XlinkCyNET: A Cytoscape Application for Visualization of Protein Interaction Networks Based on Cross-Linking Mass Spectrometry Identifications

Software tools that allow the visualization and analysis of protein interaction networks are essential for studies in systems biology. One of the most popular network visualization tools in biology is Cytoscape, which offers a great selection of plug-ins for the interpretation of network data. Chemical cross-linking coupled to mass spectrometry (XL-MS) is an increasingly important source for protein interaction data; however, to date, no Cytoscape tools are available to analyze XL-MS results. In light of the suitability of the Cytoscape platform and to expand its toolbox, here we introduce XlinkCyNET, an open-source Cytoscape Java plug-in for exploring large-scale XL-MS-based protein interaction networks. XlinkCyNET offers the rapid and easy visualization of intra- and interprotein cross-links in a rectangular-bar style as well as on the 3D structure, allowing the interrogation of protein interaction networks at the residue level. XlinkCyNET is freely available from the Cytoscape App Store (http://apps.cytoscape.org/apps/xlinkcynet) and at the Liu lab webpage (https://www.theliulab.com/software/xlinkcynet).