Flow through MS

1. A system for selecting and fragmenting a first precursor ion in a mass spectrometry/mass spectrometry/mass spectrometry (MS 3 ) experiment, comprising:

a mass spectrometer that includes an ion source that provides a continuous beam of ions and a first quadrupole Q0 ion guide that receives the continuous beam of ions and is adapted to apply dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions while passing through the first quadrupole Q0 ion guide; and

a processor in communication with the mass spectrometer that

calculates one or more first excitation parameters that define a first dipole excitation that selects a first precursor ion and fragments the first precursor ion to produce a second precursor ion,

applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions by sending a first set of data including the first excitation parameters to the mass spectrometer so that the first quadrupole Q0 ion guide applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide select and fragment the first precursor ion in the first quadrupole Q0 ion guide and to produce the second precursor ion in the first quadrupole Q0 ion guide, wherein the second precursor ion is a fragment ion of the first precursor ion,

mass selects the second precursor ion in a second quadrupole Q1,

accelerates the second precursor ion to a third quadrupole Q2 for high energy collision induced dissociation (CID), and

removes ions in a region of the second precursor ion in the first quadrupole Q0 ion guide before selecting and fragmenting the first precursor ion in the first quadrupole Q0 ion guide.

2. The system of claim 1 , wherein the first excitation parameters comprise one or more of a voltage, a frequency, and a duration.

3. The system of claim 1 , wherein the first quadrupole Q0 ion guide applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions by applying the first dipole excitation between pairs of rods.

4. The system of claim 1 , wherein the first quadrupole Q0 ion guide further includes auxiliary electrodes placed between rods of the first quadrupole Q0 ion guide.

5. The system of claim 4 , wherein the first quadrupole Q0 ion guide applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite to the continuous beam of ions by applying the first dipole excitation between pairs of the auxiliary electrodes.

6. The system of claim 4 , wherein the processor removes ions in a region of the second precursor ion in the first quadrupole Q0 ion guide before selecting and fragmenting the first precursor ion in the first quadrupole Q0 ion guide by

calculating one or more second excitation parameters that define a second dipole excitation that removes ions at a location of the second precursor ion, and

applying the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions before the first dipole excitation by additionally sending a second set of data including the second excitation parameters to the mass spectrometer so that the first quadrupole Q0 ion guide applies the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions before the first quadrupole Q0 ion guide applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions.

7. The system of claim 6 , wherein the auxiliary electrodes placed between rods of the first quadrupole Q0 ion guide are further segmented into a first set of electrodes that receive the continuous beam of ions from the ion source and a second set of electrodes located in series along the axis of the first quadrupole Q0 ion guide.

8. The system of claim 7 , wherein the processor applies the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions before the first dipole excitation by

sending the second data set to the mass spectrometer so that the first quadrupole Q0 ion guide applies the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the first set of electrodes using the second excitation parameters and the first quadrupole Q0 ion guide applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the second set of electrodes using the first excitation parameters.

9. The system of claim 6 , wherein the first quadrupole Q0 ion guide further includes entrance electrodes placed at an entrance end of the first quadrupole Q0 ion guide and an exit lens at an exit end of the first quadrupole Q0 ion guide.

10. The system of claim 9 , wherein the processor applies the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions before the first dipole excitation so that the mass spectrometer

traps ions in the first quadrupole Q0 ion guide by applying a voltage potential on the entrance electrodes and the exit lens,

applies the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the trapped ions in the first quadrupole Q0 ion guide to remove ions in a region of the second precursor ion,

applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the trapped ions in the first quadrupole Q0 ion guide to select and fragment the first precursor ion, and

lowers the voltage potential on the exit lens to transmit the trapped ions to the second quadrupole Q1.

