**XlinkCyNET** is an open-source Java plugin that generates residue-to-residue connections provided by XL-MS in protein interaction networks. Importantly, it provides an interactive interface for the exploration of cross-links and offers various options to display protein domains. XlinkCyNET works well in complex networks containing thousands of proteins.
A [video](https://www.youtube.com/embed/yLGUnLHy8rI?rel=0&showinfo=0) demonstrating how the application works can be found on the [software website](https://www.theliulab.com/software/xlinkcynet).<br/>
A detailed [tutorial](http://dx.doi.org/10.21203/rs.3.pex-1172/v1), which explains step by step the functionality of all parameters is available at *Protocol Exchange*.
↪ Visualize protein-protein interaction network based on cross-linking mass spectrometry data<br/>
↪ Apply a residue-to-residue layout to a Cytoscape interaction network
↪ Annotate protein domains to all nodes in the network
<p>Don't hesitate to send us any comments, questions or bug reports to: <img src="http://diogobor.droppages.com/emailBorderless.png" alt="email"/></p>
Any feedback is welcomed!<br/><br/>
Have fun! :)