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鲁斯蒂姆:一个开源框架,用于快速开发和处理时间TOF数据依赖的数据采集数据采集

David Teschner^1,2, David Gomez-Zepeda^3,4, Mateusz K Łącki⁵

¹Institute of Computer Science, Johannes-Gutenberg University, 55128 Mainz, Germany.

Journal of proteome research

|April 22, 2025

概括

我们开发了rustims,这是一个新的开源软件框架,用于处理 timsTOF质谱数据. 它提供了一个快速,可集成和直观的工具箱,用于分析复杂的生物样本.

科学领域:

蛋白质组学和代谢组学
计算生物学和生物信息学

背景情况:

质谱学,特别是timsTOF平台,对于生物样本分析至关重要.
处理时间TOF数据是复杂的,因为添加了离子流动性维度.
对于 timsTOF 数据的现有软件往往是专有的,阻碍了自定义工作流集成.

研究的目的:

引入rustims,一个灵活的,开源的框架,用于处理时间TOF原始数据.
为 timsTOF 数据分析提供快速,直观和可集成的解决方案,专注于 DDA-PASEF.
为了实现第三方工具和定制分析管道的无集成.

主要方法:

开发了rusttims,这是一个结合Rust和Python的双语言框架.
使用imspy用于Python脚本和sagepy用于Sage搜索引擎绑定.
实施了DDA-PASEF数据处理管道,包括Prosit的rescoring和集成以及扩展的离子移动性模型.

主要成果:

通过Rust和易于使用的Python界面,Rustims提供了高效的多线程数据处理.
该框架成功处理了三型蛋白组学和非三型免疫组学数据.
基准比较显示了与FragPipe和PEAKS等既有软件相比的竞争性表现.

结论:

Rustims提供了一个强大的开源替代方案,用于 timsTOF 数据分析.
它的灵活设计可方便集成到各种自定义生物信息学工作流程中.
该框架支持先进的分析,并且易于科学界访问.

关键词:

在DDA-PASEF之间.在这里,Python是Python.一个基本的框架框架.离子移动性的离子移动性质谱测量质谱测量质谱测量质量测量质谱测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量这是一个开源的开源软件.蛋白质组学蛋白质组学一个生的兰州.时间STOF.

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