11. A method for selecting and fragmenting a first precursor ion in a mass spectrometry/mass spectrometry/mass spectrometry (MS 3 ) experiment, comprising:

calculating one or more first excitation parameters that define a first dipole excitation that selects a first precursor ion and fragments the first precursor ion to produce a second precursor ion using a processor;

applying the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions by sending a first set of data including the first excitation parameters to a mass spectrometer so that a first quadrupole Q0 ion guide applies the first dipole excitation between rods or electrodes in the first quadrupole to select and fragment the first precursor ion in the first quadrupole Q0 ion guide and to produce the second precursor ion in the first quadrupole Q0 ion guide, wherein the second precursor ion is a fragment ion of the first precursor ion using the processor, wherein the mass spectrometer includes an ion source that provides the continuous beam of ions and the first quadrupole Q0 ion guide that receives the continuous beam of ions and is adapted to apply dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions;

mass selecting the second precursor ion in a second quadrupole Q1;

accelerating the second precursor ion to a third quadrupole Q2 for high energy collision induced dissociation (CID); and

removing ions in a region of the second precursor ion in the first quadrupole Q0 ion guide before selecting and fragmenting the first precursor ion in the first quadrupole Q0 ion guide using the processor.

12. The method of claim 11 , wherein the first quadrupole Q0 ion guide applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions by applying the first dipole excitation between pairs of rods.

13. The method of claim 11 , wherein the first quadrupole Q0 ion guide further includes auxiliary electrodes placed between rods of the first quadrupole Q0 ion guide.

14. The method of claim 13 , wherein the first quadrupole Q0 ion guide applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions by applying the first dipole excitation between pairs of the auxiliary electrodes.

15. The method of claim 13 , wherein the removing step is performed by

calculating one or more second excitation parameters that define a second dipole excitation that removes ions at a location of the second precursor ion, and

applying the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions before the first dipole excitation by additionally sending a second set of data including the second excitation parameters to the mass spectrometer so that the first quadrupole Q0 ion guide applies the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions before the first quadrupole Q0 ion guide applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions while passing through the first quadrupole Q0 ion guide.

16. The method of claim 15 , wherein the auxiliary electrodes placed between rods of the first quadrupole Q0 ion guide are further segmented into a first set of electrodes that receive the continuous beam of ions from the ion source and a second set of electrodes located in series along the axis of the first quadrupole Q0 ion guide.

17. The method of claim 16 , wherein applying the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions before the first dipole excitation comprises

sending the second data set to the mass spectrometer using the processor so that the first quadrupole Q0 ion guide applies the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the first set of electrodes using the second excitation parameters and the first quadrupole Q0 ion guide applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the second set of electrodes using the first excitation parameters.

18. The method of claim 15 , wherein the first quadrupole Q0 ion guide further includes entrance electrodes placed at an entrance end of the first quadrupole Q0 ion guide and an exit lens at an exit end of the first quadrupole Q0 ion guide.

19. The method of claim 18 , wherein applying the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions before the first dipole excitation comprises sending the second data set to the mass spectrometer using the processor so that the mass spectrometer

traps ions in the first quadrupole Q0 ion guide by applying a voltage potential on the entrance electrodes and the exit lens,

applies the second dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the trapped ions in the first quadrupole Q0 ion guide to remove ions in a region of the second precursor ion,

applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the trapped ions in the first quadrupole Q0 ion guide to select and fragment the first precursor ion, and

lowers the voltage potential on the exit lens to transmit the trapped ions to the second quadrupole Q1.

20. 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 selecting and fragmenting a first precursor ion in a mass spectrometry/mass spectrometry/mass spectrometry (MS 3 ) experiment, 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;

calculating one or more first excitation parameters that define a first dipole excitation that selects a first precursor ion and fragments the first precursor ion to produce a second precursor ion using the analysis module;

applying the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions by sending a first set of data including the first excitation parameters to a mass spectrometer so that a first quadrupole Q0 ion guide applies the first dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to select and fragment the first precursor ion in the first quadrupole and to produce the second precursor ion in the first quadrupole Q0 ion guide, wherein the second precursor ion is a fragment ion of the first precursor ion using the control module, wherein the mass spectrometer includes an ion source that provides the continuous beam of ions and the first quadrupole Q0 ion guide that receives the continuous beam of ions and is adapted to apply dipole excitation between rods or electrodes in the first quadrupole Q0 ion guide to excite the continuous beam of ions while passing through the first quadrupole Q0 ion guide;

mass selecting the second precursor ion in a second quadrupole Q1;

accelerating the second precursor ion to a third quadrupole Q2 for high energy collision induced dissociation (CID); and

removing ions in a region of the second precursor ion in the first quadrupole Q0 ion guide before selecting and fragmenting the first precursor ion in the first quadrupole Q0 ion guide.