A universal language for finding mass spectrometry data patterns.

IF 36.1 1区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Nature Methods Pub Date : 2025-05-12 DOI:10.1038/s41592-025-02660-z

Tito Damiani, Alan K Jarmusch, Allegra T Aron, Daniel Petras, Vanessa V Phelan, Haoqi Nina Zhao, Wout Bittremieux, Deepa D Acharya, Mohammed M A Ahmed, Anelize Bauermeister, Matthew J Bertin, Paul D Boudreau, Ricardo M Borges, Benjamin P Bowen, Christopher J Brown, Fernanda O Chagas, Kenneth D Clevenger, Mario S P Correia, William J Crandall, Max Crüsemann, Eoin Fahy, Oliver Fiehn, Neha Garg, William H Gerwick, Jeffrey R Gilbert, Daniel Globisch, Paulo Wender P Gomes, Steffen Heuckeroth, C Andrew James, Scott A Jarmusch, Sarvar A Kakhkhorov, Kyo Bin Kang, Nikolas Kessler, Roland D Kersten, Hyunwoo Kim, Riley D Kirk, Oliver Kohlbacher, Eftychia E Kontou, Ken Liu, Itzel Lizama-Chamu, Gordon T Luu, Tal Luzzatto Knaan, Helena Mannochio-Russo, Michael T Marty, Yuki Matsuzawa, Andrew C McAvoy, Laura-Isobel McCall, Osama G Mohamed, Omri Nahor, Heiko Neuweger, Timo H J Niedermeyer, Kozo Nishida, Trent R Northen, Kirsten E Overdahl, Johannes Rainer, Raphael Reher, Elys Rodriguez, Timo T Sachsenberg, Laura M Sanchez, Robin Schmid, Cole Stevens, Shankar Subramaniam, Zhenyu Tian, Ashootosh Tripathi, Hiroshi Tsugawa, Justin J J van der Hooft, Andrea Vicini, Axel Walter, Tilmann Weber, Quanbo Xiong, Tao Xu, Tomáš Pluskal, Pieter C Dorrestein, Mingxun Wang

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引用次数: 0

Abstract

Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community.

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用于查找质谱数据模式的通用语言。

尽管信息丰富，但绝大多数非靶向质谱数据未得到充分利用；大多数分析物在发表后不用于下游解释或再分析。由于现有软件工具的灵活性和可扩展性有限，无法深入研究这些丰富的原始质谱数据集。在这里，我们介绍了一种新的语言，质谱查询语言（MassQL），以及一个配套的软件生态系统，通过使社区能够使用一组表达性的用户定义的质谱模式直接查询质谱数据来解决这些问题。通过现实世界的例子，MassQL提供了一个数据驱动的化学多样性定义，通过重新分析所有公开的非目标代谢组学数据，使许多学科的科学家能够做出新的发现。MassQL已广泛应用于多个开源和商业质谱分析工具中，为研究社区增强了质谱数据挖掘的能力、互操作性和可重复性。

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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来源期刊

Nature Methods 生物-生化研究方法

CiteScore

58.70

自引率

1.70%

发文量

326

审稿时长

1 months

期刊介绍： Nature Methods is a monthly journal that focuses on publishing innovative methods and substantial enhancements to fundamental life sciences research techniques. Geared towards a diverse, interdisciplinary readership of researchers in academia and industry engaged in laboratory work, the journal offers new tools for research and emphasizes the immediate practical significance of the featured work. It publishes primary research papers and reviews recent technical and methodological advancements, with a particular interest in primary methods papers relevant to the biological and biomedical sciences. This includes methods rooted in chemistry with practical applications for studying biological problems.