ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics
ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics
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DOI：
10.21105/joss.03990
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发表时间：
2022
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通讯作者：
Joe Wandy;Vinny Davies;Ross McBride;S. Weidt;Simon Rogers;Rónán Daly
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作者：
Joe Wandy;Vinny Davies;Ross McBride;S. Weidt;Simon Rogers;Rónán Daly
在基于质谱学的数据采集过程中使用的碎裂策略的选择直接影响后续结构鉴定的质量和覆盖面--这是非靶向代谢组学数据分析的关键步骤。然而，开发新的裂解策略是具有挑战性的，因为运行实际质谱仪的实验成本很高，并且缺乏支持其开发的可编程模拟环境。ViMMS 2.0是一个软件框架，可用于在代谢组学中开发新的裂解策略，完全在电子计算机上以及在质谱仪上。该框架允许用户生成化学对象(合成生产或从现有mzML文件中提取)并模拟串联质谱分析过程，其中可以快速实施、测试和评估不同的裂解策略。本文介绍了ViMMS 2.0，重点介绍了该框架的软件设计选择，并通过一个例子说明了如何在ViMMS 2.0中实现一种新的碎片策略。
The choice of fragmentation strategies used during mass-spectrometry-based data acquisition directly affects the quality and coverage of subsequent structural identification – a crucial step in untargeted metabolomics data analysis. However, developing novel fragmentation strategies is challenging due to the high experimental cost of running an actual mass spectrometry instrument and the lack of a programmable simulation environment to support their development. ViMMS 2.0 is a software framework that can be used to develop new fragmentation strategies in metabolomics completely in-silico as well as on mass spectrometry instruments. The framework allows users to generate chemical objects (produced synthetically or extracted from existing mzML files) and simulate a tandem mass spectrometry process, where different fragmentation strategies can be rapidly implemented, tested and evaluated. In this paper, we present ViMMS 2.0, highlighting the software design choices of the framework and illustrate with an example how a new fragmentation strategy could be implemented in ViMMS 2.0.