Patent ID: 7586089

Claim:
A method for acquiring an improved daughter ion spectra of ions of peptides in an ion trap mass spectrometer, comprising: (a) filling the ion trap with ions and acquiring a mass spectrum of the ions; (b) analyzing the mass spectrum acquired in step (a) and, based on the results of the analysis, selecting a species of parent ion from which a daughter ion spectrum is to be measured; (c) filling the ion trap with ions and isolating the selected species of parent ion; (d) fragmenting the ions of the selected species of parent ion isolated in step (c); (e) acquiring a daughter ion spectrum of ion fragments resulting from step (d); (f) analyzing the daughter ion spectrum for the presence of a dominant daughter ion species; and (g) when a dominant daughter ion species is present, (g1) filling the ion trap with ions and isolating the selected species of parent ion; (g2) fragmenting the ions of the selected species of parent ion isolated in step (g1); (g3) resonantly exciting the dominant daughter ion species; and (g4) acquiring the improved daughter ion spectrum of ion fragments resulting from steps (g2) and (g3).