WO2012167125A1

WO2012167125A1 - Ion traps and methods of use thereof

Info

Publication number: WO2012167125A1
Application number: PCT/US2012/040519
Authority: WO
Inventors: Zheng Ouyang; Wei Xu; Linfan LI
Original assignee: Purdue Research Foundation
Current assignee: Purdue Research Foundation
Priority date: 2011-06-03
Filing date: 2012-06-01
Publication date: 2012-12-06
Anticipated expiration: 2013-12-03

Abstract

The invention generally relates to ion traps and methods of use thereof. In certain embodiments, the invention provides an ion trap that includes at least one substantially square ring electrode and a plurality of cross end electrodes.

Description

ION TRAPS AND METHODS OF USE THEREOF

Related Application

The present application claims the benefit of and priority to U.S. provisional application serial number 61/492,942, filed June 3, 2011, the content of which is incorporated by reference herein in its entirety.

Government Support

This invention was made with U.S. government support under Contract Number 0847205; awarded by the National Science Foundation. The U.S. government has certain rights in the invention.

Field of the Invention

The invention generally relates to ion traps and methods of use thereof.

Background

A quadrupole ion trap is widely used for ion storage and mass analysis in mass spectrometry systems (March, R. E.; Todd, J. F. J., Quadrupole Ion Trap Mass Spectrometry. 2nd edition ed.; John Wiley & Sons Inc.: Hoboken, New Jersey, 2005). The original 3D ion trap developed by Paul is composed of a ring electrode and 2 end cap electrodes, originally of hyperbolic shapes (Wolfgang, P.; Steinwedel, H., Ein neues

Massenspektrometer ohne Magnetfeld. RZeitschrift fiir Naturforschung A 1953, 8, (7), 448-450). The radio frequency (RF) signal is applied on the ring electrode and ions are trapped in the 3D RF trapping field. The 2D (linear) ion trap has two pairs of RF electrodes elongated in the z direction and two DC end electrodes. Ions are trapped by the RF electric field in the x-y plane and by the DC electric field in the z direction. Electrodes of both hyperbolic and round shapes have been used for linear ion traps (Schwartz, J. C;

Senko, M. W; Syka, J. E. P., A two-dimensional quadrupole ion trap mass spectrometer. Journal of the American Society for Mass Spectrometry 2002, 13, (6), 659-669; Schwartz, J. C; Senko, M. W. Two-dimensional quadrupole ion trap operated as a mass spectrometer. 2004, US patent 6797950; Hager, J. W In Mass spectrometry using a linear RF quadrupole ion trap with axial ion ejection, 46th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, FL„ 31 May-4 June, 1998; Orlando, FL„ 1998; and Hager, J. W, A new linear ion trap mass spectrometer. Rapid Communications in Mass Spectrometry 2002, 16, (6), 512-526.) In comparison with 3D ion traps, linear ion traps have enlarged trapping capacity but higher requirements to the geometry precisions. Ion traps of toroidal geometry have also been developed to allow enlarged trapping capacity (Lammert, S. A.; Plass, W. R.; Thompson, C. V.; Wise, M. B., Design, optimization and initial performance of a toroidal rf ion trap mass spectrometer. International Journal of Mass Spectrometry 2001, 212, (1-3), 25-40).

The 3D and linear ion traps with simple geometries have been developed using flat electrodes, including 3D cylindrical ion trap (CIT; Langmuir, D. B.; Langmuir, R. V.;

Shelton, H.; Wuerker, R. F. Containment device. 1962, United States Patent: 3065640) and 2D rectilinear ion trap (Ouyang, Z.; Wu, G; Song, Y.; Li, H.; Plass, W. R.; Cooks, R. G, Rectilinear Ion Trap: Concepts, Calculations, and Analytical Performance of a New Mass Analyzer. Anal. Chem. 2004, 76, (16), 4595-4605; and Cooks, G. R.; Ouyang, Z.

