piNET

piNET maps and analyzes peptide and protein sequences with annotated post-translational modification (PTM) sites to annotate enzyme–substrate relationships and relate PTM signatures to chemical and genetic perturbations.

Key Features:

• Integrated annotation and analysis: Accepts peptide or protein lists with optional PTM site annotations and abundance values and maps peptides to proteins and PTM sites.
• Network visualization: Generates high-resolution visualizations for enzyme–substrate networks, including kinase–phospho-peptide interactions.
• LINCS library integration: Integrates LINCS chemical and genetic perturbation signatures to map connectivity between PTM sites and perturbations such as chemical inhibitors and genetic knockdowns.
• Modular architecture: Implemented on a modular Spring-Boot Java platform.
• Efficient data mapping: Uses Apache Lucene indexing to map peptides into UniProt entries across multiple model organism proteomes, including human and mouse.
• Comprehensive PTM network analysis: Leverages PhosphoSitePlus, iPTMnet, and SIGNOR for validated enzyme–substrate relationships and augments kinase networks with DeepPhos predictions and sequence-based mapping of consensus motifs from PhosphoSitePlus.
• RESTful API access: Provides a RESTful API that returns results in JSON format for programmatic integration.

Scientific Applications:

• PTM network analysis: Characterizes PTM networks to investigate cellular signaling and regulatory mechanisms.
• Perturbation signature mapping: Connects proteomics-derived PTM signatures to LINCS chemical and genetic perturbation signatures to generate mechanistic hypotheses and identify potential therapeutic targets.
• Kinase and enzyme activity elucidation: Supports analysis of kinase–substrate relationships and other enzymatic processes at a systems level.

Methodology:

Accepts peptide/protein lists with optional PTM site annotations and abundance values; maps peptides to UniProt using Apache Lucene indexing; uses PhosphoSitePlus, iPTMnet, and SIGNOR for enzyme–substrate relationships; applies DeepPhos predictions and sequence-based consensus motif mapping from PhosphoSitePlus; integrates LINCS chemical and genetic perturbation signatures; implemented on Spring-Boot Java with a RESTful API returning JSON.