BICS talk – “VarMet: high-throughput annotation of small molecule mass spectra via the modification-tolerant search of chemical databases”

On Friday June 30, 2pm Azat will present his recent work on mass spectral analysis in the CBI (E2.1 ground floor), Room 001.


Secondary metabolites are a diverse class of small molecules with important biological and biomedical applications. Tandem mass spectrometry is a powerful tool in metabolomics, but the interpretation of the resulting data is challenging. Researchers rely on reference spectral libraries and in silico molecule fragmentation to annotate mass spectra with known compounds and molecular networks to propagate the annotations to novel variants. However, this approach fails if a sample or the spectral library misses a known analog.

We developed VarMet, a database search tool for identifying variants of secondary metabolites in mass spectrometry data. VarMet extends our previous molDiscovery model for small molecule fragmentation with a modification-tolerant search inspired by VarQuest but capable to handle a wide range of metabolites such as polyketides, terpenes, and lipids. The algorithmic and software solutions in VarMet enable fast screening of millions of mass spectra. In contrast to molecular networks, our tool can work even if a sample lacks known analogs and provides insights into the chemical structure of the discovered variants.

We benchmarked VarMet accuracy on annotated spectra from the GNPS spectral library. We further applied VarMet to the Smenospongia aurea metabolome and demonstrated how it identified a smenamide variant missed by the state-of-the-art approach. Overall, VarMet fills the gap in the identification of novel variants of small molecules and better addresses the chemical diversity of secondary metabolites.