Rectilinear Ion Trap and Mass Analyzer System and Method, U.S. patent number 6,838,666, 2005). Methods of using array of electrodes to vary the electric fields inside ion traps have also been developed (Austin, D. E.; Wang, M.; Tolley, S. E.; Maas, J. D.; Hawkins, A. R.; Rockwood, A. L.; Tolley, H. D.; Lee, E. D.; Lee, M. L., Halo Ion Trap Mass

Spectrometer. Anal. Chem. 2007, 79, (7), 2927-2932; Zhang, Z.; Peng, Y; Hansen, B. J.; Miller, I. W; Wang, M.; Lee, M. L.; Hawkins, A. R.; Austin, D. E., Paul Trap Mass

Analyzer Consisting of Opposing Microfabricated Electrode Plates. Analytical Chemistry 2009, 81, (13), 5241-5248; Ding, C; Ding, L. ION TRAP ARRAY. International

Application No.: PCT/CN2007/001214, 2007; and Li, X.; Jiang, G; Luo, C; Xu, F; Wang, Y; Ding, L.; Ding, C.-F, Ion Trap Array Mass Analyzer: Structure and Performance.

Analytical Chemistry 2009, 81, (12), 4840-4846). Sizes of ion traps have also been miniaturized to lower the requirement of RF voltage and power to cover the same mass-to-charge (m/z) range (Badman, E. R.; Cooks, R. G, Miniature Mass Analyzers.

Journal of Mass Spectrometry 2000, 35, 659-671; Blain, M. G; Riter, L. S.; Cruz, D.; Austin, D. E.; Wu, G; Plass, W R.; Cooks, R. G, Towards the hand-held mass spectrometer: design considerations, simulation, and fabrication of micrometer-scaled cylindrical ion traps. International Journal of Mass Spectrometry 2004, 236, (1-3), 91-104; Chaudhary, A.; van Amerom, F. H. W; Short, R. T; Bhansali, S., Fabrication and testing of a miniature cylindrical ion trap mass spectrometer constructed from low temperature co-fired ceramics. International Journal of Mass Spectrometry 2006, 251, (1), 32-39; and Lammert, S. A.; Rockwood, A. A.; Wang, M.; Lee, M. L.; Lee, E. D.; Tolley, S. E.; Oliphant, J. R.; Jones, J. L.; Waite, R. W, Miniature Toroidal Radio Frequency Ion Trap Mass Analyzer. Journal of the American Society for Mass Spectrometry 2006, 17, (7), 916-922).

Ion trap arrays have been developed to enlarge the ion trapping capacity or to allow multiplex analysis (Cooks, G. R.; Ouyang, Z. Rectilinear Ion Trap and Mass Analyzer System and Method, U.S. patent number 6,838,666, 2005; Ding, C; Ding, L. ION TRAP ARRAY. International Application No.: PCT/CN2007/001214, 2007; Li, X.; Jiang, G; Luo, C; Xu, F; Wang, Y; Ding, L.; Ding, C.-F, Ion Trap Array Mass Analyzer: Structure and Performance. Analytical Chemistry 2009, 81, (12), 4840-4846; Blain, M. G; Riter, L. S.; Cruz, D.; Austin, D. E.; Wu, G; Plass, W. R.; Cooks, R. G, Towards the hand-held mass spectrometer: design considerations, simulation, and fabrication of micrometer-scaled cylindrical ion traps. International Journal of Mass Spectrometry 2004, 236, (1-3), 91-104; Badman, E. R.; Cooks, R. G, A Parallel Miniature Cylindrical Ion Trap Array. Anal. Chem. 2000, 72, (14), 3291-3297; Fico, M.; Maas, J. D.; Smith, S. A.; Costa, A. B.; Ouyang, Z.; Chappell, W. J.; Cooks, R. G, Circular arrays of polymer-based miniature rectilinear ion traps. The Analyst 2009, 134, (7), 1338-1347; Misharin, A. S.; Laughlin, B. C; Vilkov, A.; Takats, Z.; Ouyang, Z.; Cooks, R. G, High- Throughput Mass Spectrometer Using

