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PeakForest, a digital infrastructure for metabolomic analysis and metabolite identification

​A consortium of researchers, including SPI/DMTS metabolomics specialists, presents PeakForest, a database of NMR and mass spectra, which, through its web portal, provides storage and annotation services for spectra of reference compounds and metabolic profiles of biological matrices. An open resource, developed by the French metabolomics community, which offers the possibility to address the evolving needs of the discipline.

Published on 22 November 2022


Metabolomics is the study of all metabolites (small molecules) present in an organelle, a cell, a tissue, an organ or an organism at a given time and under given conditions. It notably uses mass spectrometry (MS) and nuclear magnetic resonance (NMR). This is a powerful approach because the metabolite profiles and their concentrations, unlike other "omics" measurements, directly reflect the underlying biochemical activity and physiological state of the cells/tissues. However, the identification of metabolites in biological samples, a key element of metabolomics research, suffers from the lack of reference spectral data and logistical difficulties (data management, exchange of annotations between laboratories).


To overcome these difficulties, the researchers developed the PeakForest infrastructure, an open-source tool with a graphical interface and automatic programming interfaces that can be deployed locally to organize spectral data for metabolome annotation in laboratories. PeakForest offers for the first time the possibility to capture and store experimental NMR and MS spectral data and metadata (and, in the medium term, data from other spectroscopic techniques), to collect and display signal annotations, in a structured and centralized way at each laboratory level. This new resource thus facilitates the sharing of such data between laboratories and their integration into public databases.

PeakForest is freely accessible at : and


By removing a technical barrier, namely the annotation of large-scale spectral data and the identification of metabolites, and by relying on the expertise and experience of the members of the French national metabolomics and fluxomics infrastructure (MetaboHUB), PeakForest will promote the implementation of FAIR (Findability, Accessibility, Interoperability, Reuse) spectral databases for the benefit of the metabolomic community.

Contact CEA/Joliot : Étienne Thévenot ( )
  Annelaure Damont ( ;
  François Fenaille (

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