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METLIN-CCS Lipid Database: An authentic standards resource for lipid classification and identification

Nature Metabolism volume 6, pages 981–982 (2024)Cite this article

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Ion mobility spectrometry (IMS) has emerged as an important technology for the characterization of small molecules in biochemical and biological research. Here we present the METLIN-CCS Lipid Database, which includes collision cross section (CCS) values and IMS data for 750 unique lipid standards, many of which are not publicly available at present. Our database provides CCS values obtained by measuring each standard (in triplicate) in both positive and negative ionization modes, yielding seven different ion-types (for example, [M+H]+, [M+Na]+, [M−H]−, [M+NH4]+, [M+H−H2O]+, [M+Cl]- and [M+HCOO]−). The 2413 measured lipid CCS values in the METLIN-CCS Lipid Database expand current IMS lipid database information1,2,3,4 by adding experimental CCS values for new lipid standards and enabling the assessment of different ion types and adduction characteristics. Unlike other lipid databases that are generated from lipid extracts, the METLIN-CCS Lipid Database provides a unique resource created solely from standards, enabling more confident lipid identifications on- and off-tissue and new data for machine learning purposes.

METLIN was introduced in 2005 to provide experimental data5,6,7 to help decipher small molecule structures. METLIN currently hosts experimental MS/MS and neutral loss data on over 930,000 molecular standards6,7; however orthogonal analytical data such as CCS values are becoming increasingly important for confident identifications8,9. Lipids, with their diversity in structure and function, are vital components of cell membranes, cellular functions and signalling processes10. Notably, CCS values do present a unique alternative to MS, allowing for the separation and characterization and/or identification of isomeric lipid species (for example, in Fig. 1, phosphatidylcholine (PC) 36:2 and phosphatidylethanolamine (PE) 39:2 both have a mass of 785.5935 Da).

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Fig. 1: METLIN-CCS Lipid Database.

Data availability

The downloadable molecular standards METLIN-CCS Lipid database reported in this article are freely available at METLIN (https://metlin.scripps.edu/), the XCMS online data repository (https://xcmsonline.scripps.edu/) and PanoramaWeb (https://panoramaweb.org/ccs-library.url).

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Acknowledgements

E.S.B. would like to acknowledge support from the National Institute of Environmental Health Sciences (P42 ES027704), the National Institute of General Medicinal Sciences (RO1 GM141277 and RM1 GM145416) and the Environmental Protection Agency (STAR RD 84003201). This research was also partially funded by the National Institutes of Health grants R24 GM141156 (M.M.), P30 AG013280 (M.M), R35 GM130385 (G.S.) and U01 CA235493 (G.S.). M.G. and D.O.J. were partially funded by the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), supported by Novo Nordisk Foundation grants (NNF21CC0073729).

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Author notes

  1. Heino M. Heyman

    Present address: Metabolon Inc., 617 Davis Drive. Suite 100, Morrisville, NC, USA

Authors and Affiliations

  1. Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

    Erin S. Baker

  2. Scripps Center of Metabolomics and Mass Spectrometry, La Jolla, CA, USA

    Winnie Uritboonthai, Aries Aisporna, Corey Hoang & Gary Siuzdak

  3. Bruker Daltonics, Bruker Scientific LLC, Billerica, MA, USA

    Heino M. Heyman

  4. Avanti Polar Lipids (part of Croda International), Alabaster, AL, USA

    Lisa Connell

  5. Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands

    Damien Olivier-Jimenez & Martin Giera

  6. The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands

    Damien Olivier-Jimenez & Martin Giera

  7. Department of Chemistry, Molecular and Computational Biology Scripps Research Institute, La Jolla, CA, USA

    Gary Siuzdak

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Contributions

E.S.B., H.M.H., G.S., conceptualization; C.H., H.M.H., L.C., W.U., methodology; C.H., H.M.H., W.U., E.S.B., validation; C.H., W.U., formal analysis; G.S., resources; A.A., D.O.-J., M.G., data curation; A.A., M.G., informatics; A.A., software; C.H., W.U., A.A., investigation; E.S.B. M.G., L.C., G.S., manuscript preparation; E.S.B., C.H., G.S., figures; E.S.B., M.G., G.S., reviewing and editing manuscript; E.S.B., G.S., managed and supervised the project; E.S.B., M.G., G.S., funding.

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Correspondence to Erin S. Baker or Gary Siuzdak.

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The authors declare no competing interests.

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Nature Metabolism thanks Sunia Trauger and Zeping Hu for their contribution to the peer review of this work.

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Baker, E.S., Uritboonthai, W., Aisporna, A. et al. METLIN-CCS Lipid Database: An authentic standards resource for lipid classification and identification. Nat Metab 6, 981–982 (2024). https://doi.org/10.1038/s42255-024-01058-z

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