Atmospheric Pressure Ionization and a Cylindrical Ion Trap Array. Anal. Chem. 2005, 77, (2), 459-470; and Tabert, A. M.; Griep-Raming, J.; Guymon, A. J.; Cooks, R. G,

High- Throughput Miniature Cylindrical Ion Trap Array Mass Spectrometer. Analytical Chemistry 2003, 75, (21), 5656-5664). 2D arrays of CITs and RITs have been developed and experimentally characterized (Badman, E. R.; Cooks, R. G, A Parallel Miniature Cylindrical Ion Trap Array. Anal. Chem. 2000, 72, (14), 3291-3297; and Maas, J. D.;

Hendricks, P. I.; Ouyang, Z.; Cooks, R. G; Chappell, W. J., Miniature Monolithic Rectilinear Ion Trap Arrays by Stereolithography on Printed Circuit Board. Journal of Microelectromechanical Systems 2010, 19, (4), 951-960). Formation of multiple trapping areas using electrode array has also been implemented (Ding, C; Ding, L. ION TRAP ARRAY. International Application No.: PCT/CN2007/001214, 2007; and Li, X.; Jiang, G; Luo, C; Xu, R; Wang, Y; Ding, L.; Ding, C.-F., Ion Trap Array Mass Analyzer: Structure and Performance. Analytical Chemistry 2009, 81, (12), 4840-4846). Due to the constraints in the fabrication and implementation, ion trap arrays are typically designed in ID or 2D configuration. Summary

The invention provides ion traps that have new geometries compared to previously known ion traps. In certain aspects, the invention provides an ion trap including at least one substantially square ring electrode and a plurality of cross end electrodes. In certain embodiments, the cross end electrodes are centered with respect to the square ring electrode. In alternative embodiments, the cross end electrodes are off-set from a center of the square ring electrode.

In other aspects, the invention provides a multi-dimensional ion trap, in which each trap in each layer of traps includes at least one substantially square ring electrode and a plurality of cross end electrodes. In certain embodiments, each layer includes a plurality of traps. In certain embodiments, at least two of the traps in a layer have the same configuration. In other embodiments, all the traps in a layer have the same configuration. In alternative embodiments, at least two of the traps in a layer have different configurations. In other embodiments, at least two of the layers have the same configuration. In certain embodiments, at least two of the layers have different configurations.

Another aspect of the invention provides a mass spectrometer that includes an ion trap having at least one substantially square ring electrode and a plurality of cross end electrodes. Another aspect of the invention provides a linear ion trap including a set of quadrupole rods, and a plurality of cross end electrodes. In certain embodiments, the quadrupole rods are arranged in a rectangular configuration and the cross end electrodes are centered with respect to the quadrupole rods. In other embodiments, the quadrupole rods are arranged in a rectangular configuration and the cross end electrodes are off-set from a center of the square ring electrode.

Another aspect of the invention provides a method of analyzing a sample that involves ionizing a sample to produce sample ions, transferring the sample ions into an ion trap, in which the ion trap includes at least one substantially square ring electrode and a plurality of cross end electrodes, and analyzing the transferred ions.

Another aspect of the invention provides a method of analyzing a sample that involves ionizing a sample to produce sample ions, transferring the sample ions into a multi-dimensional ion trap, in which each trap in each layer of traps includes at least one substantially square ring electrode and a plurality of cross end electrodes, and analyzing the transferred ions. In certain embodiments, analyzing involves identifying the transferred ions in each layer by applying supplementary AC power to set different ion ejection conditions. In other embodiments, analyzing includes performing ion reactions within the trap.

