Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures

J Struct Biol. 2015 Mar;189(3):177-83. doi: 10.1016/j.jsb.2015.01.014. Epub 2015 Feb 7.


Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques. Cross-linking mass spectrometry (XL-MS) identifies proximal protein residues and thus is increasingly used to map protein interactions and determine the relative orientation of subunits within the structure of protein complexes. To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures. Xlink Analyzer enables automatic visualization of cross-links, identifies cross-links violating spatial restraints, calculates violation statistics, maps chemically modified surfaces, and allows interactive manipulations that facilitate analysis of XL-MS data and aid designing new experiments. We demonstrate these features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex. Xlink Analyzer is implemented as a plugin to UCSF Chimera, a standard structural biology software tool, and thus enables seamless integration of XL-MS data with, e.g. fitting of X-ray structures to EM maps. Xlink Analyzer is available for download at http://www.beck.embl.de/XlinkAnalyzer.html.

Keywords: Analysis; Cross-linking; Integrative modeling; Mass spectrometry; Visualization; XL-MS.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / chemistry
  • Adenosine Triphosphatases / metabolism
  • Cross-Linking Reagents / chemistry
  • DNA Helicases / chemistry
  • DNA Helicases / metabolism
  • Databases, Protein
  • Image Processing, Computer-Assisted / methods*
  • Mass Spectrometry / methods*
  • Models, Molecular
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / metabolism
  • RNA Polymerase I / chemistry
  • RNA Polymerase I / metabolism
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / metabolism
  • Software*
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism


  • Cross-Linking Reagents
  • Proteins
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • RNA Polymerase I
  • Adenosine Triphosphatases
  • RVB1 protein, S cerevisiae
  • RVB2 protein, S cerevisiae
  • DNA Helicases