Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices.

Area of Science:

• Analytical Chemistry
• Biochemistry
• Systems Biology

Background:

• Mass spectrometry-based metabolomics allows simultaneous detection and quantification of thousands of metabolite features.
• The chemical complexity and dynamic range of the metabolome complicate compound identification and reliable quantification.
• Ion suppression, fragmentation, and isomers further challenge accurate quantification in complex mixtures.

Purpose of the Study:

• To present guidelines for high-quality reporting of metabolomics-derived data.
• To address challenges in metabolite identification and quantification using mass spectrometry.
• To improve the reliability and reproducibility of metabolomics studies.

Main Methods:

• Guidelines cover sample preparation, replication, and randomization.
• Methodologies for accurate quantification, recovery, and recombination are detailed.
• Strategies to mitigate ion suppression and address peak misidentification are included.

Main Results:

• The proposed guidelines facilitate high-quality data reporting in metabolomics.
• Standardized approaches enhance the reliability of metabolite identification and quantification.
• The guidelines address common challenges encountered in LC-MS and GC-MS metabolomics.

Conclusions:

• Adherence to these guidelines is crucial for robust metabolomics research.
• Implementing these recommendations will improve the consistency and accuracy of metabolomics data.
• This work supports the advancement of mass spectrometry-based metabolomics applications.