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LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications

By Jorge Alvarez-Jarreta, Patricia Rodrigues, Eoin Fahy, Anne O'Connor, Anna Price, Caroline Gaud, Simon Andrews, Paul Benton, Gary Siuzdak, Jade Hawksworth, Maria Valdivia, Stuart Allen, Valerie O'Donnell

Posted 17 Aug 2020
bioRxiv DOI: 10.1101/2020.08.16.250878 (published DOI: 10.1093/bioinformatics/btaa856)

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 LipidFinders 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. ### Competing Interest Statement The authors have declared no competing interest.

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