An apparatus for mass analyzing molecules includes a mass spectrometer configured to select precursor ions having a mass to charge ratio range, a metastable species generator configured to generate a metastable species for introduction into the mass spectrometer, and a mass detector configured to detect a mass of the product ions. The apparatus also includes interaction region in the mass spectrometer where the precursor ions are converted into product ions via interaction of the precursor ions with the metastable species. The mass spectrometer includes at least one of a three-dimensional ion trap, a linear ion trap, or an ion guide. The interaction region is located inside the three-dimensional ion trap, the linear trap, or the ion guide; and at least one of the precursor ions or at least one of the product ions are excited by an alternating electric field or collisionally activated to produce additional product ions.