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.