Digital waveform manipulations to produce MS

1. A method of using digital waveform manipulation for selectively exciting, trapping and/or ejecting a selected ion or a range of ions in a linear ion guide, comprising:

applying pairs of digital waveforms having desired duty cycles and frequencies to configured electrodes of the linear ion guide so as to establish mass stability x-y boundary conditions for the selected ion or range of ions;

phase shifting the applied pairs of digital waveforms to provide waveform periods t 1 , t 2 and t 3 ; and

manipulating the waveform periods of the applied pairs of digital waveforms, wherein a positive potential for the t 2 portion of the waveform periods provides for an axial ejection field for the selected ion or the range of ions and a negative potential for the t 2 portion of the waveform periods provides for an axial trapping field for the selected ion or range of ions.

2. A method of using digital waveform manipulation as in claim 1 , wherein providing for a smaller difference between the t 1 and t 3 portions of the waveform periods enables a greater range of ions that can be trapped.

3. A method of using digital waveform manipulation as in claim 1 , wherein manipulating the waveforms further comprises:

switching frequencies to provide frequency hopping of the applied waveforms and/or switching the duty cycle of the applied waveforms, wherein frequency hopping and/or switching the duty cycle changes the stability boundary conditions for the selected ion or range of ions.

4. A method of using digital waveform manipulation as in claim 3 , wherein the frequency hopping further comprises:

applying the hopping frequency in a first manner so as to enable the selected ion or the range of ions to be moved into an unstable mass boundary region to energetically excite the selected ion or the range of ions;

applying the hopping frequency in a second manner so as to enable the selected ion or the range of ions to be moved back into a stable mass stability boundary wherein the energetically excited ions can undergo collisions to induce dissociation.

5. A method of using digital waveform manipulation as in claim 4 , wherein a frequency utilized for the frequency hopping is applied for a controlled number of one or more cycles before moving back to a predetermined stable frequency.

6. A method of using digital waveform manipulation as in claim 3 , wherein switching the duty cycle of the applied waveforms further comprises:

providing a frequency and a first duty cycle so that selected ion or the range of ions are in a stable mass region;

switching to a second duty cycle but keeping the frequency constant so as to induce the selected ion or the range of ions to no longer be stable;

applying the switched second duty cycle waveform for a controlled number of one or more cycles; and

switching back to the first duty cycle so as to enable translational excitation to induce dissociation of the selected ion or the range of ions.

7. A method of using digital waveform manipulation as in claim 6 , further comprising:

switching the duty cycle to the second duty cycle so as to introduce a high mass cutoff and a desired range of stable m/z;

manipulating the applied frequency to place the ions just inside a stable boundary region; and

maintaining the manipulated applied frequency for a fixed time period to enable the selected ion or range of ions to undergo disposed buffer gas collisions within the linear ion guide so as to increase their internal energy until they dissociate.

8. A method of using digital waveform manipulation as in claim 7 , wherein the manipulated applied frequency can be applied for the fixed time period of up to hundreds of milliseconds without loss of the precursor ions provided by the selected ion or the range of ions.

9. A method of using digital waveform manipulation as in claim 1 , wherein during the t 1 and t 3 portions of the waveform periods, radial trapping is provided and during the t 2 portion of the waveform periods, a resultant potential creates an axial force near end electrodes of the linear ion guide.

10. A method of using digital waveform manipulation as in claim 1 , wherein desired one or more ions resultant from the linear ion guide can be followed by controlled ion injection into a time-of flight (TOF) instrument for resolved mass analysis.

11. A method of using digital waveform manipulation as in claim 10 , wherein the TOF configured with the linear ion guide provides a sampling duty cycle of about 1.

12. A method of using digital waveform manipulation as in claim 1 , wherein the applied pairs of digital waveforms are provided with up to 48 bit of direct digital synthesis for trapping frequency control.

13. A method of using digital waveform manipulation as in claim 1 , wherein the linear ion guide comprises a linear ion guide selected from: a quadrupole, a hexapole, an octupole, and a decapole.