Identifying variants of molecules through database search of mass spectra

Mass spectrometry is a widely used method for the identification of molecules in complex samples. Current tools for database search of experimental spectra against libraries of molecules are not scalable. Moreover, these tools are often limited to known molecules and only perform an exact search. Here, to address this, we introduce Variable Interpretation of Spectrum-Molecule Couples, or VInSMoC, a mass spectral database search algorithm for the identification of variants of molecules. VInSMoC removes some false identifications by estimating the statistical significance of matches between spectra and molecular structures. Benchmarking VInSMoC in a search of 483 million spectra from GNPS against 87 million molecules from PubChem and COCONUT revealed 43,000 known molecules and 85,000 variants that were previously unreported. VInSMoC further facilitates identifying putative microbial biosynthesis pathways of promothiocin B and depsidomycin in Streptomyces bellus and Streptomyces sp. F-2747, respectively.