Implementation of an algorithm for modeling disulfide bond patterns using mass spectrometry

The paper describes the implementation of a software system based on the Fenyö disulfide bond assignment algorithm. The system allows an investigator to enter data derived from mass spectrum peak assignments, a target protein sequence and other experimental conditions. The output of the system is the set of disulfide bonding pattern models that are consistent with the experimental evidence. The software and code are available through a public web site, which also has a functioning, publicly accessible version of the disulfide bond modeler. This implementation was tested as part of a project to check homology-based assignments disulfide bonding patterns of human integrins.