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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 2021. LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications. Bioinformatics 37 (10) , pp. 1478-1479. 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: Publication
Status: Published
Schools: Computer Science & Informatics
Medicine
Additional Information: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/)
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 Jul 2021 12:48
URI: http://orca.cardiff.ac.uk/id/eprint/135819

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