Effects of fragile ions on mass resolution and on isolation for tandem mass spectrometry in the quadrupole ion trap mass spectrometer

In the quadrupole ion trap, it has been noted that factors other than an ion's mass and charge may affect its measured m/z, resulting in compound-dependent, or chemical, mass shifts. We propose that ions can exhibit a chemical mass shift because they are fragile and may fragment during the application of resonance ejection during mass analysis; these effects were studied using ions that include protonated, deprotonated, and adduct ions of explosives, acylcarnitines, and macrolide antibiotics. Fragile ions affect mass resolution by causing broader peaks than nonfragile ions, especially at slower scan speeds, as the result of the application of resonance ejection. Fragile ions may also be fragmented by the application of the isolation waveform during selection of the parent ion for tandem mass spectrometry experiments, making it impossible to achieve unit isolation of a fragile ion. To obtain adequate isolation intensity, the isolation waveform notch width must be increased and the time period of isolation must be decreased. Fragile ions also require lower optimum collision energy to achieve efficient collision-induced dissociation. We have developed criteria for the determination of the degree of ion fragility based upon experimental results.