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. 2021 Oct 14;40(3):411–421. doi: 10.1038/s41587-021-01045-9

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 7 — Shown is the query spectrum (bottom) from the independent dataset, plus the top-scoring reference spectrum (top) from the spectral library, that is, the CSI training dataset without merging spectra. Cosine scores were calculated using regular intensities (cosine) as well as square root of intensities (cosine-sqrt). All query spectra consist of a single 20 eV collision energy measurement with medium noise added. Reference spectra consist of a single collision energy measurement with no added noise; shown is the spectrum with the highest cosine, among all spectra in the spectral library for this compound. (a) Spectra of Thiophanate, PubChem CID 3032792, molecular formula C₁₄H₁₈N₄O₄S₂. Reference spectrum NIST 1191658, query spectrum Agilent PCDL 345. Correct COSMIC annotation with confidence 0.9092, cosine 0.0637, cosine-sqrt 0.3165. (b) Spectra of Chlorbufam, PubChem CID 16073, molecular formula C₁₁H₁₀ClNO₂. Reference spectrum NIST 1537783, query spectrum Agilent PCDL 3113. Correct COSMIC annotation with confidence 0.9347, cosine 0.1949, cosine-sqrt 0.3523. (c) Spectra of Duloxetine, PubChem CID 60835, molecular formula C₁₈H₁₉NOS. Reference spectrum NIST 1245947, query spectrum Agilent PCDL 2545. Correct COSMIC annotation with confidence 0.9283, cosine 0.5197, cosine-sqrt 0.4767. (d) Spectra of Proscillaridin, PubChem CID 5284613, molecular formula C₃₀H₄₂O₈. Reference spectrum NIST 1519862, query spectrum Agilent PCDL 781. Correct COSMIC annotation with confidence 0.9720, cosine 0.6312, cosine-sqrt 0.4852. Unlike the commercial Agilent library, the query spectra shown here are uncurated and artificial noise was added.