Automatic precursor-ion switching in a four-sector tandem mass spectrometer and its application to acquisition of the MS/MS product ions derived from a partially (18)O-labeled peptide for their facile assignments.

We developed an acquisition processor unit to control MS1 and MS2 in a four-sector tandem mass spectrometer simultaneously. The magnetic field strength of MS1 corresponding to the precise centers of the precursor ions, whose masses are determined by MS1 in advance, is recalibrated using an appropriate standard just before an MS/MS experiment, which allows consecutive acquisition of the MS/MS spectra from multiprecursor ions by B2/E2-linked scanning of MS2 synchronized with automatic B1 switching to the centers of each precursor ion on MS1. The accuracy of the automatic precursor-ion switching and the efficiency of consecutive B2/E2-linked scannings were demonstrated by measurement of a peptide mixture. The new MS/MS control system was further applied to rapid acquisition of the MS/MS spectra of isotopic ions of MH+ and (M + 3)+ with normal oxygen and (18)O at the alpha-carboxyl group of a partly (18)O-labeled peptide, which can be easily prepared by enzymatic hydrolysis of a protein in buffer containing 40 atom % H2(18)O. MS/MS analysis of an (18)O-labeled peptide by the present system allowed facile and reliable assignment of MS/MS product ions to a peptide sequence. The usefulness of the method was also demonstrated by measurement of some peptides that give MS/MS product ions incidentally observed at the same mass or assignable to some incorrect sequence.