{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:01Z","timestamp":1772138041452,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2020,10,7]],"date-time":"2020-10-07T00:00:00Z","timestamp":1602028800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["203014\/Z\/16\/Z"],"award-info":[{"award-number":["203014\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Royal Society Wolfson Research Merit Award"},{"name":"Avanti Polar Lipids"},{"name":"Cayman Chemical Co and Merck"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We present LipidFinder 2.0, incorporating four new modules that apply artefact filters, remove lipid and contaminant stacks, in-source fragments and salt clusters, and a new isotope deletion method which is significantly more sensitive than available open-access alternatives. We also incorporate a novel false discovery rate method, utilizing a target\u2013decoy strategy, which allows users to assess data quality. A renewed lipid profiling method is introduced which searches three different databases from LIPID MAPS and returns bulk lipid structures only, and a lipid category scatter plot with color blind friendly pallet. An API interface with XCMS Online is made available on LipidFinder\u2019s online version. We show using real data that LipidFinder 2.0 provides a significant improvement over non-lipid metabolite filtering and lipid profiling, compared to available tools.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>LipidFinder 2.0 is freely available at https:\/\/github.com\/ODonnell-Lipidomics\/LipidFinder and http:\/\/lipidmaps.org\/resources\/tools\/lipidfinder.<\/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\/btaa856","type":"journal-article","created":{"date-parts":[[2020,9,22]],"date-time":"2020-09-22T19:49:33Z","timestamp":1600804173000},"page":"1478-1479","source":"Crossref","is-referenced-by-count":11,"title":["LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications"],"prefix":"10.1093","volume":"37","author":[{"given":"Jorge","family":"Alvarez-Jarreta","sequence":"first","affiliation":[{"name":"School of Medicine, Systems Immunity Research Institute, School of Medicine, Cardiff University , Cardiff CF14 4XN, UK"},{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton CB10 1SD, UK"}]},{"given":"Patricia R S","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"School of Medicine, Systems Immunity Research Institute, School of Medicine, Cardiff University , Cardiff CF14 4XN, UK"}]},{"given":"Eoin","family":"Fahy","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California , San Diego, CA 92037, USA"}]},{"given":"Anne","family":"O\u2019Connor","sequence":"additional","affiliation":[{"name":"School of Medicine, Systems Immunity Research Institute, School of Medicine, Cardiff University , Cardiff CF14 4XN, UK"}]},{"given":"Anna","family":"Price","sequence":"additional","affiliation":[{"name":"School of Biosciences, Cardiff University , Cardiff CF10 3AX, UK"}]},{"given":"Caroline","family":"Gaud","sequence":"additional","affiliation":[{"name":"Bioinformatics, Babraham Institute , Cambridge CF24 3AA, UK"}]},{"given":"Simon","family":"Andrews","sequence":"additional","affiliation":[{"name":"Bioinformatics, Babraham Institute , Cambridge CF24 3AA, UK"}]},{"given":"Paul","family":"Benton","sequence":"additional","affiliation":[{"name":"The Scripps Research Institute, Center for Metabolomics , La Jolla, CA 92037, USA"}]},{"given":"Gary","family":"Siuzdak","sequence":"additional","affiliation":[{"name":"The Scripps Research Institute, Center for Metabolomics , La Jolla, CA 92037, USA"}]},{"given":"Jade I","family":"Hawksworth","sequence":"additional","affiliation":[{"name":"School of Medicine, Systems Immunity Research Institute, School of Medicine, Cardiff University , Cardiff CF14 4XN, UK"}]},{"given":"Maria","family":"Valdivia-Garcia","sequence":"additional","affiliation":[{"name":"School of Medicine, Systems Immunity Research Institute, School of Medicine, Cardiff University , Cardiff CF14 4XN, UK"}]},{"given":"Stuart M","family":"Allen","sequence":"additional","affiliation":[{"name":"School of Computer Science and Informatics, Cardiff University , Cardiff CF24 3AA, UK"}]},{"given":"Valerie B","family":"O\u2019Donnell","sequence":"additional","affiliation":[{"name":"School of Medicine, Systems Immunity Research Institute, School of Medicine, Cardiff University , Cardiff CF14 4XN, UK"}]}],"member":"286","published-online":{"date-parts":[[2020,12,10]]},"reference":[{"key":"2023051709344646400_btaa856-B1","doi-asserted-by":"crossref","first-page":"2275","DOI":"10.1194\/jlr.M079012","article-title":"Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-metabolites in frozen human plasma","volume":"58","author":"Bowden","year":"2017","journal-title":"J. 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