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Updated: May 18, 2026

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome
Published on: September 20, 2022
Fragmentation trees for the structural characterisation of metabolites
Piotr T Kasper1, Miguel Rojas-Chertó, Robert Mistrik
1Netherlands Metabolomics Centre, Einsteinweg 55, Leiden, The Netherlands.
This study introduces a new method using multistage mass spectrometry and fragmentation trees for accurate metabolite identification in metabolomics. This approach enhances the analysis of complex samples, improving compound characterization and distinguishing structural isomers.
Area of Science:
- Analytical Chemistry
- Metabolomics
- Bioinformatics
Background:
- Metabolite identification is essential for interpreting metabolomics data.
- Electrospray mass spectrometry is a common technique in metabolomics.
- Current methods require enhancement for complex analyses.
Purpose of the Study:
- To integrate multistage mass spectrometry into metabolite identification workflows.
- To develop novel software for analyzing multistage mass spectra.
- To create a robust and generic method for metabolite identification.
Main Methods:
- Development and implementation of new software tools for multistage mass spectrometry data analysis.
- Efficient removal of spectral artifacts from mass spectra.
- Generation and analysis of fragmentation trees representing molecular structures.
Main Results:
- Successfully pre-processed fragmentation patterns into characteristic fragmentation trees.
- Demonstrated reproducibility and robustness of fragmentation tree acquisition using a model compound.
- Showcased the specificity of fragmentation trees in distinguishing structural isomers, exemplified by isomeric prostaglandins.
Conclusions:
- Multistage mass spectrometry, coupled with fragmentation tree analysis, offers a powerful approach for metabolite identification.
- The developed software tools facilitate efficient and accurate spectral analysis.
- This method represents a significant advancement towards a universal metabolite identification strategy.
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