In certain embodiments, the ions are transferred between the different layers of the multi-dimensional ion trap. Transferring the ions between the different layers of the multi-dimensional ion trap may be accomplished by gas flow; DC pulses, and/or AC waveform excitation.

In certain embodiments, methods of the invention further involve sorting the ions. In certain embodiments, the ions are sorted during ion transfer. In certain embodiments, sorting is accomplished by varying ion trapping conditions within the layers of the trap.

Brief Description of the Drawings

Figure 1. Geometry of the 3D ion trap and using it to construct a single trapping layer, (a) top view of the trapping layer; (b) 3D view of the trapping layer; (c) simulated electric field in a single trap.

Figure 2. 3D array of ion traps, (a) schematic drawing of the 3D array of ion traps with 3 trapping layers; (b) a fabricated 3D array of ion traps with 4 trapping layers and 121 individual ion traps in each trapping layer.

Figure 3. Geometry optimization of a single 3D ion trap, (a) geometry of a symmetric design and its performances: mass analysis (b) and ion ejection efficiency (c). (d) geometry of an asymmetric design and its performances: mass analysis (e) and ion ejection efficiency (f).

Figure 4. (a) Instrument setup for testing of the 3D array of ion traps, (b) Simulated supersonic expansion at the exit of the discontinuous atmospheric pressure interface

(DAPI). (c) Ion distributions in the x-y plane of the 3D array of ion traps as a function of the distance between the capillary and the 3D array (d).

Figure 5. Mass spectrum of DEET using atmosphere pressure chemical ionization (APCI) method (a) and MRFA using nano-Electrospray (Nano-ESI) ionization method (b).

Figures 6a-c. Ion distribution manipulation by introducing ions from different locations of the 3D array of ion traps.

Figure 7. Differentiating ions with the same m/z but trapped in different trapping layers of the 3D array of ion traps, (a) Boundary ejection in trapping layer 1 and 2, and the resulted mass spectrum of DEET (b). (c) Boundary ejection in trapping layer 1 and resonance ejection in trapping layer 2, and the resulted mass spectrum of DEET (d).

Figure 8. Ion transfer between layers. (a,b) Ions trapped in layer 2 were ejected using a broadband waveform. (c,d) A portion of the ions trapped in layer 1 were transferred to layer 2.

Figures 9a-c. Ion sorting during the ion introduction period.

Figure 10. Ion molecule reaction inside the 3D array of ion traps, demonstrated using

/7-bromobenzoic acid and diethylmethoxyborane. (a) Reaction pathway, (b) Protonated /7-bromobenzoic acid isolated in the 3D array of ion traps, (c) Mass spectrum after the ion molecule reaction.

Figure 11. (a) The geometry of the linear ion trap, (b) ID array of the linear ion trap.

Figure 12. (a) The 3D array of ion traps with 2 trapping layers; (b) resonance ejection of imatinib ions (m/z 494); collision induced dissociation with AC resonance excitation of 86 kHz at (c) 380 mV and (d) 450 mV. RF frequence of 826 kHz, resonance ejection with AC of 335 kHz and 480 mV on both layers.

Figure 13. (a) The 3D array of ion traps with 3 trapping layers; (b) resonance ejection of imatinib (m/z 494); (c) collision induced dissociation with AC resonance excitation of 99 kHz at 800 mV.

Figure 14. (a) The 3D array of ion traps with 3 trapping layers (independent AC associated to electrode plate 7 for resonance excitation and resonance ejection of layer 3); (b) resonance ejection of imatinib ions (m/z 494); collision induced dissociation with 99 kHz AC resonance excitation at (c) 900 mV and (d) 2500 mV.

Figure 15. (a) The 3D array of ion traps with 3 trapping layers (independent AC associated to electrode plate 5 for resonance excitation and resonance ejection of both layer 2 and layer 3); (b) resonance ejection of imatinib ions (m/z 494); collision induced dissociation with 99 kHz AC resonance excitation at (c) 400 mV and (d) 1000 mV.

