PINE: An Automation Tool to Extract & Visualize Functionally Enriched Networks from Mass Spectrometry-Based Proteomics Datasets

Recent surges in mass spectrometry-based proteomics studies demands a concurrent rise in speedy and optimized data processing tools and pipelines. While several stand-alone databases exist that store gene interaction and annotation information, we developed Protein Interaction Network Extractor (PINE) as a fully-automated, user-friendly, graphical interface-based bioinformatics tool that has an easily adoptable framework suitable for study of all proteins and post-translational modifications (PTMs) sites enabling simple, quick and robust visualization of differentially expressed proteins or PTMs and their interaction or functionally enriched networks. PINE tool can be applied not only to better understand protein functional interaction networks but also to analyze PTMs involved and their effect. To illustrate the relevance of the tool, we explore the total proteome and its PTM -associated relationships in two different nonalcoholic steatohepatitis (NASH) mouse models to show different context-specific use cases. The strength of this tool relies in its ability to (1) perform accurate protein identifier mapping to resolve any ambiguity, (2) retrieve interaction data from multiple publicly available protein-protein interaction databases, (3) assimilate these complex networks into meaningful functionally enriched pathways. Ultimately this tool can be used as an extremely powerful approach for novel hypothesis generation towards understanding disease mechanisms and potential therapeutics.