Dataset Information

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

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 .

SUBMITTER: Paulhe N

PROVIDER: S-EPMC9197906 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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Publications

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

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

Metabolomics : Official journal of the Metabolomic Society 20220614 6

<h4>Introduction</h4>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.<h4>Objectives</h4>To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and ma ...[more]

PMID: 35699774

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Dataset Information

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

Introduction

Objectives

Methods

Results

Conclusion

Publications

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

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