Patent ID: 8909481

Claim:
A method of mass spectrometry for identifying a plurality of polypeptides in a sample, said method comprises the steps of: subjecting the sample comprising a plurality of parent polypeptides to a mass spectrometer; mass analyzing said polypeptides by continuously alternating the mass spectrometer between: (i) a parent ion scan mode of operation including generating a first mass spectrum by mass analyzing a plurality of parent polypeptide ions of different masses; and (ii) a Collision Induced Dissociation (CID) scan mode of operation including simultaneously fragmenting a plurality of parent polypeptide ions of different masses without selecting a specific ion to form resulting fragment ions and then generating a second mass spectrum by mass analyzing the resulting fragment ions; determining the masses of said parent polypeptide ions from the first mass spectrum generated in step (i); determining the masses of said fragment ions from the second mass spectrum generated in step (ii); comparing the masses of said parent polypeptide ions and the masses of said fragment ions to an annotated polypeptide index; and identifying one or more of the plurality of parent polypeptides in said sample on the basis of comparison.