xiNET: cross-link network maps with residue resolution

Mol Cell Proteomics. 2015 Apr;14(4):1137-47. doi: 10.1074/mcp.O114.042259. Epub 2015 Feb 3.


xiNET is a visualization tool for exploring cross-linking/mass spectrometry results. The interactive maps of the cross-link network that it generates are a type of node-link diagram. In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures.

Availability: xiNET is open source, released under the Apache version 2 license. Results can be viewed by uploading data to or by downloading the software from and running it locally.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / metabolism*
  • Cross-Linking Reagents / metabolism*
  • Mass Spectrometry
  • Protein Interaction Maps*
  • Protein Multimerization
  • Protein Structure, Tertiary
  • Software*
  • Transcription Factors, TFII / chemistry
  • Transcription Factors, TFII / metabolism


  • Amino Acids
  • Cross-Linking Reagents
  • Transcription Factors, TFII
  • transcription factor TFIIF