. 2024 Sep;65(9):100621.

doi: 10.1016/j.jlr.2024.100621. Epub 2024 Aug 14.

The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data

Dominik Kopczynski¹, Christer S Ejsing², Jeffrey G McDonald³, Takeshi Bamba⁴, Erin S Baker⁵, Justine Bertrand-Michel⁶, Britta Brügger⁷, Cristina Coman¹, Shane R Ellis⁸, Timothy J Garrett⁹, William J Griffiths¹⁰, Xue Li Guan¹¹, Xianlin Han¹², Marcus Höring¹³, Michal Holčapek¹⁴, Nils Hoffmann¹⁵, Kevin Huynh¹⁶, Rainer Lehmann¹⁷, Jace W Jones¹⁸, Rima Kaddurah-Daouk¹⁹, Harald C Köfeler²⁰, Peter J Meikle¹⁶, Thomas O Metz²¹, Valerie B O'Donnell²², Daisuke Saigusa²³, Dominik Schwudke²⁴, Andrej Shevchenko²⁵, Federico Torta²⁶, Juan Antonio Vizcaíno²⁷, Ruth Welti²⁸, Markus R Wenk²⁹, Denise Wolrab¹, Yu Xia³⁰, Kim Ekroos³¹, Robert Ahrends³², Gerhard Liebisch³³

Affiliations

¹ Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
² Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
³ Center for Human Nutrition and Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, Texas, USA.
⁴ Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
⁵ Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
⁶ MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Inserm I2MC, Toulouse, France.
⁷ Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany.
⁸ Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
⁹ Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA.
¹⁰ Swansea University Medical School, Swansea, Wales, UK.
¹¹ Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
¹² Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA.
¹³ Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany.
¹⁴ Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic.
¹⁵ Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, Jülich, Germany.
¹⁶ Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC, Australia.
¹⁷ Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany.
¹⁸ Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA.
¹⁹ Department of Psychiatry and Behavioural Sciences, Duke University, Durham, North Carolina, USA; Duke Institute of Brain Sciences, Duke University, Durham, North Carolina, USA; Department of Medicine, Duke University, Durham, North Carolina, USA.
²⁰ Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria.
²¹ Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
²² Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
²³ Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan.
²⁴ Division of Bioanalytical Chemistry, Research Center Borstel - Leibniz Lung Center, Borstel, Germany; German Center for Infection Research, Thematic Translational Unit Tuberculosis, Partner Site Hamburg-Lübeck-Borstel-Riems, Germany; German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany.
²⁵ Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
²⁶ Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore; Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
²⁷ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
²⁸ Kansas Lipidomics Research Center, Division of Biology, Kansas State University, Manhattan, Kansas, USA.
²⁹ Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore.
³⁰ MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China.
³¹ Lipidomics Consulting Ltd., Esbo, Finland. Electronic address: kim@lipidomicsconsulting.com.
³² Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria. Electronic address: robert.ahrends@univie.ac.at.
³³ Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany. Electronic address: gerhard.liebisch@ukr.de.

PMID: 39151590
PMCID: PMC11417233
DOI: 10.1016/j.jlr.2024.100621

The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data

Dominik Kopczynski et al. J Lipid Res. 2024 Sep.

. 2024 Sep;65(9):100621.

doi: 10.1016/j.jlr.2024.100621. Epub 2024 Aug 14.

Authors

Affiliations

¹ Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
² Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
³ Center for Human Nutrition and Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, Texas, USA.
⁴ Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
⁵ Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
⁶ MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Inserm I2MC, Toulouse, France.
⁷ Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany.
⁸ Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
⁹ Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA.
¹⁰ Swansea University Medical School, Swansea, Wales, UK.
¹¹ Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
¹² Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA.
¹³ Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany.
¹⁴ Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic.
¹⁵ Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, Jülich, Germany.
¹⁶ Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC, Australia.
¹⁷ Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany.
¹⁸ Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA.
¹⁹ Department of Psychiatry and Behavioural Sciences, Duke University, Durham, North Carolina, USA; Duke Institute of Brain Sciences, Duke University, Durham, North Carolina, USA; Department of Medicine, Duke University, Durham, North Carolina, USA.
²⁰ Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria.
²¹ Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
²² Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
²³ Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan.
²⁴ Division of Bioanalytical Chemistry, Research Center Borstel - Leibniz Lung Center, Borstel, Germany; German Center for Infection Research, Thematic Translational Unit Tuberculosis, Partner Site Hamburg-Lübeck-Borstel-Riems, Germany; German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany.
²⁵ Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
²⁶ Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore; Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
²⁷ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
²⁸ Kansas Lipidomics Research Center, Division of Biology, Kansas State University, Manhattan, Kansas, USA.
²⁹ Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore.
³⁰ MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China.
³¹ Lipidomics Consulting Ltd., Esbo, Finland. Electronic address: kim@lipidomicsconsulting.com.
³² Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria. Electronic address: robert.ahrends@univie.ac.at.
³³ Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany. Electronic address: gerhard.liebisch@ukr.de.

