Parsing events during MS

1. A system for segmenting a collision-induced dissociation (CID) event of a mass spectrometry/mass spectrometry/mass spectrometry (MS 3 ) experiment, comprising:

a mass spectrometer that performs an MS 3 experiment on a sample;

a processor in communication with the mass spectrometer that

divides a CID event of the MS 3 experiment into two time periods,

at the beginning of a first time period of the CID event, instructs the mass spectrometer to both open a pulse valve in order to pulse a collision gas and apply a first CID voltage, and

at the beginning of a second time period of the CID event, instructs the mass spectrometer to both close the pulse valve and apply a second CID voltage, wherein the mass spectrometer is pumped down during the second time period allowing pump down and CID to overlap in time,

receives a plurality of second generation fragmentation spectra from the MS 3 experiment, and

selects second generation fragment ions from the plurality of second generation fragmentation spectra that have an intensity above a threshold intensity level and a signal-to-noise ratio (S/N) above a threshold S/N level for quantitation.

2. The system of claim 1 , wherein the first CID voltage and the second CID voltage are the same CID voltage.

3. The system of claim 1 , wherein the first CID voltage and the second CID voltage are different CID voltages.

4. The system of claim 1 , wherein the first CID voltage and the second CID voltage are different CID voltages and the difference in voltage between the first CID voltage and the second CID voltage causes a step in collision energy across the CID event.

5. The system of claim 1 , wherein the first time period and the second time period have different lengths.

6. The system of claim 1 , wherein the first time period is longer than the second time period.

7. A method for segmenting a collision-induced dissociation (CID) event of a mass spectrometry/mass spectrometry/mass spectrometry (MS 3 ) experiment, comprising:

dividing a CID event of an MS 3 experiment performed on a sample by a mass spectrometer into two time periods using a processor;

at the beginning of a first time period of the CID event, instructing the mass spectrometer to both open a pulse valve in order to pulse a collision gas and apply a first CID voltage using the processor;

at the beginning of a second time period of the CID event, instructing the mass spectrometer to both close the pulse valve and apply a second CID voltage using the processor wherein the mass spectrometer is pumped down during the second time period allowing pump down and CID to overlap in time thereby;

receiving a plurality of second generation fragmentation spectra from the MS 3 experiment using the processor; and

selecting second generation fragment ions from the plurality of second generation fragmentation spectra that have an intensity above a threshold intensity level and a signal-to-noise ratio (S/N) above a threshold S/N level for quantitation using the processor.

8. The method of claim 7 , wherein the first CID voltage and the second CID voltage are the same CID voltage.

9. The method of claim 7 , wherein the first CID voltage and the second CID voltage are different CID voltages.

10. The method of claim 7 , wherein the first CID voltage and the second CID voltage are different CID voltages and the difference in voltage between the first CID voltage and the second CID voltage causes a step in collision energy across the CID event.

11. The method of claim 7 , wherein the first time period and the second time period have different lengths.

12. The method of claim 7 , wherein the first time period is longer than the second time period.

13. A computer program product, comprising a non-transitory and tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for segmenting a collision-induced dissociation (CID) event of a mass spectrometry/mass spectrometry/mass spectrometry (MS 3 ) experiment, the method comprising:

providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise an analysis module and a control module;

dividing a CID event of an MS 3 experiment performed on a sample by a mass spectrometer into two time periods using the analysis module;

at the beginning of a first time period of the CID event, instructing the mass spectrometer to both open a pulse valve in order to pulse a collision gas and apply a first CID voltage using the control module;

at the beginning of a second time period of the CID event, instructing the mass spectrometer to both close the pulse valve and apply a second CID voltage using the control module; wherein the mass spectrometer is pumped down during the second time period allowing pump down and CID to overlap in time;

receiving a plurality of second generation fragmentation spectra from the MS 3 experiment using the analysis module; and

selecting second generation fragment ions from the plurality of second generation fragmentation spectra that have an intensity above a threshold intensity level and a signal-to-noise ratio (S/N) above a threshold S/N level for quantitation using the analysis module.

14. The computer program product of claim 13 , wherein the first CID voltage and the second CID voltage are the same CID voltage.

15. The computer program product of claim 13 , wherein the first CID voltage and the second CID voltage are different CID voltages.

16. The computer program product of claim 13 , wherein the first CID voltage and the second CID voltage are different CID voltages and the difference in voltage between the first CID voltage and the second CID voltage causes a step in collision energy across the CID event.

17. The computer program product of claim 13 , wherein the first time period and the second time period have different lengths.

18. The computer program product of claim 13 , wherein the first time period is longer than the second time period.