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LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications

Alvarez-Jarreta, Jorge, Rodrigues, Patricia R.S., Fahy, Eoin, O'Connor, Anne, Price, Anna, Gaud, Caroline, Andrews, Simon, Benton, Paul, Siuzdak, Gary, Hawksworth, Jade I., Valdivia-Garcia, Maria, Allen, Stuart M., O'Donnell, Valerie B. and Valencia, Alfonso 2020. LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications. Bioinformatics 10.1093/bioinformatics/btaa856

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Abstract

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 (FDR) method, utilizing a target-decoy 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’s 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.

Item Type: Article
Date Type: Published Online
Status: In Press
Schools: Computer Science & Informatics
Medicine
Publisher: Oxford University Press
ISSN: 1367-4803
Funders: Wellcome Trust
Date of First Compliant Deposit: 21 October 2020
Date of Acceptance: 20 September 2020
Last Modified: 05 Nov 2020 14:21
URI: http://orca-mwe.cf.ac.uk/id/eprint/135819

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