MSLib: efficient generation of open multi-stage fragmentation mass spectral libraries.

Untargeted high-resolution mass spectrometry is a key tool in clinical metabolomics, natural product discovery and exposomics, with compound identification remaining the major bottleneck. Currently, the standard workflow applies spectral library matching against tandem mass spectrometry (MS) fragmentation data. Multi-stage fragmentation (MS) yields more profound insights into substructures, enabling validation of fragmentation pathways; however, the community lacks open MS reference data of diverse natural products and other chemicals. Here we describe MSLib, a machine learning-ready open resource of >2 million spectra in MS trees of 30,008 unique small molecules, built with a high-throughput data acquisition and processing pipeline in the open-source software mzmine.