A method of processing mass spectrographs data regarding reaction pairs in an ion sample, the method comprising: a) obtaining a first mass spectrum of the ion sample at a first fragmentation level, the first mass spectrum comprising a sequence of first mass signals defined over a mass axis such that each first mass signal represents an associated first signal magnitude for an associated mass on the mass axis; b) obtaining a second mass spectrum of the ion sample at a second fragmentation level that is higher than the first fragmentation level, the second mass spectrum comprising a sequence of second mass signals defined over the mass axis such that each second mass signal represents an associated second signal magnitude for an associated mass in the mass axis; c) selecting a neutral loss difference; and, d) subtracting the first mass spectrum from the second mass spectrum to create a differential mass spectrum, shifting the differential mass spectrum by the neutral loss difference relative to the first mass spectrum of the ion sample to provide a shifted mass spectrum and then multiplying the shifted mass spectrum with the first mass spectrum of the ion sample, the individual shifted mass signal and the individual first mass signal being aligned along the mass axis and each mass signal in one spectrum is multiplied with the corresponding aligned mass signal in the other spectrum to obtain a probability mass spectrum to determine at least one reaction pair based on the neutral loss difference, wherein a precursor ion is selected from the at least one reaction pair in a mass spectrometer system and an MS/MS analysis is performed on the precursor ion. a) obtaining a first mass spectrum of the ion sample at a first fragmentation level, the first mass spectrum comprising a sequence of first mass signals defined over a mass axis such that each first mass signal represents an associated first signal magnitude for an associated mass on the mass axis; b) obtaining a second mass spectrum of the ion sample at a second fragmentation level that is higher than the first fragmentation level, the second mass spectrum comprising a sequence of second mass signals defined over the mass axis such that each second mass signal represents an associated second signal magnitude for an associated mass in the mass axis; c) selecting a neutral loss difference; and, d) subtracting the first mass spectrum from the second mass spectrum to create a differential mass spectrum, shifting the differential mass spectrum by the neutral loss difference relative to the first mass spectrum of the ion sample to provide a shifted mass spectrum and then multiplying the shifted mass spectrum with the first mass spectrum of the ion sample, the individual shifted mass signal and the individual first mass signal being aligned along the mass axis and each mass signal in one spectrum is multiplied with the corresponding aligned mass signal in the other spectrum to obtain a probability mass spectrum to determine at least one reaction pair based on the neutral loss difference, wherein a precursor ion is selected from the at least one reaction pair in a mass spectrometer system and an MS/MS analysis is performed on the precursor ion.