MS1FA: Shiny app for the annotation of redundant features in untargeted metabolomics datasets.

Bioinformatics (Oxford, England) Pub Date : 2025-05-06 DOI:10.1093/bioinformatics/btaf161

Ruibing Shi, Frank Klawonn, Mark Brönstrup, Raimo Franke

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Abstract

Motivation: Untargeted metabolomics, the comprehensive analysis of small molecules in biological systems, has become an invaluable tool for understanding physiology and metabolism. However, the annotation of metabolomic data is often confounded by the presence of redundant features, which can arise from e.g. multimerization, in-source fragments (ISFs), and adducts.

Results: MS1FA uniquely integrates all major annotation approaches for redundant features within a single interactive platform. It combines correlation-based grouping with reliable ISF annotation using MS2 data and operates with MS1 data only, MS2 data only, or both. Additionally, it offers a distinctive method for grouping features based on relational criteria. As the only web-based platform with these capabilities, MS1FA provides easy access and allows users to explore and annotate the feature table interactively, with options to download the results.

Availability and implementation: MS1FA is freely accessible at https://ms1fa.helmholtz-hzi.de. The source code and data are available at https://github.com/RuibingS/MS1FA_RShiny_dashboard and are archived with the DOI 10.5281/zenodo.15118962.

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MS1FA：闪亮的应用程序，用于注释非目标代谢组学数据集中的冗余特征。

动机：非靶向代谢组学是对生物系统中小分子的综合分析，已成为理解生理和代谢的宝贵工具。然而，代谢组学数据的注释经常被冗余特征的存在所混淆，这些特征可能来自例如多聚合、源内片段（isf）和加合物。结果：MS1FA独特地将所有主要的冗余特性注释方法集成在一个单一的交互平台中。它结合了基于关联的分组和使用MS2数据的可靠ISF注释，并且仅使用MS1数据、仅使用MS2数据或同时使用两者进行操作。此外，它还提供了一种基于关系标准对特征进行分组的独特方法。作为唯一具有这些功能的基于web的平台，MS1FA提供了方便的访问，并允许用户交互式地探索和注释功能表，并提供下载结果的选项。可用性和实现：MS1FA可在https://ms1fa.helmholtz-hzi.de免费访问。源代码和数据可在https://github.com/RuibingS/MS1FA_RShiny_dashboard上获得，并以DOI 10.5281/zenodo.15118962存档。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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