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METLIN-CCS: an ion mobility spectrometry collision cross section database

Nature Methods volume 20, pages 1836–1837 (2023)Cite this article

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Ion mobility spectrometry (IMS) and the corresponding calculated collision cross section (CCS) values have emerged as an important resource for small molecule characterization in biochemical research. Here we present the METLIN-CCS database, which includes CCS values derived from IMS data for over 27,000 molecular standards, representing 79 chemical classes. METLIN-CCS provides CCS values measured in triplicate for these standards in both positive and negative ionization modes and yielding multiple ion types (for example, [M+H]+, [M+Na]+ and [M–H]–). With over 185,000 CCS values, the METLIN-CCS database is a unique resource for small molecule characterization and IMS-based machine learning.

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Fig. 1: METLIN-CCS.

Data availability

The downloadable molecular standards METLIN-CCS 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). The ion mobility data conversion to CCS values software is available at Skyline (https://skyline.ms/skyline.url).

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Acknowledgements

The authors appreciate the assistance of Bruker in facilitating the timsTOF data acquisition. We also thank Ulrike Schweiger-Hufnagel (Bruker) for her invaluable support during this process. E.S.B. acknowledges support from the US National Institute of Environmental Health Sciences (P42 ES027704), US National Institute of General Medicinal Sciences (RO1 GM141277 and RM1 GM145416) and US Environmental Protection Agency (STAR RD 84003201). This research was also partially funded by US National Institutes of Health grants R24 GM141156 (M.M.), P30 AG013280 (M.M), R35 GM130385 (G.S.) and U01 CA235493 (G.S.).

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Author notes

  1. Heino M. Heyman

    Present address: Metabolon Inc., 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

    Corey Hoang, Winnie Uritboonthai, Aries Aisporna & Gary Siuzdak

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

    Heino M. Heyman

  4. Department of Genome Sciences, University of Washington, Seattle, WA, USA

    Brian Pratt, Michael MacCoss & Brendan MacLean

  5. Waters Corporation, Scientific Operations, IMMERSE, Cambridge, MA, USA

    Robert Plumb

  6. 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., 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., B.P. M.M., B.M., data curation; A.A., B.P. M.M., B.M., informatics; A.A., B.P. M.M., B.M., software; C.H., W.U., A.A., investigation; E.S.B. and G.S., manuscript preparation; E.S.B., C.H., G.S., figures; E.S.B., R.P., G.S., reviewing and editing manuscript; E.S.B., G.S., management and supervision of project; E.S.B., G.S., funding.

Corresponding authors

Correspondence to Erin S. Baker or Gary Siuzdak.

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The authors declare no competing interests.

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Nature Methods thanks the anonymous reviewers for their contribution to the peer review of this work.

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Supplementary Methods, Supplementary Table 1 and Supplementary References.

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Baker, E.S., Hoang, C., Uritboonthai, W. et al. METLIN-CCS: an ion mobility spectrometry collision cross section database. Nat Methods 20, 1836–1837 (2023). https://doi.org/10.1038/s41592-023-02078-5

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