MASSyPupX

MASSyPupX provides a free and open-source, portable Debian-based Linux distribution for processing and analyzing shotgun proteomics data from data-dependent acquisition (DDA) and data-independent acquisition (DIA) mass spectrometry experiments.

Key Features:

• Portable deployment: The complete software collection runs directly from a USB drive without installation, or can be set up as a workstation or server.
• Pre-installed proteomics tools: Includes Comet, PeptideProphet, ProteinProphet, ProtyQuant, DIA-NN, and the Trans-Proteomic Pipeline for peptide and protein identification and quantification.
• Data format conversion: Supports conversion of raw Thermo files to the HUPO community standard mzML format.
• Custom workflow development: Installed programming languages and libraries including Bash, Python, and R support development of custom mass spectrometry software and workflows.
• Post-processing and visualization: Custom scripts in Bash, Python, and R enable result post-processing and visualization.

Scientific Applications:

• Shotgun proteomics data analysis: Processes DDA and DIA shotgun proteomics data for peptide identification, protein inference, and quantification.
• Decentralized informatics workflows: Enables off-site, scalable data processing without reliance on commercial software infrastructure.
• Reproducible research: Provides a ready-to-use and reproducible mass spectrometry analysis platform with standardized tool configurations.
• Computational method development: Supports creation and testing of novel data interpretation approaches including artificial intelligence integration.

Methodology:

Raw Thermo files are converted to mzML format. DDA data are evaluated with Comet, PeptideProphet, ProteinProphet, ProtyQuant, and the Trans-Proteomic Pipeline. DIA shotgun proteomics data are analyzed with DIA-NN. Custom Bash, Python, and R scripts are used for post-processing and visualization.