MassSpecGym: A benchmark for the discovery and identification of molecules

TL;DR

MassSpecGym introduces a comprehensive benchmark dataset and evaluation framework for molecular discovery and identification from MS/MS spectra, aiming to standardize and advance machine learning methods in this challenging field.

Contribution

It provides the first large-scale, labeled MS/MS dataset with standardized tasks and metrics, facilitating progress in molecular structure prediction from spectra.

Findings

Largest publicly available MS/MS dataset for benchmarking.

Defines three key MS/MS annotation challenges.

Introduces new evaluation metrics and data splits.

Abstract

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 https://github.com/pluskal-lab/MassSpecGym.