence":"first","affiliation":[{"name":"Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fraser","family":"Morton","sequence":"additional","affiliation":[{"name":"Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R\u00f3n\u00e1n","family":"Daly","sequence":"additional","affiliation":[{"name":"Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ross","family":"Gurden","sequence":"additional","affiliation":[{"name":"Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, UK"},{"name":"Centre for Cell Engineering, University of Glasgow, Glasgow, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Rogers","sequence":"additional","affiliation":[{"name":"School of Computing Science, University of Glasgow, Glasgow, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3068-4664","authenticated-orcid":false,"given":"Joe","family":"Wandy","sequence":"additional","affiliation":[{"name":"Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, UK"},{"name":"School of Computing Science, University of Glasgow, Glasgow, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Wilson","sequence":"additional","affiliation":[{"name":"Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Barrett","sequence":"additional","affiliation":[{"name":"Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, UK"},{"name":"Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karl","family":"Burgess","sequence":"additional","affiliation":[{"name":"Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,8,14]]},"reference":[{"key":"2023020207504500900_btx499-B1","doi-asserted-by":"crossref","first-page":"W132","DOI":"10.1093\/nar\/gkq312","article-title":"MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks","volume":"38","author":"Cottret","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023020207504500900_btx499-B2","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1038\/nprot.2011.335","article-title":"Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry","volume":"6","author":"Dunn","year":"2011","journal-title":"Nat. Protoc"},{"key":"2023020207504500900_btx499-B3","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1093\/bioinformatics\/btu813","article-title":"Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics","volume":"31","author":"Giacomoni","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020207504500900_btx499-B4","doi-asserted-by":"crossref","first-page":"D199","DOI":"10.1093\/nar\/gkt1076","article-title":"Data, information, knowledge and principle: back to metabolism in KEGG","volume":"42","author":"Kanehisa","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020207504500900_btx499-B5","doi-asserted-by":"crossref","first-page":"3422","DOI":"10.1002\/rcm.5245","article-title":"Pathos: A web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry","volume":"25","author":"Leader","year":"2011","journal-title":"Rapid Commun. Mass Spectrom"},{"key":"2023020207504500900_btx499-B6","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/S0167-7799(98)01214-1","article-title":"Systematic functional analysis of the yeast genome","volume":"16","author":"Oliver","year":"1998","journal-title":"Trends Biotechnol"},{"key":"2023020207504500900_btx499-B7","doi-asserted-by":"crossref","first-page":"2786","DOI":"10.1021\/ac2000994","article-title":"PeakML\/mzMatch: a file format, java library, R library, and tool-chain for mass spectrometry data analysis","volume":"83","author":"Scheltema","year":"2011","journal-title":"Anal. Chem"},{"key":"2023020207504500900_btx499-B8","first-page":"779","article-title":"XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification","volume-title":"Anal. chem.","author":"Smith"},{"key":"2023020207504500900_btx499-B9","doi-asserted-by":"crossref","first-page":"W481","DOI":"10.1093\/nar\/gkn194","article-title":"MassTRIX: mass translator into pathways","volume":"36","author":"Suhre","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023020207504500900_btx499-B10","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":"2023020207504500900_btx499-B11","doi-asserted-by":"crossref","first-page":"W127","DOI":"10.1093\/nar\/gks374","article-title":"MetaboAnalyst 2.0\u2013a comprehensive server for metabolomic data analysis","volume":"40","author":"Xia","year":"2012","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/24\/4007\/49041963\/bioinformatics_33_24_4007.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/24\/4007\/49041963\/bioinformatics_33_24_4007.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T07:52:20Z","timestamp":1675324340000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/24\/4007\/4082268"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,8,14]]},"references-count":11,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2017,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx499","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,12,15]]},"published":{"date-parts":[[2017,8,14]]}}}