Polynomial-time disulfide bond determination using mass spectrometry data

We present an algorithmic approach for determining, in polynomial time, disulfide bonds in proteins using mass spectrometry data. The proposed technique is based on matching the set of all theoretically possible disulfide bonded structures with precursor ions derived from a tandem MS/MS experiment. For each match found, theoretical fragments from a disulfide bonded peptide structure are matched with precursor ion fragments obtained from the same tandem MS/MS data set in order to determine a protein´s disulfide linkage pattern. A polynomial-time approximation strategy is proposed to selectively generate the set of theoretically possible disulfide bonded linkages for matching. Experiments demonstrate the efficacy of the method.