Method of operating a linear ion trap to provide low pressure short time high amplitude excitation

1. A method for fragmenting ions in an ion trap of a mass spectrometer comprising

a) selecting parent ions for fragmentation;

b) retaining the parent ions within the ion trap for a retention time interval, the ion trap having an operating pressure of less than about 1×10 −4 Torr;

c) providing a RF trapping voltage to the ion trap to provide a Mathieu stability parameter q at an excitement level during an excitement time interval within the retention time interval;

d) providing a resonant excitation voltage to the ion trap during the excitement time interval to excite and fragment the parent ions; and,

e) within the retention time interval and after the excitement time interval, terminating the resonant excitation voltage and changing the RF trapping voltage applied to the ion trap to reduce the Mathieu stability parameter q to a hold level less than the excitement level to retain fragments of the parent ions within the ion trap.

2. The method as defined in claim 1 wherein the excitement time interval is between about 1 ms and about 150 ms in duration.

3. The method as defined in claim 2 wherein the excitement time interval is less than about 50 ms in duration.

4. The method as defined in claim 2 wherein the excitement time interval is greater than about 2 ms in duration.

5. The method as defined in claim 2 wherein the excitement time interval is greater than about 10 ms in duration.

6. The method as defined in claim 2 wherein the resonant excitation voltage has an amplitude of between about 50 mV and about 250 mV, peak to peak.

7. The method as defined in claim 2 wherein the resonant excitation voltage has an amplitude of between about 50 mV and about 100 mV, peak to peak.

8. The method as defined in claim 2 wherein the excitement level of q is between about 0.15 and about 0.9.

9. The method as defined in claim 2 wherein the hold level of q is above about 0.015.

10. The method as defined in claim 2 wherein

c) comprises determining the excitement time interval based at least partly on the operating pressure in the ion trap, such that the excitement time interval varies inversely with the operating pressure in the ion trap; and,

d) comprises determining an amplitude of the resonant excitation voltage based at least partly on the operating pressure in the ion trap, such that the amplitude of the resonant excitation voltage varies inversely with the operating pressure in the ion trap.

11. The method as defined in claim 2 wherein e) comprises determining the hold level of q to be i) sufficiently high to retain the parent ions within the ion trap, and ii) sufficiently low to retain within the ion trap fragments of the parent ions having a fragment m/z less than about one fifth of a parent m/z of the parent ions.

12. The method as defined in claim 2 wherein the excitement level of q is between about 0.15 and about 0.39.

13. The method as defined in claim 12 wherein the excitement time interval is greater than about 10 ms.

14. The method as defined in claim 13 wherein the resonant excitation voltage has an amplitude of between about 50 mV and about 100 mV, peak to peak.

15. The method as defined in claim 2 wherein the resonant excitation voltage has an amplitude of between about 50 mV and about 700 mV, peak to peak.

16. The method as defined in claim 2 wherein the resonant excitation voltage is terminated substantially concurrently with the RF trapping voltage applied to the ion trap being changed to reduce the Mathieu stability parameter q to the hold level.

17. The method as defined in claim 2 wherein, in b), the ion trap has an operating pressure of less than about 5×10 −5 Torr.

18. The method as defined in claim 2 wherein the hold level of q is at least about ten percent less than the excitement level of q.