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METLIN MS2 molecular standards database: a broad chemical and biological resource

Nature Methods volume 17, pages 953–954 (2020)Cite this article

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To the Editor — Tandem mass spectrometry (MS2) data provide high-confidence molecular identification of known molecules and preliminary characterization of novel, unknown molecules (unknowns). However, for databases to be an effective resource, broad chemical space coverage is necessary. Consequently, we have created METLIN (http://metlin.scripps.edu) a highly annotated and structurally diverse database of over 850,000 molecular standards. METLIN’s tandem mass spectral library numerically covers almost 1% of PubChem’s 93 million compounds, essentially a number that can be characterized as the known chemical space.

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Fig. 1: The METLIN MS2 database.

Data availability

The data in the METLIN database are available at http://metlin.scripps.edu. The data in other databases mentioned in this study were obtained from their websites (accessed in February 2020) or published papers: MoNA (https://mona.fiehnlab.ucdavis.edu/), mzCloud (https://www.mzcloud.org/), GNPS (https://gnps.ucsd.edu/)9, HMDB (https://hmdb.ca/)10 and NIST 17 (https://chemdata.nist.gov/).

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Acknowledgements

This research was partially funded by US National Institutes of Health grants R35 GM130385 (G.S.), P30 MH062261 (G.S.), P01 DA026146 (G.S.) and U01 CA235493 (G.S.) and by Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA), a Scientific Focus Area Program at Lawrence Berkeley National Laboratory for the US Department of Energy, Office of Science, Office of Biological and Environmental Research, under contract number DE-AC02-05CH11231 (G.S.).

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Author notes

  1. These authors contributed equally: Jingchuan Xue, Carlos Guijas.

Authors and Affiliations

  1. Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research Institute, La Jolla, CA, USA

    Jingchuan Xue, Carlos Guijas, H. Paul Benton & Gary Siuzdak

  2. Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria

    Benedikt Warth

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

    Gary Siuzdak

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  1. Jingchuan Xue
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  2. Carlos Guijas
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  3. H. Paul Benton
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  5. Gary Siuzdak
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Contributions

J.X., C.G., H.P.B., B.W. and G.S. contributed to data collection, analysis, and manuscript writing. J.X. and C.G. share first authorship.

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Correspondence to Gary Siuzdak.

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The authors declare no competing interests.

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Editorial note: This article has been peer reviewed.

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Xue, J., Guijas, C., Benton, H.P. et al. METLIN MS2 molecular standards database: a broad chemical and biological resource. Nat Methods 17, 953–954 (2020). https://doi.org/10.1038/s41592-020-0942-5

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