Figure 16. (a) The 3D array of ion traps with 3 trapping layers (independent AC associated to electrode plate 7 for resonance excitation and resonance ejection of layer 3); resonance ejection of daughter ions (m/z 394) of imatinib (m/z 494) at AC frequency of 225 kHz at (b) 800 mV and (c) 100 mV after the collision induced dissociation with 99 kHz AC resonance excitation at 2500 mV.

Detailed Description

The invention generally relates to ion traps and methods of use thereof. Figure 1 shows a schematic drawing of one layer of the ion trap array (Figure la and b) and the simulated electric field of a single trap unit. The RF is applied between the square ring electrode and the cross electrodes to trap the ions. The mechanic drawing of an assembly of 3 layers of ion trap arrays with 3 electron multipliers are shown in Figure 2a. A photo of a fabricated 3D array of 484 ion traps, 4 layers with 121 traps on each layer, is shown in Figure 2b. Each layer of ion traps is composed of three layers of electrodes, with one ring and two end electrodes for each trap. Each electrode layer is a mesh with square holes of 7.5x7.5 mm and 0.25 wire width. The centers of the square holes on the end electrode plates are aligned but the there is an offset (3.75mm in the case shown in Figure 1) in both x and y directions between the end electrodes and the ring electrode. Each ion trap unit have two cross end electrodes and one square ring electrode. A single -phase RF signal (798 kHz) was applied on all the RF plates, and AC or DC signals were applied on the ground plates to facilitate ion transfer between layers or ion ejection for detection.

This design allows simple geometry of ion traps and simple configuration for the trap array with ease of fabrication. Each trap in the array is highly transparent, which would allow efficient ion introduction into the traps from any direction, efficient ion transfer between traps, and introduction of laser beams into an inner trap unit in the 3D array. 3D array with a much large number of ion traps can also be easily fabricated.

The design of the ion trap was assisted with numerical simulation, and the optimization was made with a balance among the simplicity of the trap array, trapping efficiency, inter-trap ion transfer efficiency, and mass selectivity or mass resolution. The first design (Figure 3 a) has a symmetric geometry, where the cross end electrode (blue cross) is placed at the center of the ring electrode (brown square) in the x-y plane, with a 3.75 mm displacement in the z direction (Figure 1). The second design (Figure 3b) has a similar geometry but with the end cap offset from the center of the ring electrode. The first design has a better mass analysis capability (Figure 3b) but lower ion ejection efficiency (Figure 3c). By offsetting the end electrodes in the second design (Figure 3d), the ion ejection efficiency was improved (Figure 3f) with minimum effect on the mass analysis capability (Figure 3e).

The 3D array of ion traps was characterized (Figure 4a) using a mass spectrometer with multiple discontinuous atmospheric pressure (DAPI) interfaces (Ouyang, Z.; Gao, L.; Cooks, R. G. Discontinuous Atmospheric Pressure Interface. US Pat. App 12622776, 2009; Gao, L.; Cooks, R. G; Ouyang, Z., Breaking the Pumping Speed Barrier in Mass

Spectrometry: Discontinuous Atmospheric Pressure Interface. Anal. Chem. 2008, 80, (11), 4026-4032; and Xu, W.; Charipar, N.; Kirleis, M. A.; Xia, Y; Ouyang, Z., Study of

Discontinuous Atmospheric Pressure Interfaces for Mass Spectrometry Instrumentation Development. Analytical Chemistry 2010, 82, (15), 6584-6592). Ions were injected into the vacuum chamber through capillaries. There is a supersonic expansion effect due to the high pressure difference between inside and outside of the vacuum chamber (Figure 4b). By tuning the distance between the capillary and the ion trap array (d depicted in Figure 4), the distribution of the trapped ions inside the 3D array of ion traps can be modified. An ion detector array was also assembled to measure the ion distribution inside the 3D array of ion traps. As shown in Figure 4c, the ion distribution will vary when changing the distance, d. Results showed that ions introduced through DAPI were spread in a relatively large space due to the supersonic gas expansion but could be captured and trapped by the 3D array of ion traps with an enlarged coverage of trapping space.

