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. 2021 Jun 16;37(10):1478-1479.
doi: 10.1093/bioinformatics/btaa856.

LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications

Jorge Alvarez-Jarreta  1   2 , Patricia R S Rodrigues  1 , Eoin Fahy  3 , Anne O'Connor  1 , Anna Price  4 , Caroline Gaud  5 , Simon Andrews  5 , Paul Benton  6 , Gary Siuzdak  6 , Jade I Hawksworth  1 , Maria Valdivia-Garcia  1 , Stuart M Allen  7 , Valerie B O'Donnell  1
Affiliations

LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications

Jorge Alvarez-Jarreta et al. Bioinformatics. .

Abstract

Summary: 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-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.

Availability and implementation: LipidFinder 2.0 is freely available at https://github.com/ODonnell-Lipidomics/LipidFinder and http://lipidmaps.org/resources/tools/lipidfinder.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Common pipeline for untargeted lipidomics incorporating LipidFinder 2.0. It also shows LipidFinder’s new main workflow
See this image and copyright information in PMC

References

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