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

被引：9

作者：

Paulhe, Nils ^{[1
]}

Canlet, Cecile ^{[2
]}

Damont, Annelaure ^{[3
]}

Peyriga, Lindsay ^{[4
]}

Durand, Stephanie ^{[1
]}

Deborde, Catherine ^{[5
]}

Alves, Sandra ^{[3
]}

Bernillon, Stephane ^{[5
]}

Berton, Thierry ^{[5
]}

Bir, Raphael ^{[1
]}

Bouville, Alyssa ^{[2
]}

Cahoreau, Edern ^{[4
]}

Centeno, Delphine ^{[1
]}

Costantino, Robin ^{[2
]}

Debrauwer, Laurent ^{[2
]}

Delabriere, Alexis ^{[3
]}

Duperier, Christophe ^{[1
]}

Emery, Sylvain ^{[1
]}

Flandin, Amelie ^{[5
]}

Hohenester, Ulli ^{[3
]}

Jacob, Daniel ^{[5
]}

Joly, Charlotte ^{[1
]}

Jousse, Cyril ^{[1
]}

Lagree, Marie ^{[1
]}

Lamari, Nadia ^{[5
]}

Lefebvre, Marie ^{[5
]}

Lopez-Piffet, Claire ^{[1
]}

Lyan, Bernard ^{[1
]}

Maucourt, Mickael ^{[5
]}

Migne, Carole ^{[1
]}

Olivier, Marie-Francoise ^{[3
]}

Rathahao-Paris, Estelle ^{[3
]}

Petriacq, Pierre ^{[5
]}

Pinelli, Julie ^{[5
]}

Roch, Lea ^{[5
]}

Roger, Pierrick ^{[3
]}

Roques, Simon ^{[5
]}

Tabet, Jean-Claude ^{[3
]}

Tremblay-Franco, Marie ^{[2
]}

Traikia, Mounir ^{[1
]}

Warnet, Anna ^{[3
]}

Zhendre, Vanessa ^{[5
]}

Rolin, Dominique ^{[5
]}

Jourdan, Fabien ^{[2
]}

Thevenot, Etienne ^{[3
]}

Moing, Annick ^{[5
]}

Jamin, Emilien ^{[2
]}

Fenaille, Francois ^{[3
]}

Junot, Christophe ^{[3
]}

Pujos-Guillot, Estelle ^{[1
]}

机构：

[1] Univ Clermont Auvergne, INRAE, UNH, Plateforme Explorat Metab,MetaboHUB Clermont, Clermont Ferrand, France

[2] Univ Toulouse, Toxalim Res Ctr Food Toxicol, INRAE, ENVT,INP Purpan,UPS,MetaboHUB, F-31300 Toulouse, France

[3] Univ Paris Saclay, Dept Medicaments & Technol Sante DMTS, CEA, INRAE,MetaboHUB, F-91191 Gif Sur Yvette, France

[4] Natl Infrastruct Metabol & Flux ANR 11 INBS 0010, MetaboHUB MetaToul, F-31077 Toulouse, France

[5] Univ Bordeaux, INRAE, Biol Fruit & Pathol, UMR 1332,Bordeaux Metab,MetaboHUB,PHENOME EMPHASI, 71 Ave E Bourlaux, Bordeaux, France

来源：

METABOLOMICS | 2022年 / 18卷 / 06期

关键词：

Curation; Database; FAIR; Interoperability; Metabolite identification; Spectral library; MASS-SPECTROMETRY; METABOLOMICS; IDENTIFICATION; HMDB; STANDARDS; DATABASES; GUIDE; TOOL;

D O I：

10.1007/s11306-022-01899-3

中图分类号：

R5 [内科学];

学科分类号：

1002 ; 100201 ;

摘要：

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.

引用

页数：15

共 64 条

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