Patent ID: 8686349

Claim:
A method of tandem mass spectrometry (MS/MS) for use in a mass spectrometer characterized by the steps: (a) repeating, a finite number of times, the steps of: (a1) selecting a distinct mass to charge (m/z) ratio; (a2) isolating a set of precursor ions of a precursor ion type, said precursor ions of said precursor ion type comprising said m/z ratio; (a3) estimating an elemental composition for the precursor ions comprising said (m/z) ratio, the estimation based on said m/z ratio and an estimated charge state; and (a4) transferring said isolated precursor ions into an ion storage device, so as to create a mixture of precursor ion types therein, the mixture including any precursor ions previously transferred into the ion storage device; (b) generating fragment ions comprising plurality of fragment ion types by fragmenting the plurality of precursor ion types of the mixture; (c) generating a mass spectrum of the fragment ion types so as to determine a respective m/z ratio or m/z ratio range for each respective fragment ion type; (d) estimating an elemental composition for each of the fragment ion types based on the determined m/z ratio or m/z ratio range and an estimated charge state for each respective fragment ion type; and (e) calculating a set of probability values for each precursor ion type, each probability value representing a probability that a respective fragment ion type or a respective pair of fragment ion types was derived from the precursor ion type.