TY - INPR A1 - Bushuiev, Roman A1 - Bushuiev, Anton A1 - de Jonge, Niek F. A1 - Young, Adamo A1 - Kretschmer, Fleming A1 - Samusevich, Raman A1 - Heirman, Janne A1 - Wang, Fei A1 - Zhang, Luke A1 - Dührkop, Kai A1 - Ludwig, Marcus A1 - Haupt, Nils A. A1 - Kalia, Apurva A1 - Brungs, Corinna A1 - Schmid, Robin A1 - Greiner, Russell A1 - Wang, Bo A1 - Wishart, David S. A1 - Liu, Li-Ping A1 - Rousu, Juho A1 - Bittremieux, Wout A1 - Röst, Hannes A1 - Mak, Tytus D. A1 - Hassoun, Soha A1 - Huber, Florian A1 - van der Hooft, Justin J.J. A1 - Stravs, Michael A. A1 - Böcker, Sebastian A1 - Sivic, Josef A1 - Pluskal, Tomáš T1 - MassSpecGym: A benchmark for the discovery and identification of molecules T2 - arXiv N2 - The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: de novo molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at this https URL [https://github.com/pluskal-lab/MassSpecGym]. KW - Maschinelles Lernen KW - Benchmark KW - Computational chemistry KW - Massenspektrometrie KW - Molekülstruktur Y1 - 2025 UR - https://opus4.kobv.de/opus4-hs-duesseldorf/frontdoor/index/index/docId/5550 N1 - Open Review: https://web.archive.org/web/20250521010648/https://openreview.net/forum?id=AAo8zAShX3#discussion PB - arXiv ER -