Comment

. 2021 Aug 6;12(1):4771.

doi: 10.1038/s41467-021-24984-y.

Quality control requirements for the correct annotation of lipidomics data

Harald C Köfeler¹, Thomas O Eichmann², Robert Ahrends³, John A Bowden⁴, Niklas Danne-Rasche⁵, Edward A Dennis⁶, Maria Fedorova^{7

8}, William J Griffiths⁹, Xianlin Han¹⁰, Jürgen Hartler^{6

11}, Michal Holčapek¹², Robert Jirásko¹², Jeremy P Koelmel¹³, Christer S Ejsing^{14

15}, Gerhard Liebisch¹⁶, Zhixu Ni^{7

8}, Valerie B O'Donnell¹⁷, Oswald Quehenberger⁶, Dominik Schwudke^{18

19

20}, Andrej Shevchenko²¹, Michael J O Wakelam²², Markus R Wenk²³, Denise Wolrab¹², Kim Ekroos²⁴

Affiliations

¹ Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria. harald.koefeler@medunigraz.at.
² Institute for Molecular Biosciences, Karl-Franzens University of Graz, Graz, Austria.
³ Department for Analytical Chemistry, University of Vienna, Vienna, Austria.
⁴ Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA.
⁵ University Duisburg Essen, Essen, Germany.
⁶ Department of Pharmacology, University of California, San Diego, CA, USA.
⁷ Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany.
⁸ Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany.
⁹ Swansea Univerity Medical School, Swansea, UK.
¹⁰ Barshop Inst Longev & Aging Studies, Univ Texas Hlth Sci Ctr San Antonio, San Antonio, TX, USA.
¹¹ Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria.
¹² Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic.
¹³ Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT, USA.
¹⁴ Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.
¹⁵ Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
¹⁶ Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany.
¹⁷ Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom.
¹⁸ Bioanalytical Chemistry, Research Center Borstel, Borstel, Germany.
¹⁹ German Center for Infection Research, Borstel, Germany.
²⁰ German Centre for Lung Research, Airway Research Center North, Borstel, Germany.
²¹ Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
²² Babraham Institute, Babraham Research Campus, Cambridge, UK.
²³ Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore.
²⁴ Lipidomics Consulting Ltd., Esbo, Finland.

PMID: 34362906
PMCID: PMC8346590
DOI: 10.1038/s41467-021-24984-y

Comment

Quality control requirements for the correct annotation of lipidomics data

Harald C Köfeler et al. Nat Commun. 2021.

. 2021 Aug 6;12(1):4771.

doi: 10.1038/s41467-021-24984-y.

Authors

Affiliations

¹ Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria. harald.koefeler@medunigraz.at.
² Institute for Molecular Biosciences, Karl-Franzens University of Graz, Graz, Austria.
³ Department for Analytical Chemistry, University of Vienna, Vienna, Austria.
⁴ Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA.
⁵ University Duisburg Essen, Essen, Germany.
⁶ Department of Pharmacology, University of California, San Diego, CA, USA.
⁷ Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany.
⁸ Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany.
⁹ Swansea Univerity Medical School, Swansea, UK.
¹⁰ Barshop Inst Longev & Aging Studies, Univ Texas Hlth Sci Ctr San Antonio, San Antonio, TX, USA.
¹¹ Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria.
¹² Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic.
¹³ Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT, USA.
¹⁴ Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.
¹⁵ Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
¹⁶ Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany.
¹⁷ Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom.
¹⁸ Bioanalytical Chemistry, Research Center Borstel, Borstel, Germany.
¹⁹ German Center for Infection Research, Borstel, Germany.
²⁰ German Centre for Lung Research, Airway Research Center North, Borstel, Germany.
²¹ Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
²² Babraham Institute, Babraham Research Campus, Cambridge, UK.
²³ Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore.
²⁴ Lipidomics Consulting Ltd., Esbo, Finland.

PMID: 34362906
PMCID: PMC8346590
DOI: 10.1038/s41467-021-24984-y

No abstract available

PubMed Disclaimer

Conflict of interest statement

H.K., R.A., X.H., M.H., G.L., M.R.W., and K.E. are board members of the International Lipidomics Society. H.K., R.A., J.A.B., M.F., J.H., X.H., M.H., C.S.E., G.L., V.O.D., D.S., A.S., M.R.W., and K.E. are members of ILS Interest Group steering committees. E.D., W.J.G., V.O.D., and O.Q. are members of the LIPID MAPS consortium. H.K. R.A. J.A.B., M.F., W.J.G., X.H., M.H., C.S.E, G.L., V.O.D., D.S., A.S., M.R.W., and K.E. are members of the Lipidomics Standards Initiative. The other authors declare no competing interests.

Figures

**Fig. 1. Plot of retention times versus number of fatty acyl carbons.**
Shown are data for (a) triacylglycerols and (b) diacyl phosphatidylcholines in plasma. DB0 through DB8 represent the cumulative number of double bonds in the fatty acyl chains. For each individual DB assignment the relationship should be close to linear on a C18 stationary phase colum.

See this image and copyright information in PMC

Comment in

Reply to "Quality control requirements for the correct annotation of lipidomics data".
Vasilopoulou CG, Sulek K, Brunner AD, Meitei NS, Schweiger-Hufnagel U, Meyer SW, Barsch A, Mann M, Meier F. Vasilopoulou CG, et al. Nat Commun. 2021 Aug 6;12(1):4772. doi: 10.1038/s41467-021-24985-x. Nat Commun. 2021. PMID: 34362889 Free PMC article. No abstract available.

Comment on

Trapped ion mobility spectrometry and PASEF enable in-depth lipidomics from minimal sample amounts.
Vasilopoulou CG, Sulek K, Brunner AD, Meitei NS, Schweiger-Hufnagel U, Meyer SW, Barsch A, Mann M, Meier F. Vasilopoulou CG, et al. Nat Commun. 2020 Jan 16;11(1):331. doi: 10.1038/s41467-019-14044-x. Nat Commun. 2020. PMID: 31949144 Free PMC article.

References

1. Vasilopoulou CG, et al. Trapped ion mobility spectrometry and PASEF enable in-depth lipidomics from minimal sample amounts. Nat. Commun. 2020;11:331. doi: 10.1038/s41467-019-14044-x. - DOI - PMC - PubMed
1. Hartler J, et al. Deciphering lipid structures based on platform-independent decision rules. Nat. Methods. 2017;14:1171–1174. doi: 10.1038/nmeth.4470. - DOI - PMC - PubMed
1. Hartler J, et al. Automated annotation of sphingolipids including accurate identification of hydroxylation sites using MS(n) data. Anal. Chem. 2020;92:14054–14062. doi: 10.1021/acs.analchem.0c03016. - DOI - PMC - PubMed
1. Ni Z, Angelidou G, Lange M, Hoffmann R, Fedorova M. LipidHunter identifies phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets. Anal. Chem. 2017;89:8800–8807. doi: 10.1021/acs.analchem.7b01126. - DOI - PubMed
1. Herzog, R. et al. A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol. 12 (2011). - PMC - PubMed

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Quality control requirements for the correct annotation of lipidomics data

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Quality control requirements for the correct annotation of lipidomics data

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