Intelligent saturation control for compound specific optimization of MRM

1. A system for automatically determining mass spectrometer parameters used to tune a mass spectrometer for multiple reaction monitoring, comprising:

a mass spectrometer that receives a single injection of a sample and performs two or more precursor ion scans and a plurality of product ion scans for each precursor ion scan of the two or more precursor ion scans from the single injection, wherein the each precursor ion scan is produced with different mass spectrometer parameters that create a different level of ion current for a same precursor ion,

a processor that is in communication with the mass spectrometer, wherein

the processor analyzes mass spectra of the two or more precursor ion scans to determine if saturation has occurred in any of the two or more precursor ion scans and performs saturation correction for a precursor ion scan of the two or more precursor ion scans if saturation has occurred in the precursor ion scan,

the processor selects a precursor ion scan of the two or more precursor ion scans that produces the highest ion current with the least amount of saturation, and

the processor determines mass spectrometer parameters used to tune the mass spectrometer for multiple reaction monitoring from mass spectrometer parameters of the selected precursor ion scan and mass spectrometer parameters of one or more product ion scans from one or more fragments produced from the selected precursor ion scan.

2. The system of claim 1 , wherein the spectrometer comprises a triple quadrupole.

3. The system of claim 1 , wherein the spectrometer comprises a triple quadrupole linear ion trap hybrid instrument.

4. The system of claim 1 , wherein the different mass spectrometer parameters that produce a different level of ion current for a sample precursor ion comprise an ion source condition.

5. The system of claim 1 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise an interface voltage.

6. The system of claim 1 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise an axial path ion voltage.

7. The system of claim 1 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise an isolation mass.

8. The system of claim 1 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise a quadrupole resolution.

9. A method for automatically determining mass spectrometer parameters used to tune a mass spectrometer for multiple reaction monitoring, comprising:

receiving a single injection of a sample using a mass spectrometer;

performing one or more precursor ion scans and a plurality of product ion scans for each precursor ion scan of the two or more precursor ion scans from the single injection using the mass spectrometer, wherein the each precursor ion scan is produced with different mass spectrometer parameters that create a different level of ion current for a same precursor ion;

analyzing mass spectra of the two or more precursor ion scans to determine if saturation has occurred in any of the two or more precursor ion scans and performing saturation correction for a precursor ion scan of the two or more precursor ion scans if saturation has occurred in the precursor ion scan using a processor;

selecting a precursor ion scan of the two or more precursor ion scans that produces the highest ion current with the least amount of saturation using the processor; and

determining mass spectrometer parameters used to tune the mass spectrometer for multiple reaction monitoring from mass spectrometer parameters of the selected precursor ion scan and mass spectrometer parameters of one or more product ion scans from one or more fragments produced from the selected precursor ion scan using the processor.

10. The method of claim 9 , wherein the different mass spectrometer parameters that produce a different level of ion current for a sample precursor ion comprise an ion source condition.

11. The method of claim 9 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise an interface voltage.

12. The method of claim 9 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise an axial path ion voltage.

13. The method of claim 9 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise an isolation mass.

14. The method of claim 9 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise a quadrupole resolution.

15. A computer program product, comprising a tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for automatically determining mass spectrometer parameters used to tune a mass spectrometer for multiple reaction monitoring, the method comprising:

providing a system, wherein the system comprises distinct software modules, and wherein the distinct software modules comprise a measurement control module, a saturation analysis module, and a parameter acquisition module;

instructing a mass spectrometer to receive a single injection of a sample using the measurement control module;

instructing the mass spectrometer to perform one or more precursor ion scans and a plurality of product ion scans for each precursor ion scan of the two or more precursor ion scans from the single injection using the measurement control module, wherein the each precursor ion scan is produced with different mass spectrometer parameters that create a different level of ion current for a same precursor ion;

analyzing mass spectra of the two or more precursor ion scans to determine if saturation has occurred in any of the two or more precursor ion scans and performing saturation correction for a precursor ion scan of the two or more precursor ion scans if saturation has occurred in the precursor ion scan using the saturation analysis module;

selecting a precursor ion scan of the two or more precursor ion scans that produces the highest ion current with the least amount of saturation using the saturation analysis module; and

determining mass spectrometer parameters used to tune the mass spectrometer for multiple reaction monitoring from mass spectrometer parameters of the selected precursor ion scan and mass spectrometer parameters of one or more product ion scans from one or more fragments produced from the selected precursor ion scan using the parameter acquisition module module.

16. The computer program product of claim 15 , wherein the different mass spectrometer parameters that produce a different level of ion current for a sample precursor ion comprise an ion source condition.

17. The computer program product of claim 15 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise an interface voltage.

18. The computer program product of claim 15 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise an axial path ion voltage.

19. The computer program product of claim 15 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise an isolation mass.

20. The computer program product of claim 15 , wherein the different mass spectrometer parameters that produce a different level of ion current for a same precursor ion comprise a quadrupole resolution.