PMID: 39151590
PMCID: PMC11417233
DOI: 10.1016/j.jlr.2024.100621

Abstract

The rapid increase in lipidomic studies has led to a collaborative effort within the community to establish standards and criteria for producing, documenting, and disseminating data. Creating a dynamic easy-to-use checklist that condenses key information about lipidomic experiments into common terminology will enhance the field's consistency, comparability, and repeatability. Here, we describe the structure and rationale of the established Lipidomics Minimal Reporting Checklist to increase transparency in lipidomics research.

Keywords: FAIR; checklist; lipid metabolism; lipidomics; mass spectrometry; metabolomics; quality control; reference standards.

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Conflict of interest statement

Conflict of interests Kaddurah-Daouk is an inventor on key patents in the field of metabolomics and hold equity in Metabolon, a biotech company in North Carolina. In addition, she holds patents licensed to Chymia LLC and PsyProtix with royalties and ownership. Kim Ekroos is the owner of Lipidomics Consulting Ltd.

Figures

**Fig. 1**
Scope and aim of the lipidomics reporting checklist.

**Fig. 2**
Outline of lipidomics workflow.

**Fig. 3**
Preanalytics, sample handling and preservation.

**Fig. 4**
A: Methods and conditions applied for lipid extraction. B: Solubility and recovery in lipid extractions are determined by the polarity of the lipids and solvents. Solvents (polarity index) and lipid classes are ordered by increasing polarity (gray triangle).

**Fig. 5**
Definition of the analytical platform.

**Fig. 6**
Reducing the complexity of the lipidome using mass spectrometry and separation-based analysis. For this computational experiment, all phospholipids, sphingolipids, sterols, and free fatty acids from LIPID MAPS (46) were considered. Here, PC 16:1_18:0 serves as a reference. For computing precursor masses, combinations of both lipid class common adducts and up to two ¹³C isotopes were taken into consideration. Interfering lipids are lipids that share the same set of features (mass-to-charge ratio; *m/z*) with the reference lipid within a given mass tolerance. Features are: positive/negative precursor ions, positive fragment ions *m/z* 184.07 (head group HG), negative fragment ions at *m/z* 255.23 (fatty acyl FA₁) and *m/z* 281.24 (FA₂). With increasing resolution and pre-separation the number of interfering lipids clearly can be reduced. Separation in the reversed phase is related to the lipophilicity or hydrophobicity of the compound displayed as a logP value.

**Fig. 7**
Sufficient mass resolving power (R) can separate isobaric overlaps that are commonly present in lipidomic analysis, such as (A) Type-II overlaps occurring for double bond series and (B) isobars resulting from different bond types as seen for diacyl PC 16:0/17:1 and alkyl/acyl PC O-16:1/18:0.

**Fig. 8**
Elucidation of lipid molecule structure and related annotation/structure level. Source: Adapted from Zhang *et al.* (31).

**Fig. 9**
Lipid molecule quantification.

**Fig. 10**
Blank and QC samples used for analytical evaluation of the workflow. Blanks provide insight into background lipids/contaminants and their origin. Quality Control (QC) samples are used to evaluate the reliability of the analysis.

**Fig. 11**
Parameters that are typically evaluated in method validations and related guidelines.

**Fig. 13**
Reporting checklist data handling.

See this image and copyright information in PMC

References

1. Liebisch G., Ahrends R., Arita M., Arita M., Bowden J.A., Ejsing C.S., et al. Lipidomics needs more standardization. Nat. Metab. 2019;1:745–747. - PubMed
1. Köfeler H.C., Eichmann T.O., Ahrends R., Bowden J.A., Danne-Rasche N., Dennis E.A., et al. Quality control requirements for the correct annotation of lipidomics data. Nat. Commun. 2021;12:4771. - PMC - PubMed
1. Liebisch G., Fahy E., Aoki J., Dennis E.A., Durand T., Ejsing C.S., et al. Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures. J. Lipid Res. 2020;61:1539–1555. - PMC - PubMed
1. Kofeler H.C., Ahrends R., Baker E.S., Ekroos K., Han X., Hoffmann N., et al. Recommendations for good practice in MS-based lipidomics. J. Lipid Res. 2021;62 - PMC - PubMed
1. Wilkinson M.D., Dumontier M., Aalbersberg I.J., Appleton G., Axton M., Baak A., et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data. 2016;3 - PMC - PubMed

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The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data

Affiliations

The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data

Authors

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Abstract

Conflict of interest statement

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