We highlight the BUDDY software, which was developed to accurately determine the molecular formulae of unknown chemicals in mass spectrometry data. BUDDY is a bottom-up approach that shows superior annotation performance on reference spectra and experimental datasets. Incorporation of global peak annotation could enable BUDDY to refine formula annotations and reveal feature interrelationships.
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References
da Silva, R. R., Dorrestein, P. C. & Quinn, R. A. Illuminating the dark matter in metabolomics. Proc. Natl Acad. Sci. USA 112, 12549–12550 (2015). A commentary paper that presents the concept of “dark matter” in chemical discovery.
Dührkop, K. et al. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nat. Methods 16, 299–302 (2019). A benchmarking tool for molecular formula determination and chemical structure annotation.
Huan Lab. GitHub https://github.com/HuanLab/BUDDY (2022). The free BUDDY software.
Huan Lab Bioinformatics. YouTube https://www.youtube.com/watch?v=Ne_Y0vZ0WKI (2022). BUDDY quick-start video tutorial.
Giné, R. et al. HERMES: a molecular-formula-oriented method to target the metabolome. Nat. Methods 18, 1370–1376 (2021). A new MS data acquisition approach that relies on large-scale targeted molecular formulae.
Chen, L. et al. Metabolite discovery through global annotation of untargeted metabolomics data. Nat. Methods 18, 1377–1385 (2021). A research article that inspired our implementation of global peak annotation in BUDDY.
Hoffmann, M. A. et al. High-confidence structural annotation of metabolites absent from spectral libraries. Nat. Biotechnol. 40, 411–421 (2022). A research article that incorporates confidence scores in metabolite annotation.
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This is a summary of: Xing, S., Shen, S., Xu, B., Li, X. & Huan, T. BUDDY: molecular formula discovery via bottom-up MS/MS interrogation. Nat. Methods https://doi.org/10.1038/s41592-023-01850-x (2023).
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Accurate determination of molecular formulae using tandem mass spectrometry. Nat Methods 20, 799–800 (2023). https://doi.org/10.1038/s41592-023-01851-w
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DOI: https://doi.org/10.1038/s41592-023-01851-w
