PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata...

Area of Science:

• Metabolomics
• Bioinformatics
• Data Management

Background:

• Metabolomics research relies heavily on accurate feature annotation and metabolite identification.
• Challenges include a lack of spectral reference data and difficulties in data management and inter-laboratory exchange.

Purpose of the Study:

• To develop an open-source infrastructure for hosting nuclear magnetic resonance (NMR) and mass spectra (MS).
• To provide a web interface and web services for metabolite annotation and laboratory data management.

Main Methods:

• Developed PeakForest, an open-source Java tool with APIs for local deployment.
• Incorporated standardized operating procedures and formats for data quality and interoperability, adhering to FAIR principles.

Main Results:

• PeakForest captures and stores experimental MS and NMR metadata and signal annotations.
• Provides a structured database for curating, browsing, and reusing spectral information.
• Facilitates data formalization, centralization, and sharing across laboratories.

Conclusions:

• PeakForest addresses the bottleneck of large-scale spectral data annotation and metabolite identification in metabolomics.
• It integrates with data analysis pipelines like Galaxy for evolving research needs.
• Freely available, it supports the French metabolomics community and beyond.