Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples

J Proteome Res. 2013 Dec 6;12(12):5923-33. doi: 10.1021/pr4003867. Epub 2013 Oct 4.


Chemical cross-linking of proteins combined with mass spectrometry provides an attractive and novel method for the analysis of native protein structures and protein complexes. Analysis of the data however is complex. Only a small number of cross-linked peptides are produced during sample preparation and must be identified against a background of more abundant native peptides. To facilitate the search and identification of cross-linked peptides, we have developed a novel software suite, named Hekate. Hekate is a suite of tools that address the challenges involved in analyzing protein cross-linking experiments when combined with mass spectrometry. The software is an integrated pipeline for the automation of the data analysis workflow and provides a novel scoring system based on principles of linear peptide analysis. In addition, it provides a tool for the visualization of identified cross-links using three-dimensional models, which is particularly useful when combining chemical cross-linking with other structural techniques. Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data. Further validation was carried out on known structural elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight into the previously uncharacterized C-terminal domain of the protein.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Cattle
  • Cross-Linking Reagents / chemistry
  • Cytochromes c / chemistry*
  • DNA Polymerase III / chemistry*
  • Escherichia coli / chemistry
  • Escherichia coli / enzymology
  • Escherichia coli Proteins / chemistry*
  • Mass Spectrometry / statistics & numerical data*
  • Models, Molecular*
  • Molecular Sequence Data
  • Software*


  • Cross-Linking Reagents
  • Escherichia coli Proteins
  • Cytochromes c
  • DNA polymerase III, alpha subunit
  • DNA Polymerase III

Associated data

  • UniProtKB/P10443
  • UniProtKB/P62894