CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry–based protein–protein interaction/association data

Abstract

The elucidation of a protein's interaction/association network is important for defining its biological function. Mass spectrometry-based proteomic approaches have emerged as powerful tools for identifying protein-protein interactions (PPIs) and protein-protein associations (PPAs). However, interactome/association experiments are difficult to interpret considering the complexity and abundance of data that is generated. Although tools have been developed to quantitatively identify protein interactions/associations, there is still a pressing need for easy-to-use tools that allow users to contextualize their results. To address this, we developed CANVS, a computational pipeline that cleans, analyzes, and visualizes mass spectrometry-based interactome/association data. CANVS is wrapped as an interactive Shiny dashboard, allowing users to easily interface with the pipeline. With simple requirements, users can analyze complex experimental data and create PPI/A networks. The application integrates systems biology databases like BioGRID and CORUM to contextualize the results. Furthermore, CANVS features a Gene Ontology tool that allows users to identify relevant GO terms in their results and create visual networks with proteins associated with relevant GO terms. Overall, CANVS is an easy-to-use application that benefits all researchers, especially those who lack an established bioinformatic pipeline and are interested in studying interactome/association data.