Multi-scale Sinusoidal Embeddings Enable Learning on High Resolution Mass Spectrometry Data

Gennady Voronov, Rose Lightheart, Joe Davison, Christoph A. Krettler, David Healey, Thomas Butler

Keywords: Cheminformatics for Life Sciences, Tandem Mass Spectrometry, Transformers

Abstract: Small molecules in biological samples are studied to provide information about disease states, environmental toxins, natural product drug discovery, and many other applications. The primary window into the composition of small molecule mixtures is tandem mass spectrometry (MS2), which produces high sensitivity and part per million resolution data. We adopt multi-scale sinusoidal embeddings of the mass data in MS2 designed to meet the challenge of learning from the full resolution of MS2 data. Using these embeddings, we provide a new state of the art model for spectral library search, the standard task for initial evaluation of MS2 data. We also investigate the task of chemical property prediction from MS2 data, that has natural applications in high-throughput MS2 experiments and show that an average $R^2$ of 80\% for novel compounds can be achieved across 10 chemical properties prioritized by medicinal chemists. We vary the resolution of the input spectra directly by using different floating point representations of the MS2 data, and show that the resulting sinusoidal embeddings are able to learn from high resolution portion of the input MS2 data. We apply dimensionality reduction to the embeddings that result from different resolution input masses to show the essential role multi-scale sinusoidal embeddings play in learning from MS2 data.