Mass selective instability scan was performed with a dipolar resonance ejection at

398 kHz and an RF scan rate of 3600 Da/s. In the mass spectrum in Figure 5a, a peak width at half maximum of 0.22Da was observed for the protonated molecular ion (m/z 192) of DEET. The Figure 5b shows the mass spectrum of a peptide, MRFA (Met-Arg-Phe-Ala) using Nano-ESI ionization method. Mass analysis could also be performed using boundary ejection, where the RF voltage was scanned to eject ions out of the ion trap without supplementary AC signals.

Ions generated using different ionization methods can be introduced simultaneously into the 3D array and trapped in the same or different locations. As shown in Figure 6a, protonated cocaine ions by nano-ESI were introduced toward the center of the x-y plane of the trap array and were mainly trapped in the center of the 3D array; protonated DEET ions were introduced toward a corner of the trap array and were trapped in the corner region. The simulated data are shown in Figure 6b while the experimentally characterization is shown in Figure 6c.

The ion distribution on the cross-section (the x-y plane) of the 3D array of ion traps can be monitored by a detector array. Ion distribution in the z direction could be characterized using the combination of DC pulses and waveform excitations. As shown in Figure 7c, when every trapping layer is experiencing the same operating conditions (such as the same RF signal, AC and DC signals, dimensions, etc.), the mass spectrum recorded shows peaks representing ions trapped in the whole device. However, ions with the same m/z value but trapped in different trapping layers are not differentiated. Supplementary AC or DC signals can be applied differently to each trap layer to generate different peaks for the ions of the same m/z value but from different layers. For example, boundary ejection was applied on trap layer 1 and resonance ejection using a monopolar AC was applied on trap layer 2 (Figure 7c). With this method, the mass spectrum will have two sets of peaks (Figure 7d). The peaks labeled with LI and L2 attribute to the ions trapped in layer 1 and 2, respectively.

Ion transfer between sections of the 3D array of ion traps could be facilitated or hindered by pulsed gas flow, DC field and/or AC excitations. As an example, DEET ions were first introduced into the ion trap array. A broadband SWIFT waveform (stored waveform inverse Fourier transform; Guan, S.; Marshall, A. G, Stored waveform inverse Fourier transform (SWIFT) ion excitation in trapped-ion mass spectometry: Theory and applications. International Journal of Mass Spectrometry and Ion Processes 1996, 157-158, 5-37) was then applied on the second trapping layer to eject all ions in layer 2 (Figure 8a). Ion peaks from layer 2 will not be present in the mass spectrum recorded with RF scan (Figure 8b). If a 1 ms 110 V DC pulse was applied on the front end electrode of trapping layer 1 and an 1 ms 30 V DC pulse on the back electrode of trapping layer 2 (Figure 8c), a portion of the ions trapped in layer 1 were transferred to layer 2. An efficiency of -30% was obtained for transferring DEET protonated dimmer ions m/z 383 between layers in this particular case (Figure 8).

