CLIPPER 2.0

CLIPPER 2.0 annotates peptide-level outputs from positional proteomics LC-MS/MS degradomics experiments to identify natural and neo-termini and support protease signaling analysis.

Key Features:

• Enhanced data analysis: Builds on previous algorithms for MS-based protein termini analysis to provide peptide-level annotation compatible with diverse sample preparation workflows and proteomics search algorithms.
• Automated database retrieval: Automates retrieval of database information for annotated peptides and termini.
• Comprehensive statistical analysis: Provides capabilities for detailed statistical analysis of positional proteomics datasets.
• Network analysis: Supports network analysis to explore protease systems, interactions, and signaling pathways.
• Visualization tools: Generates visualizations for terminomic datasets to aid interpretation of cleavage sites and termini.

Scientific Applications:

• Protease research: Enables characterization of enzyme–substrate interactions and mapping of proteolytic processing at natural and neo-termini.
• Degradomics studies: Facilitates system-wide analysis of protein degradation pathways from LC-MS/MS positional proteomics data.
• Protease signaling characterization: Supports interrogation of protease signaling networks and pathway-level effects of proteolysis.
• Experimental demonstration: Applied to analysis of GluC and MMP9 cleavages in HeLa cell lysates to evaluate terminomic profiles.

Methodology:

Builds on MS-based protein termini analysis algorithms and automates database retrieval, statistical analysis, network exploration, and visualization of LC-MS/MS positional proteomics datasets.