PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics...

Area of Science:

• Proteomics
• Bioinformatics
• Computational Biology

Background:

• Mass spectrometry (MS)-based proteomics is crucial for identifying protein complexes in biological processes.
• Tandem MS methods accurately detect protein-protein interactions (PPIs).
• Current methods often yield only peptide fragment lists, lacking discrimination between physical or functional PPIs.

Purpose of the Study:

• To introduce the PPI-MASS web server, an interactive platform for identifying pharmacologically relevant PPIs.
• To provide a tool for filtering large protein datasets based on biological features.
• To facilitate the discovery of novel PPIs and protein complexes for therapeutic applications.

Main Methods:

• The PPI-MASS server integrates an automated pipeline using data from accessible databases.
• It collects protein sequence, functional, structural, pathological, and expression data.
• Users can apply interactive filters to identify candidate proteins for physical interactions.

Main Results:

• The web server successfully identified PPIs for TRPM4 and TMPRSS11a proteins.
• Identified PPIs were validated through biochemical and bioinformatic analyses.
• The platform demonstrates its utility in discovering and validating PPIs.

Conclusions:

• PPI-MASS offers a powerful, user-friendly tool for detecting novel PPIs.
• It significantly reduces the time and effort required for data postprocessing.
• The server serves as a valuable resource for identifying protein complexes and designing therapies.