Hydrogen–deuterium exchange (HDX) has become a pivotal method for investigating the structural and dynamic properties of proteins. The versatility and sensitivity of mass spectrometry (MS) made the technique the ideal companion for HDX, and today HDX-MS is addressing a growing number of applications in both academic research and industrial settings. The prolific generation of experimental data has spurred the concurrent development of numerous computational tools, designed to automate parts of the workflow while employing different strategies to achieve common objectives. Various computational methods are available to perform automated peptide searches and identification; different statistical tests have been implemented to quantify differences in the exchange pattern between two or more experimental conditions; alternative strategies have been developed to deconvolve and analyze peptides showing multimodal behavior; and different algorithms have been proposed to computationally increase the resolution of HDX-MS data, with the ultimate aim to provide information at the level of the single residue. This review delves into a comprehensive examination of the merits and drawbacks associated with the diverse strategies implemented by software tools for the analysis of HDX-MS data.

中文翻译：

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用于氢-氘交换质谱数据分析的计算工具


氢-氘交换 （HDX） 已成为研究蛋白质结构和动力学特性的关键方法。质谱 （MS） 的多功能性和灵敏度使该技术成为 HDX 的理想伴侣，如今，HDX-MS 正在解决学术研究和工业环境中越来越多的应用。实验数据的大量生成刺激了众多计算工具的并发开发，这些工具旨在自动化部分工作流程，同时采用不同的策略来实现共同目标。有多种计算方法可用于执行自动肽搜索和鉴定;已经实施了不同的统计检验来量化两个或多个实验条件之间交换模式的差异;已经开发了替代策略来去卷积和分析显示多模式行为的肽;并且已经提出了不同的算法来通过计算提高 HDX-MS 数据的分辨率，最终目的是提供单个残基水平的信息。本综述深入探讨了与软件工具实施的用于分析 HDX-MS 数据的不同策略相关的优缺点。