ArticleMetabolomics : Official journal of the Metabolomic Society2022
PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management.
Article in Metabolomics : Official journal of the Metabolomic Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed, 15 citations in OpenAlex.
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- ChemFOnt: the chemical functional ontology resource.Nucleic acids research · 2023Article
- Bridging data management platforms and visualization tools to enable ad-hoc and smart analytics in life sciences.Journal of integrative bioinformatics · 2022Article
- NMR-based metabolomics: Where are we now and where are we going?Progress in nuclear magnetic resonance spectroscopyReview
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Authors and funding
51 authors at 6 institutions in 1 country.
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Abstract
introductionAccuracy 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.
objectivesTo 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.
methodsWe 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.
resultsPeakForest 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.
conclusionPeakForest 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 .
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Registered trials
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