{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T08:19:01Z","timestamp":1778055541048,"version":"3.51.4"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: A major challenge for mass spectrometric-based lipidomics, aiming at describing all lipid species in a biological sample, lies in the computational and bioinformatic processing of the large amount of data that arises after data acquisition. Lipid-Pro is a software tool that supports the identification of lipids by interpreting large datasets generated by liquid chromatography\u2014tandem mass spectrometry (LC\u2013MS\/MS) using the advanced data-independent acquisition mode MSE. In the MSE mode, the instrument fragments all molecular ions generated from a sample and records time-resolved molecular ion data as well as fragment ion data for every detectable molecular ion. Lipid-Pro matches the retention time-aligned mass-to-charge ratio data of molecular- and fragment ions with a lipid database and generates a report on all identified lipid species. For generation of the lipid database, Lipid-Pro provides a module for construction of lipid species and their fragments using a flexible building block approach. Hence, Lipid-Pro is an easy to use analysis tool to interpret complex MSE lipidomics data and also offers a module to generate a user-specific lipid database.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0Lipid-Pro is freely available at: http:\/\/www.neurogenetics.biozentrum.uni-wuerzburg.de\/en\/project\/services\/lipidpro\/<\/jats:p>\n               <jats:p>Contact: \u00a0zeeshan.ahmed@uni-wuerzburg.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu796","type":"journal-article","created":{"date-parts":[[2014,11,30]],"date-time":"2014-11-30T01:39:32Z","timestamp":1417311572000},"page":"1150-1153","source":"Crossref","is-referenced-by-count":28,"title":["<i>Lipid-Pro:<\/i> a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms"],"prefix":"10.1093","volume":"31","author":[{"given":"Zeeshan","family":"Ahmed","sequence":"first","affiliation":[{"name":"1 Department of Neurobiology and Genetics, Biocenter, 2Department of Bioinformatics, Biocenter and 3Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany"},{"name":"1 Department of Neurobiology and Genetics, Biocenter, 2Department of Bioinformatics, Biocenter and 3Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany"}]},{"given":"Michel","family":"Mayr","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology and Genetics, Biocenter, 2Department of Bioinformatics, Biocenter and 3Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany"}]},{"given":"Saman","family":"Zeeshan","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology and Genetics, Biocenter, 2Department of Bioinformatics, Biocenter and 3Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany"}]},{"given":"Thomas","family":"Dandekar","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology and Genetics, Biocenter, 2Department of Bioinformatics, Biocenter and 3Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany"}]},{"given":"Martin J.","family":"Mueller","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology and Genetics, Biocenter, 2Department of Bioinformatics, Biocenter and 3Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany"}]},{"given":"Agnes","family":"Fekete","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology and Genetics, Biocenter, 2Department of Bioinformatics, Biocenter and 3Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2014,11,29]]},"reference":[{"key":"2023051309142730200_btu796-B1","doi-asserted-by":"crossref","first-page":"e61951","DOI":"10.1371\/journal.pone.0061951","article-title":"LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics","volume":"8","author":"Foster","year":"2013","journal-title":"PLoS One"},{"key":"2023051309142730200_btu796-B2","doi-asserted-by":"crossref","first-page":"19","DOI":"10.3390\/metabo2010019","article-title":"Mass spectrometry based lipidomics: an overview of technological platforms","volume":"2","author":"Harald","year":"2012","journal-title":"Metabolites"},{"key":"2023051309142730200_btu796-B3","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1093\/bioinformatics\/btq699","article-title":"Lipid data analyser: unattended identification and quantification of lipids in LC-MS data","volume":"27","author":"Hartler","year":"2011","journal-title":"Bioinformatics"},{"key":"2023051309142730200_btu796-B4","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1038\/nmeth.2551","article-title":"LipidBlast in silico tandem mass spectrometry database for lipid identification","volume":"10","author":"Kind","year":"2013","journal-title":"Nat. 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