Different operating conditions at different regions within the 3D array of ion traps can be achieved using various methods, such as different ion trap dimensions, different RF signals, and different supplementary AC and DC signals. A 3D array of ion traps with different ion trap dimensions for layer 1 and 2 was demonstrated as shown in Figure 9. In trap layer 2, each trapping cell has the same dimension as described earlier (Figure 1). For trap layer 1, the electrode width was increased to 2.25 mm and the spacing between ring and end electrode layers was also decreased to2.75 mm (Figure 9a). When applying the same RF voltage onto the ring electrodes, the traps in layer 1 and 2 operate at different conditions (q values) and have different trapping well depth for the same ions (Figure 9b). The RF voltage can be optimized to allow the sorting of ions based on their m/z ratios during the ion introduction process. At a lower RF voltage, both monomer and dimmer ions of DEET can be trapped in layer 1 while none of them trapped in layer 2 (Figure 9c top panel). When the trapping voltage was increased, DEET protonated monomer ions could only be trapped in layer 2, while dimmer ions could only be observed in layer 1. When the RF voltage was further increased, both monomer and dimmer ions of DEET can be trapped in layer 2 but only dimmer ions were observed from layer 1. Gas-phase ion reaction could also be performed inside the 3D array of ion traps. As an example, the protonated molecular ion of p-bromobenzoic acid (m/z 202) was trapped and isolated in the 3D array of ion traps, and then reacted with the neutral diethylmethoxyborane molecules introduced as a reactant. After some (10ms to 10s) reaction time, the reaction product ion m/z 270 was observed (Figure 10).

A linear ion trap was also proposed and depicted in Figure 11a. The linear ion trap consisted of four wire electrodes and two end electrodes. To operate the ion trap, a single phase RF signal can be applied on one set of the wire electrodes (red or blue set).

Alternatively, a dual phase RF signal can be applied, with one of the RF signal applied on the red set of wire electrodes and the other (opposite phase) RF signal applied on the blue set of wire electrodes. A set of DC signal can be applied on the end electrodes to trap ions in the z direction. Similarly, supplementary DC and AC signals could be applied on electrodes to manipulate ion distributions and motions. Figure lib shows a IDarray of the linear ion trap. The 2D and 3D arrays of the linear ion trap can also be fabricated in a similar fashion by sharing RF electrode layers and end electrode layers. Ion transfer and distribution manipulation could also be performed using the methods proposed earlier.

Incorporation by Reference

References and citations to other documents, such as patents, patent applications, patent publications, journals, books, papers, web contents, have been made throughout this disclosure. All such documents are hereby incorporated herein by reference in their entirety for all purposes.

Equivalents

The invention may be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting on the invention described herein. EXAMPLES

Example 1 : MS/MS in a two - layer trap array

The ions were trapped using an RF at 826 kHz. The excitation AC at 86 kHz was applied between the endcap plates as shown in Figure 12a. The precursor ion of protonated imatinib m/z 494 (Figure 12b) was fragmented to generated m/z 394. When the excitation amplitude increased to 450 mV, the precursor ions were completely fragmented. The ions in both layers were scanned with a resonance ejection with an AC at 335 kHz and 480 mV.

Example 2: MS/MS in a three - layer trap array

The ions were trapped using an RF at 758 kHz. The excitation AC at 99 kHz was applied between the endcap plates as shown in Figure 13 a. The precursor ion of protonated imatinib m/z 494 (Figure 13b) was fragmented to generate m/z 394. The ions in three layers were scan with a resonance ejection with an AC at 225 kHz and 900 mV.

Example 3: MS/MS in a selected layer of a three - layer trap array

The ions were trapped using an RF at 758 kHz. The excitation AC at 99 kHz was applied at the seventh endcap plate as shown in Figure 14a. The precursor ion of protonated imatinib m/z 494 (Figure 14b) was fragmented to generate m/z 394. When the excitation amplitude increased to 2500 mV, the precursor ions were completely fragmented. The ions in the third layer were scanned with a resonance ejection with an AC at 225 kHz and 800 mV. The ions in the first and second layers were scanned with boundary ejection.

Example 4: MS/MS in the second and third layer

The ions were trapped using an RF at 758 kHz. The excitation AC at 99 kHz was applied at the fifth endcap plate as shown in Figure 15 a. The precursor ion of protonated imatinib m/z 494 (Figure 15b) was fragmented to m/z 394. When the excitation amplitude increased to 1000 mV, the precursor ions were completely fragmented. The ions in the second and third layer were scanned with a resonance ejection with an AC at 225 kHz and 500 mV. The ions in the first layer were scanned with boundary ejection.

