LinX: A Software Tool for Uncommon Cross-Linking Chemistry

J Proteome Res. 2021 Apr 2;20(4):2021-2027. doi: 10.1021/acs.jproteome.0c00858. Epub 2021 Mar 3.


Chemical cross-linking mass spectrometry has become a popular tool in structural biology. Although several algorithms exist that efficiently analyze data-dependent mass spectrometric data, the algorithm to identify and quantify intermolecular cross-links located at the interaction interface of homodimer molecules was missing. The algorithm in LinX utilizes high mass accuracy for ion identification. In contrast with standard data-dependent analysis, LinX enables the elucidation of cross-linked peptides originating from the interaction interface of homodimers labeled by 14N/15N, including their ratio or cross-links from protein-nucleic acid complexes. The software is written in Java language, and its source code and a detailed user's guide are freely available at or Data are accessible via the ProteomeXchange server with the data set identifier PXD023522.

Keywords: chemical cross-linking; data interpretation; high resolution; homo oligomers; mass spectrometry; nucleic acids; proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cross-Linking Reagents
  • Mass Spectrometry
  • Peptides*
  • Software*


  • Cross-Linking Reagents
  • Peptides