PPI-MASS

PPI-MASS identifies and prioritizes candidate protein–protein interactions from tandem mass spectrometry-based proteomics data, distinguishing potential physical interactors from functional associations while integrating sequence, structural, pathology, drug and tissue-expression annotations.

Key Features:

• Automated Data Integration: Integrates protein sequences, functional and structural properties, associated pathologies and drugs, and tissue-specific location and expression from publicly accessible databases.
• Customizable Filtering: Applies biological filters based on function, structure, disease association, and drug interaction potential to refine candidate protein interactors.
• Post-processing of Mass Spectrometry Data: Associates tandem mass spectrometry peptide lists with target proteins to identify putative protein–protein interactions.
• Automated High-throughput Processing: Automates integration and filtering steps to support large-scale post-processing of proteomics results.
• Validation through Case Studies: Includes reported interactome analyses such as TRPM4 and TMPRSS11a with interactions validated by biochemical and bioinformatic studies.

Scientific Applications:

• Proteomics: Identification and prioritization of novel protein–protein interactions from mass spectrometry datasets.
• Systems Biology: Reconstruction and analysis of interactomes to study molecular networks.
• Drug Discovery: Highlighting proteins with pharmacological potential and drug-interaction annotations to inform targeted therapy design.
• Disease Mechanism Studies: Linking PPIs with pathology and tissue-specific expression to investigate disease-related molecular mechanisms.

Methodology:

Automated integration of protein information (sequences, functional and structural properties, pathologies, drugs, tissue-specific expression) from public databases and application of customizable biological filters (function, structure, disease association, drug interaction potential) to prioritize candidate interactors from tandem mass spectrometry peptide lists.