PINE

PINE extracts and visualizes protein–protein interaction (PPI) and post-translational modification (PTM)-based functional networks from mass spectrometry-based proteomics datasets to support proteome-wide analysis.

Key Features:

• Automated Data Processing: Automates extraction and visualization of protein-centric functional networks from large-scale mass spectrometry proteomics datasets.
• Integration of Differential Expression Data: Overlays differential expression values and statistical significance thresholds onto functional networks.
• PTM Site Visualization: Maps and displays post-translational modification (PTM) sites within protein networks.
• Comprehensive Data Retrieval: Retrieves interaction data from multiple publicly available protein–protein interaction (PPI) databases.
• Functional Enrichment and Ontology Mapping: Performs functional enrichment and maps ontology categories and terms onto networks.
• Accurate Protein Identifier Mapping: Resolves ambiguity in protein identifiers to ensure precise mapping and interaction retrieval.

Scientific Applications:

• Proteome-wide interaction analysis: Supports analysis and visualization of proteome-scale PPI networks derived from mass spectrometry data.
• PTM-mediated network analysis: Enables exploration of post-translational modification-mediated network relationships and site-specific effects.
• Disease mechanism exploration: Facilitates hypothesis generation and investigation of regulatory mechanisms underlying disease processes.
• Context-specific proteome and PTM analysis: Has been applied to contextualize proteome and PTM-associated relationships in nonalcoholic steatohepatitis (NASH) mouse models.

Methodology:

Integrates interaction data from multiple PPI databases, maps protein identifiers to resolve ambiguities, incorporates differential expression and PTM-site information, and visualizes interactions within functionally enriched networks.