Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

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

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

Subjects

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.

In the last two decades, there has been a substantial increase in metabolomic and exposomic analyses, driven by a growing interest in how small molecules directly affect personal and population health1. These studies have highlighted the potential of small molecules, including primary metabolites, secondary metabolites and xenobiotics. And while mass spectrometry (MS) is typically the technology of choice in evaluating small molecules, orthogonal analytical methods are important for more confident identification. The use of IMS has therefore recently increased2 because of its orthogonal nature to chromatography, MS and tandem mass spectrometry (MS/MS) data. IMS data are generated by separating ions based on the interplay of an electric field pulling force and frictional drag force resulting from collisions with buffer gas molecules3. The resulting CCS values provide a size-based characteristic that further facilitates experimental small molecule identification.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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).

References

  1. Suhre, K. et al. Nature 477, 54–60 (2011).

    Article  CAS  PubMed  Google Scholar 

  2. Dodds, J. N. & Baker, E. S. J. Am. Soc. Mass Spectrom. 30, 2185–2195 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Zheng, X. et al. Annu. Rev. Anal. Chem. (Palo Alto, Calif.) 10, 71–92 (2017).

    Article  CAS  PubMed  Google Scholar 

  4. Guijas, C. et al. Anal. Chem. 90, 3156–3164 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Xue, J., Guijas, C., Benton, H. P., Warth, B. & Siuzdak, G. Nat. Methods 17, 953–954 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. MacLean, B. X. et al. J. Am. Soc. Mass Spectrom. 29, 2182–2188 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Picache, J. A. et al. Chem. Sci. 10, 983 (2019).

    Article  CAS  PubMed  Google Scholar 

  8. Kirkwood, K. I. et al. J. Proteome Res. 21, 232–242 (2022).

    Article  CAS  PubMed  Google Scholar 

  9. Stow, S. M. et al. Anal. Chem. 89, 9048–9055 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Zheng, X. et al. Anal. Bioanal. Chem. 409, 467–476 (2017).

    Article  CAS  PubMed  Google Scholar 

Download references

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.).

Author information

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

Authors
  1. Erin S. Baker
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Corey Hoang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Winnie Uritboonthai
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Heino M. Heyman
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Brian Pratt
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Michael MacCoss
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Brendan MacLean
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Robert Plumb
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Aries Aisporna
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Gary Siuzdak
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

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

Supplementary information

Supplementary Information

Supplementary Methods, Supplementary Table 1 and Supplementary References.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41592-023-02078-5

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research