García-Chávez Jorge Noé, Winkler Robert
Advanced Genomics Unit, Cinvestav, km 9.6 Libr. Nte. Irapuato-León, Irapuato, 36824, Gto., Mexico; Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), Camino a la Presa San José 2055, Lomas 4ta Sección, San Luis Potosí, 78216, S.L.P., Mexico.
Advanced Genomics Unit, Cinvestav, km 9.6 Libr. Nte. Irapuato-León, Irapuato, 36824, Gto., Mexico.
J Proteomics. 2025 Aug 5;321:105494. doi: 10.1016/j.jprot.2025.105494.
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.
鸟枪法蛋白质组学数据生成的快速步伐给及时的数据分析带来了挑战。与此同时，科学界正在创建尚未集成到商业软件中的新型数据解释工具，如人工智能。使用免费和开源软件（FOSS）进行异地数据处理能够实现信息学工作流程的去中心化和扩展。FOSS平台还降低了教育和研究成本。MASSyPupX是一个FOSS质谱（MS）软件集合，可直接从USB驱动器运行。或者，设置一个MASSyPupX工作站或服务器可提供一个即用型且可重现的MS分析平台。已安装的编程语言和库支持定制MS软件和工作流程的开发。本文展示了使用MASSyPupX来转换和处理原始鸟枪法蛋白质组学数据。原始的赛默飞世尔文件从ProteomeXchange下载并转换为HUPO社区格式mzML。使用Comet、PeptideProphet、ProteinProphet、ProtyQuant和跨蛋白质组学管道对数据依赖型采集（DDA）数据进行评估。使用DIA-NN分析数据非依赖型采集（DIA）鸟枪法蛋白质组学数据。使用定制的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可从https://doi.org/10.5281/zenodo.14618430下载。MASSyPupX平台通过提供一个免费、开源、便携、可扩展且易于访问的软件（FOSS）解决方案，显著推进了鸟枪法蛋白质组学数据处理。这个基于Debian的Linux发行版可直接从USB驱动器或服务器运行，使研究人员能够在无需安装的情况下分析数据依赖型（DDA）和数据非依赖型（DIA）采集的蛋白质组学数据，实现工作流程的去中心化，降低成本，并促进协作和质谱数据处理培训。借助预安装的编程语言、库以及对Comet、PeptideProphet、DIA-NN和ProtyQuant等工具的支持，MASSyPupX便于进行可重现的分析，集成前沿计算技术，并为教育、研究和定制工作流程开发提供一个用户友好的环境。MASSyPupX使高级蛋白质组学分析的获取更加普及，通过去中心化且具有成本效益的工作流程，成为推进生物学和医学研究的通用工具。
