Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry

Anal Chem. 2006 Apr 1;78(7):2145-9. doi: 10.1021/ac051339c.


To facilitate structural analysis of proteins and protein-protein interactions, we developed Pro-CrossLink, a suite of software tools consisting of three programs (Figure 1), DetectShift, IdentifyXLink, and AssignXLink. DetectShift was developed to detect ions of cross-linked peptide pairs in a mixture of 18O-labeled peptides obtained from protein proteolytic digests. The selected candidate ions of cross-linked peptide pairs subsequently undergo tandem mass spectrometric (MS/MS) analysis for sequence determination. Based on the masses of candidate ions as well as y- and b-type ions in the tandem mass spectra, IdentifyXLink assigns the candidate ions to cross-linked peptide pairs. For an identified cross-linked peptide pair, AssignXLink generates an extensive fragment ion list, including a-, b-, c-type, x-, y-, z-type, internal, and immonium ions with associated common losses of H2O, NH3, CO, and CO2, and facilitates a precise location of the cross-linked residues. Pro-CrossLink is automated, highly configurable by the user, and applicable to many studies that map low-resolution protein structures and molecular interfaces in protein complexes.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Ammonia / chemistry
  • Automation
  • Carbon Dioxide / chemistry
  • Carbon Monoxide / chemistry
  • Cross-Linking Reagents / chemistry*
  • Ions
  • Mass Spectrometry / methods*
  • Molecular Sequence Data
  • Peptides / analysis*
  • Protein Interaction Mapping / methods*
  • Proteins / chemistry*
  • Software*
  • Water / chemistry


  • Cross-Linking Reagents
  • Ions
  • Peptides
  • Proteins
  • Water
  • Carbon Dioxide
  • Ammonia
  • Carbon Monoxide