利用MASSyPupX对数据依赖和数据独立采集的散弹枪蛋白质组学数据进行非现场处理。

IF 2.8 2区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of proteomics Pub Date : 2025-08-05 DOI:10.1016/j.jprot.2025.105494

Jorge Noé García-Chávez , Robert Winkler

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引用次数: 0

摘要

霰弹枪蛋白质组学数据生成的快速步伐为及时的数据分析提出了挑战。与此同时，科学界正在创造新的数据解释工具，如人工智能，这些工具尚未集成到商业软件中。使用免费和开源软件（FOSS）进行场外数据处理可以实现信息学工作流程的分散和扩展。自由/开源软件平台还降低了教育和研究的成本。MASSyPupX是一个自由/开源软件质谱（MS）软件集合，直接从USB驱动器运行。另外，设置MASSyPupX工作站或服务器提供了一个即用型和可重复的MS分析平台。已安装的编程语言和库支持自定义MS软件和工作流的开发。本文演示了使用MASSyPupX转换和处理原始鸟枪蛋白质组学数据。原始Thermo文件从ProteomeXchange下载并转换为HUPO社区格式mzML。使用Comet、PeptideProphet、ProteinProphet、ProtyQuant和Trans-Proteomic Pipeline对数据依赖采集（DDA）数据进行评估。数据独立采集（DIA）散弹枪蛋白质组学数据用DIA- nn进行分析。使用自定义Bash、Python和R脚本对结果进行后处理和可视化。MASSyPupX项目托管在https://codeberg.org/LabABI/MASSyPupX，当前的ISO可以从https://doi.org/10.5281/zenodo.14618430下载。MASSyPupX平台通过提供可移植、可扩展和可访问的免费开源软件（FOSS）解决方案，显著推进了霰弹枪蛋白质组学数据处理。直接从USB驱动器或服务器操作，这个基于debian的Linux发行版使研究人员能够分析数据依赖（DDA）和数据独立（DIA）采集蛋白质组学数据，而无需安装，分散工作流程，降低成本，并促进协作和质谱数据处理培训。通过预先安装的编程语言、库和对Comet、PeptideProphet、DIA-NN和ProtyQuant等工具的支持，MASSyPupX促进了可重复分析，集成了尖端的计算技术，并为教育、研究和自定义工作流开发提供了一个用户友好的环境。MASSyPupX使先进的蛋白质组学分析大众化，通过分散和具有成本效益的工作流程，作为推进生物和医学研究的有用工具。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

Off-site processing of data-dependent and data-independent acquisition shotgun proteomics data with MASSyPupX

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Off-site processing of data-dependent and data-independent acquisition shotgun proteomics data with MASSyPupX

The rapid pace of shotgun proteomics data generation presents challenges for timely data analysis. In parallel, the scientific community is creating novel data interpretation tools, such as artificial intelligence, that have not yet been integrated into commercial software. Off-site data processing with free and open-source software (FOSS) enables the decentralization and scaling of informatics workflows. FOSS platforms also lower the costs of education and research. MASSyPupX is a FOSS mass spectrometry (MS) software collection that runs directly from a USB drive. Alternatively, setting up a MASSyPupX workstation or server provides a ready-to-use and reproducible MS analysis platform. Installed programming languages and libraries support the development of custom MS software and workflows. This paper demonstrates using MASSyPupX to convert and process raw shotgun proteomics data. Raw Thermo files were downloaded from ProteomeXchange and converted to the HUPO community format mzML. Data-dependent acquisition (DDA) data were evaluated with Comet, PeptideProphet, ProteinProphet, ProtyQuant, and the Trans-Proteomic Pipeline. Data-independent acquisition (DIA) shotgun proteomics data were analyzed with DIA-NN. Custom Bash, Python, and R scripts were used to post-process and visualize the results. The MASSyPupX project is hosted at https://codeberg.org/LabABI/MASSyPupX, and the current ISO can be downloaded from https://doi.org/10.5281/zenodo.14618430.

The MASSyPupX platform significantly advances shotgun proteomics data processing by offering a free and open-source software (FOSS) solution that is portable, scalable, and accessible. Operating directly from a USB drive or server, this Debian-based Linux distribution enables researchers to analyze data-dependent (DDA) and data- independent (DIA) acquisition proteomics data without installation, decentralizing workflows, reducing costs, and fostering collaboration and mass spectrometry data processing training. With pre-installed programming languages, libraries, and support for tools like Comet, PeptideProphet, DIA-NN, and ProtyQuant, MASSyPupX facilitates reproducible analyses, integrates cutting-edge computational techniques, and provides a user-friendly environment for education, research, and custom workflow development.

MASSyPupX democratizes access to advanced proteomics analysis, serving as a versatile tool for advancing biological and medical research through decentralized and cost-effective workflows.

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来源期刊

Journal of proteomics 生物-生化研究方法

CiteScore

7.10

自引率

3.00%

发文量

227

审稿时长

73 days

期刊介绍： Journal of Proteomics is aimed at protein scientists and analytical chemists in the field of proteomics, biomarker discovery, protein analytics, plant proteomics, microbial and animal proteomics, human studies, tissue imaging by mass spectrometry, non-conventional and non-model organism proteomics, and protein bioinformatics. The journal welcomes papers in new and upcoming areas such as metabolomics, genomics, systems biology, toxicogenomics, pharmacoproteomics. Journal of Proteomics unifies both fundamental scientists and clinicians, and includes translational research. Suggestions for reviews, webinars and thematic issues are welcome.