Systems and methods for regulating the ion population in an ion trap for MS

1. A mass spectrometry apparatus comprising:

an ion source configured to generating ions;

an ion trap configured to:

trap ions within a RF field;

eject unwanted ion while retaining target ions; and

fragment target ions;

a mass spectrometer controller configured to:

determine an injection time for the ion trap based on a precursor ion flux and a product ion flux;

fill the ion trap with ions from the ion source for an amount of time equal to the injection time;

isolate target precursor ions in the ion trap;

fragment the target precursor ions to generate product ions; and

mass analyzing the product ions.

2. The mass spectrometry system of claim 1 wherein the mass spectrometry controller is further configured to perform a scan cycle without fragmentation to determine the precursor ion flux.

3. The mass spectrometry system of claim 1 wherein the mass spectrometry controller is further configured to perform a scan cycle with fragmentation to determine the product ion flux.

4. The mass spectrometry system of claim 1 wherein the injection time is further based on a maximum injection time.

5. The mass spectrometry system of claim 1 wherein the injection time is calculated to keep the number of precursor ions below an isolation space charge limit, an activation space charge limit, or any combination thereof, and to keep the number of product ions below a spectral space charge limit.

6. The mass spectrometry system of claim 5 wherein the injection time is long enough for the precursor ions to exceed the spectral space charge limit.

7. The mass spectrometry system of claim 1 wherein to fragment the target precursor ions, the mass spectrometer controller is further configured to isolate ion fragments and fragment the isolated ion fragments to generate product ions.

8. A method of analyzing ion fragments, comprising:

determining an injection time for an ion trap based on a precursor ion flux and a product ion flux;

supplying ions to an ion trap for an amount of time equal to the injection time;

isolating target precursor ions in the ion trap;

fragmenting the target precursor ions in the ion trap to generate product ions; and

mass analyzing the product ions.

9. The method of claim 7 wherein fragmenting the target precursor ions further includes isolating ion fragments and further fragmenting the isolated ion fragments to generate product ions.

10. The method of claim 8 further comprising performing a scan cycle without fragmentation to determine the precursor ion flux.

11. The method of claim 8 further comprising performing a scan cycle with fragmentation to determine the product ion flux.

12. The method of claim 8 wherein injection time is further based on a maximum injection time.

13. The method of claim 8 wherein the injection time is calculated to keep the precursor ions below an isolation space charge limit, an activation space charge limit, or any combination thereof, and to keep the product ions below a spectral space charge limit.

14. The method of claim 13 wherein the injection time is long enough for the precursor ions to exceed the spectral space charge limit.

15. A non-transitory computer readable medium containing instructions that when implemented by a processor perform the steps of:

determining an injection time for an ion trap based on a precursor ion flux and a product ion flux;

filling the ion trap for an amount of time equal to the injection time;

isolating target precursor ions in the ion trap;

fragmenting the target precursor ions in the ion trap to generate product ions; and

mass analyzing the product ions.

16. The non-transitory computer readable medium of claim 15 further comprising instructions for the step of performing a scan cycle without fragmentation to determine the precursor ion flux.

17. The non-transitory computer readable medium of claim 15 further comprising instructions for the step of performing a scan cycle with fragmentation to determine the product ion flux.

18. The non-transitory computer readable medium of claim 15 wherein injection time is further based on a max injection time.

19. The non-transitory computer readable medium of claim 15 wherein the injection time is calculated to keep the precursor ions below an isolation space charge limit, an activation space charge limit, or any combination thereof, and to keep the product ions below a spectral space charge limit.

20. The non-transitory computer readable medium of claim 19 wherein the injection time is long enough for the precursor ions to exceed the spectral space charge limit.