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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. 3 — Queries are cross-validation data, merged spectra, medium noise, biomolecule structure database, structure-disjoint evaluation. (a–i) Incorrect hits with lowest confidence scores. Top-ranked structure on the right and corresponding true structure on the left. ‘PubChem CID’ is PubChem compound identifier number. Instances where the true structure was not contained in the biomolecule structure database are marked by an asterisk. For (g), the structure of the top hit is not contained in PubChem; we report the KNApSAcK compound identifier (‘C_ID’) instead. For (a) and (e), molecular graphs of incorrect hit and true structure differ by the theoretical minimum of two edge deletions. For (a), the query spectrum was heavily distorted, and only 8.6 % of peak intensities were explained by the fragmentation tree. For (e), the three top-ranked candidates — including the correct one — were structurally highly similar and received almost identical CSI:FingerID score. Hence, COSMIC rightfully showed little confidence in these (incorrect) hits. Query spectra: (a) NIST 1544714/19/23, (b) NIST 1322859/64/69, (c) NIST 1627646/51/56, (d) NIST 1462584/87/93, (e) NIST 1340388/91/96, (f) NIST 1320854/56/62, (g) NIST 1386503/07/12, (h) NIST 1305770/72/78, (i) NIST 1325235/37/43.