Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France.
Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, 31300, Toulouse, France.
Metabolomics. 2022 Jun 14;18(6):40. doi: 10.1007/s11306-022-01899-3.
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.
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.
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.
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.
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 .
在代谢组学研究中，生物样本中特征注释和代谢物鉴定的准确性是一个关键要素。然而，注释过程常常受到实验条件下缺乏光谱参考数据以及光谱数据管理和注释在实验室之间交换的后勤困难的阻碍。
设计一个开源基础设施，允许同时托管核磁共振（NMR）和质谱（MS）谱，具有符合人体工程学的 Web 界面和 Web 服务，以支持代谢物注释和实验室数据管理。
我们开发了 PeakForest 基础设施，这是一个具有自动编程接口的开源 Java 工具，可以在本地部署以组织代谢组注释的光谱数据。包括了标准化操作程序和格式，以确保数据质量和互操作性，符合国际建议和 FAIR 原则。
PeakForest 能够捕获和存储实验光谱 MS 和 NMR 元数据以及收集和显示信号注释。这个模块化系统提供了一个带有内置工具的结构化数据库，用于管理信息、浏览和在数据处理中重复使用光谱信息。PeakForest 在实验室级别提供了数据形式化和集中化，促进了实验室之间共享光谱数据和集成到公共数据库中。
PeakForest 是一个全面的资源，解决了一个技术瓶颈，即具有多台仪器的代谢组学实验室的大规模光谱数据注释和代谢物鉴定。PeakForest 数据库可以与 Galaxy 环境中的定制数据分析管道一起使用，为满足代谢组学研究不断发展的需求提供了机会。由法国代谢组学社区开发和测试，PeakForest 可在 https://github.com/peakforest 免费获得。
