Česká společnost pro hmotnostní spektrometrii

(13. ročník České konference hmotnostní spektrometrie a 11. Neformální proteomické setkání - WeS-06)
A Comprehensive timsTOF MS/MS Spectral Library for Improving Metabolite Annotation in Non-Targeted Metabolomics

Aninda Mazumdar ^1 *, Tommaso Stefani ¹, Michaela Plechatá ¹, Zdenek Kamenik ¹

1. Institute of Microbiology, Academy of Sciences of the Czech Republic

Abstrakt

Metabolite annotation, or tentative identification, remains a major bottleneck in non-targeted mass spectrometry-based metabolomics due to the limited availability of authentic standards. Spectral libraries2, which rely on matching accurate mass-to-charge ratios (m/z) and MS/MS fragmentation spectra between experimental and reference data, are therefore essential for this process. However, existing libraries encompass only a small portion of chemical space, typically allowing annotation of just a few percent of features detected in a sample.

To address this limitation, we established a high-resolution MS/MS spectral library comprising over 10,000 bioactive compounds. Compounds were analyzed using reverse-phase liquid chromatography coupled to a Bruker timsTOF HT system operated in both positive and negative ionization modes, and the resulting data were processed with MZmine1.

Through several case studies, including fecal samples from gut microbiota studies and microbial culture broths, we assess the performance of our library relative to the largest public GNPS spectral database and Bruker’s commercial MetaboBASE library. These comparisons highlight the critical importance of instrument-specific spectral acquisition for improving annotation rates. The resulting dataset substantially expands the chemical and instrumental diversity represented in current spectral resources and provides a robust foundation for the development of advanced, AI-driven approaches to bioactivity prediction and natural product discovery.

* Korespondující autor: anindamazumdar@gmail.com

Literatura

1. Bittremieux, W. et al. "The critical role that spectral libraries play in capturing the metabolomics community knowledge." Metabolomics 18.12 : 94 (2022).
2. Brungs, C. et al. "MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries." Nature Methods: 1-4 (2025).

Poděkování:

This study was supported by the project National Institute of Virology and Bacteriology (Programme EXCELES, ID Project No. LX22NPO5103) - Funded by the European Union - Next Generation EU and by a grant from the Programme Johannes Amos Comenius under the Ministry of Education, Youth and Sports of the Czech Republic (project Nr CZ.02.01.01/00/22_008/0004597).