Ms/Ms-Based Identification of Trisulfide Bonds

A system for analyzing a sample comprising:

• a tandem mass spectrometer comprising:
• an ion filter,
• at least one of a collision cell and an electron activated dissociation device, and
• a mass analyzer,
• a processor configured to:
• instruct the tandem mass spectrometer to perform a MS1 scan of the sample by mass analyzing the sample,
• receive from the tandem mass spectrometer an MS1 spectra of the sample,
• identify at least one pair of peaks in the MS1 spectra that differ from one another in m/z by 32 units,
• for each of said at least one pair of peaks, instructs the tandem mass spectrometer to isolate a precursor ion representative of each of the peaks in each pair of the at least one pair of peaks and perform an electron activated fragmentation on each precursor ion and to generate fragment ions and to mass analyze said fragment ions,
• receive from the tandem mass spectrometer an MSMS spectra of said fragment ions,
• survey the MSMS spectra for one or more fragment peaks pairs, wherein in each fragment peak pair, the m/z for each differs from the other by 32,
• determines whether the fragment peak pairs correlates by determining whether said fragment peaks were derived from the precursor ion of any of the at least one pair of peaks in the MS1 spectra and if so, determining that a tri-sulfide linkage exists in said sample.