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.

Multi‐omics approach to understand the impact of sun exposure on an in vitro skin ecosystem and evaluate a new broad‐spectrum sunscreen

“…Structural identifications of discriminant metabolites were achieved on a LTQ Orbitrap XL MS coupled to a U3000 LC system (Thermo Scientific). Tandem MS/MS analyses were tentatively identified according to the nomenclature of the metabolomics standards initiative, 13 using an in‐house database (Peakforest) of retention times, and MS/MS spectra of standards 14 …”

“…Tandem MS/MS analyses were tentatively identified according to the nomenclature of the metabolomics standards initiative, 13 using an in-house database (Peakforest) of retention times, and MS/MS spectra of standards. 14 Pathway enrichment analysis using Metexplore v.2.27.5, with the human network Recon 2.2, was performed to identify the metabolic pathways altered by irradiation. 15…”

ChemFOnt: the chemical functional ontology resource

“…Similarly, efforts will also be made to ensure that ChemFOnt is more widely used in other popular, online chemical databases such as PubChem ( 30 ), ChemSpider ( 31 ), LIPID MAPS ( 34 ), the CompTox Chemicals Dashboard ( 35 ), COCONUT ( 27 ) and ChEBI ( 7 ). A major effort will also be undertaken to integrate ChemFOnt into a variety of multi-omics data analysis tools such as MetaboAnalyst ( 36 ), Galaxy for Metabolomics ( 37 ) and various metabolite set enrichment tools ( 38 , 39 ).…”

FragHub: A Mass Spectral Library Data Integration Workflow

“…The processed libraries are compatible with metabolomics data processing software such as MS-Dial, MZmine3, or Flash Entropy Search 16 but also interoperable with spectral data management software such as PeakForest. 17 A PeakForest instance for FragHub is accessible online, providing tools for viewing, browsing, and filtering spectral data through a Web portal or application programming interfaces (APIs) (available at https://fraghub.peakforest.org/).…”