Example 5: Adjustment of the peak width

MS/MS was performed in the third layer of a three - layer trap array. The amplitude of the AC for resonance ejection was varied and peaks of narrower width were observed at 100 mV in comparison with 800 mV.

The ions were trapped using an RF at 758 kHz. The excitation AC at 99 kHz was applied at the seventh endcap plate as shown in Figure 16a. When the excitation amplitude increased to 2500 mV, the precursor ions (protonated imatinib m/z 494) were completely fragmented. The ions in the third layer were scanned with a resonance ejection with an AC of 800 mV 100 mV at 225 kHz.

Claims

What is claimed is:

1. An ion trap comprising at least one substantially square ring electrode and a plurality of cross end electrodes.

2. The trap according to claim 1, wherein the cross end electrodes are centered with respect to the square ring electrode.

3. The trap according to claim 1, wherein the cross end electrodes are off-set from a center of the square ring electrode.

4. A multi-dimensional ion trap, wherein each trap in each layer of traps comprises at least one substantially square ring electrode and a plurality of cross end electrodes.

5. The trap according to claim 4, wherein each layer comprises a plurality of traps.

7. The trap according to claim 5, wherein at least two of the traps in a layer have the same configuration.

8. The trap according to claim 5, wherein all the traps in a layer have the same

configuration.

9. The trap according to claim 5, wherein at least two of the traps in a layer have different configurations.

10. The trap according to claim 4, wherein at least two of the layers have the same configuration.

11. The trap according to claim 4, wherein at least two of the layers have different configurations.

12. The trap according to claim 4, wherein at least one of the traps is configured such that the cross end electrodes are centered with respect to the square ring electrode.

13. The trap according to claim 4, wherein at least one of the traps is configured such that the cross end electrodes are off-set from a center of the square ring electrode.

14. A mass spectrometer, the mass spectrometer comprising an ion trap that comprises at least one substantially square ring electrode and a plurality of cross end electrodes.

15. A linear ion trap comprising: a set of quadrupole rods; and a plurality of cross end electrodes.

16. The trap according to claim 15, wherein the quadrupole rods are arranged in a rectangular configuration and the cross end electrodes are centered with respect to the quadrupole rods.

17. The trap according to claim 15, wherein the quadrupole rods are arranged in a rectangular configuration and the cross end electrodes are off-set from a center of the square ring electrode.

18. A method of analyzing a sample, the method comprising:

ionizing a sample to produce sample ions;

transferring the sample ions into an ion trap, wherein the ion trap comprises at least one substantially square ring electrode and a plurality of cross end electrodes; and

analyzing the transferred ions.

19. A method of analyzing a sample, the method comprising:

ionizing a sample to produce sample ions;

transferring the sample ions into a multi-dimensional ion trap, wherein each trap in each layer of traps comprise at least one substantially square ring electrode and a plurality of cross end electrodes; and

analyzing the transferred ions.

20. The method according to claim 19, wherein analyzing comprises identifying the transferred ions in each layer by applying supplementary AC power to set different ion ejection conditions.

21. The method according to claim 19, wherein the ions are transferred between the different layers of the multi-dimensional ion trap.

22. The method according to claim 21, wherein transferring the ions between the different layers of the multi-dimensional ion trap is accomplished by at least one mechanism selected from the group consisting of: gas flow; DC pulses, AC waveform excitation, and a combination thereof.

23. The method according to claim 19, further comprising sorting the ions.

24. The method according to claim 23, wherein the ions are sorted during ion transfer.

25. The method according to claim 23, wherein sorting is accomplished by varying ion trapping conditions within the layers of the trap.

26. The method according to claim 19, wherein analyzing comprises performing ion reactions within the trap.