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

2022; Springer Science+Business Media; Volume: 18; Issue: 6 Linguagem: Inglês

10.1007/s11306-022-01899-3

1573-3890

Nils Paulhe, Cécile Canlet, Annelaure Damont, Lindsay Peyriga, Stéphanie Durand, Catherine Deborde, Sandra Alvès, Stéphane Bernillon, Thierry Berton, Raphael Bir, Alyssa Bouville, Edern Cahoreau, Delphine Centeno, Robin Costantino, Laurent Debrauwer, Alexis Delabrière, Christophe Dupérier, Sylvain Emery, Amélie Flandin, Ulli Martin Hohenester, Daniel Jacob, Charlotte Joly, Cyril Jousse, Marie Lagrée, Nadia Lamari, Marie Lefebvre, Claire Lopez-Piffet, Bernard Lyan, Mickaël Maucourt, Carole Migné, Marie‐Françoise Olivier, Estelle Rathahao, Pierre Pétriacq, Julie Pinelli, Léa Roch, Pierrick Roger, Simon Roques, Jean‐Claude Tabet, Marie Tremblay‐Franco, Mounir Traı̈kia, Anna Warnet, Vanessa Zhendre, Dominique D. Rolin, Fabien Jourdan, Etienne Thévenot, Annick Moing, Emilien L. Jamin, François Fenaille, Christophe Junot, Estelle Pujos‐Guillot, Franck Giacomoni,

Spectroscopy and Chemometric Analyses

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 .