A method includes obtaining a first mass spectrum; selecting a first peak of the first mass spectrum; fragmenting and analyzing ions of the first peak to obtain a second mass spectrum; performing a real-time spectral search for compounds corresponding to peaks in the second mass spectrum; identifying fragments for the compounds identified based on the real-time spectral search; adding mass-to-charge ratios for the fragments to an exclusion list; selecting a second peak present in the first mass spectrum and not on the exclusion list; and fragmenting and analyzing ions of the second peak to obtain a third mass spectrum.