{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T05:58:37Z","timestamp":1791266317433,"version":"4.1.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2024,7,17]],"date-time":"2024-07-17T00:00:00Z","timestamp":1721174400000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Independent Research Funds Denmark","award":["2032-00062B"],"award-info":[{"award-number":["2032-00062B"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The post-processing and analysis of large-scale untargeted metabolomics data face significant challenges due to the intricate nature of correction, filtration, imputation, and normalization steps. Manual execution across various applications often leads to inefficiencies, human-induced errors, and inconsistencies within the workflow.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Addressing these issues, we introduce MetaboLink, a novel web application designed to process LC-MS metabolomics datasets combining established methodologies and offering flexibility and ease of implementation. It offers visualization options for data interpretation, an interface for statistical testing, and integration with PolySTest for further tests and with VSClust for clustering analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Fully functional tool is publicly available at https:\/\/computproteomics.bmb.sdu.dk\/Metabolomics\/. The source code is available at https:\/\/github.com\/anitamnd\/MetaboLink and a detailed description of the app can be found at https:\/\/github.com\/anitamnd\/MetaboLink\/wiki. A tutorial video can be found at https:\/\/youtu.be\/ZM6j10S6Z8Q.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae459","type":"journal-article","created":{"date-parts":[[2024,7,17]],"date-time":"2024-07-17T12:14:51Z","timestamp":1721218491000},"source":"Crossref","is-referenced-by-count":11,"title":["MetaboLink: a web application for streamlined processing and analysis of large-scale untargeted metabolomics data"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-5170-0927","authenticated-orcid":false,"given":"Ana","family":"Mendes","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark , 5230 Odense M, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9797-5431","authenticated-orcid":false,"given":"Jesper Foged","family":"Havelund","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark , 5230 Odense M, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonas","family":"Lemvig","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark , 5230 Odense M, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9708-6722","authenticated-orcid":false,"given":"Veit","family":"Schw\u00e4mmle","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark , 5230 Odense M, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9281-5287","authenticated-orcid":false,"given":"Nils J","family":"F\u00e6rgeman","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark , 5230 Odense M, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,7,17]]},"reference":[{"key":"2024072505120808700_btae459-B1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate\u2014a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J R Stat Soc B"},{"key":"2024072505120808700_btae459-B2","doi-asserted-by":"crossref","first-page":"357","DOI":"10.3390\/metabo12040357","article-title":"Guide to metabolomics analysis: a bioinformatics workflow","volume":"12","author":"Chen","year":"2022","journal-title":"Metabolites"},{"key":"2024072505120808700_btae459-B3","doi-asserted-by":"crossref","first-page":"4281","DOI":"10.1021\/ac051632c","article-title":"Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics","volume":"78","author":"Dieterle","year":"2006","journal-title":"Anal Chem"},{"key":"2024072505120808700_btae459-B4","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":"2024072505120808700_btae459-B5","doi-asserted-by":"crossref","first-page":"W398","DOI":"10.1093\/nar\/gkae253","article-title":"MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation","volume":"52","author":"Pang","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2024072505120808700_btae459-B6","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2024072505120808700_btae459-B7","doi-asserted-by":"crossref","first-page":"1897","DOI":"10.1007\/s13361-016-1469-y","article-title":"Untargeted metabolomics strategies-challenges and emerging directions","volume":"27","author":"Schrimpe-Rutledge","year":"2016","journal-title":"J Am Soc Mass Spectrom"},{"key":"2024072505120808700_btae459-B8","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1074\/mcp.RA119.001777","article-title":"PolySTest: robust statistical testing of proteomics data with missing values improves detection of biologically relevant features","volume":"19","author":"Schw\u00e4mmle","year":"2020","journal-title":"Mol Cell Proteomics"},{"key":"2024072505120808700_btae459-B9","doi-asserted-by":"crossref","first-page":"2965","DOI":"10.1093\/bioinformatics\/bty224","article-title":"VSClust: feature-based variance-sensitive clustering of omics data","volume":"34","author":"Schwammle","year":"2018","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae459\/58575879\/btae459.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/7\/btae459\/58644455\/btae459.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/7\/btae459\/58644455\/btae459.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T02:19:26Z","timestamp":1721873966000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae459\/7715873"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,7,1]]},"references-count":9,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2024,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae459","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,7]]},"published":{"date-parts":[[2024,7,1]]},"article-number":"btae459"}}