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. 2022 Jun 14;18(6):40.
doi: 10.1007/s11306-022-01899-3.

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

Nils Paulhe  1 , Cécile Canlet  2 , Annelaure Damont  3 , Lindsay Peyriga  4 , Stéphanie Durand  1 , Catherine Deborde  5 , Sandra Alves  3 , Stephane Bernillon  5 , Thierry Berton  5 , Raphael Bir  1 , Alyssa Bouville  2 , Edern Cahoreau  4 , Delphine Centeno  1 , Robin Costantino  2 , Laurent Debrauwer  2 , Alexis Delabrière  3 , Christophe Duperier  1 , Sylvain Emery  1 , Amelie Flandin  5 , Ulli Hohenester  3 , Daniel Jacob  5 , Charlotte Joly  1 , Cyril Jousse  1 , Marie Lagree  1 , Nadia Lamari  5 , Marie Lefebvre  5 , Claire Lopez-Piffet  1 , Bernard Lyan  1 , Mickael Maucourt  5 , Carole Migne  1 , Marie-Francoise Olivier  3 , Estelle Rathahao-Paris  3 , Pierre Petriacq  5 , Julie Pinelli  5 , Léa Roch  5 , Pierrick Roger  3 , Simon Roques  5 , Jean-Claude Tabet  3 , Marie Tremblay-Franco  2 , Mounir Traïkia  1 , Anna Warnet  3 , Vanessa Zhendre  5 , Dominique Rolin  5 , Fabien Jourdan  2 , Etienne Thévenot  3 , Annick Moing  5 , Emilien Jamin  2 , François Fenaille  3 , Christophe Junot  3 , Estelle Pujos-Guillot  1 , Franck Giacomoni  6
Affiliations

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

Nils Paulhe et al. Metabolomics. .

Abstract

Introduction: Accuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However, the annotation process is often hampered by the lack of spectral reference data in experimental conditions, as well as logistical difficulties in the spectral data management and exchange of annotations between laboratories.

Objectives: To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with an ergonomic Web interface and Web services to support metabolite annotation and laboratory data management.

Methods: We developed the PeakForest infrastructure, an open-source Java tool with automatic programming interfaces that can be deployed locally to organize spectral data for metabolome annotation in laboratories. Standardized operating procedures and formats were included to ensure data quality and interoperability, in line with international recommendations and FAIR principles.

Results: PeakForest is able to capture and store experimental spectral MS and NMR metadata as well as collect and display signal annotations. This modular system provides a structured database with inbuilt tools to curate information, browse and reuse spectral information in data treatment. PeakForest offers data formalization and centralization at the laboratory level, facilitating shared spectral data across laboratories and integration into public databases.

Conclusion: PeakForest is a comprehensive resource which addresses a technical bottleneck, namely large-scale spectral data annotation and metabolite identification for metabolomics laboratories with multiple instruments. PeakForest databases can be used in conjunction with bespoke data analysis pipelines in the Galaxy environment, offering the opportunity to meet the evolving needs of metabolomics research. Developed and tested by the French metabolomics community, PeakForest is freely-available at https://github.com/peakforest .

Keywords: Curation; Database; FAIR; Interoperability; Metabolite identification; Spectral library.

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Conflict of interest statement

All authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
PeakForest database inputs and outputs
Fig. 2
Fig. 2
Example of a chemical compound card (L-tryptophan) with compound basic information (A), related names and spectra parts (B) and externals identifiers and related Metabolights studies (C)
Fig. 3
Fig. 3
Spectral card examples related to L-Tryptophan; pH 7.0; HSQC-2D (hsqcetgp)—600 MHz card (A) and Urea; GC-EI-QTOF; MS; 2 TMS card (B)
Fig. 4
Fig. 4
Screenshot of the PeakForest search modules with the “quick search” tool (A), and the advanced search tool for compounds (B) and for NMR data (C)
Fig. 5
Fig. 5
Example of an inter-platform workflow strategy used to generate LC-HRMS/MS, NMR and other orthogonal data related to unknown metabolites in biological matrices, and subsequent PeakForest database enrichment with biological compounds identified with a confidence “MSI level 2”
See this image and copyright information in PMC

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