Patent Publication Number: US-11651948-B2

Title: Systems and methods of operation of linear ion traps in dual balanced AC/unbalanced RF mode for 2D mass spectrometry

Description:
CROSS-REFERENCE TO RELATED APPLICATION 
     This application is a divisional under 35 U.S.C. § 121 and claims the priority benefit of co-pending U.S. patent application Ser. No. 16/552,614, filed Aug. 27, 2019. The disclosure of the foregoing application is incorporated herein by reference. 
    
    
     FIELD 
     The present disclosure generally relates to the field of mass spectrometry including system and method of operation of linear ion traps in dual balanced AC/unbalanced RF mode for 2D mass spectrometry. 
     INTRODUCTION 
     An ion trap as an analytical instrument can provide invaluable opportunities for use in data-independent analysis (DIA) due to its ability to maintain good ions&#39; m/z separation during scan-out under large ion loads in the ion trap. This can open opportunities for extended functionality for the ion trap, especially for a linear ion trap, beyond the routine analytical scan. This functionality can include post-ejection trapping, CID fragmentation and final mass analysis of fragments with a second mass analyzer. Key factors can include ensuring highly efficient trapping of injected ions and maintaining tight control of the kinetic energy of ejected ions. However, the optimal conditions for trapping injected ions may not correspond to the optimal conditions to maintain tight control over the kinetic energy of ejection ions. From the foregoing it will be appreciated that a need exists for improved operation of linear ion traps. 
     SUMMARY 
     In a first aspect, a mass selective ion trapping device can include a linear ion trap and an RF control circuitry. The linear ion trap can include a plurality of trap electrodes spaced apart from each other and surrounding a trap interior. The plurality of trap electrodes can include a first pair of trap electrodes and a second pair of trap electrodes. At least a first trap electrode of the first pair of trap electrodes can include a trap exit aperture. The trap electrodes can be configured for generating a quadrupolar trapping field in the trap interior and for mass selective ejection of ions from the trap interior. The RF control circuitry can be configured to apply a balanced AC voltage to the trap electrodes during a first period of time such that a first AC voltage applied to the first pair of trap electrodes is of opposite sign and of substantially the same magnitude to a second AC voltage to the second pair of trap electrodes; apply unbalanced RF voltage to the second pair of trap electrodes during a second period of time; ramp the balanced AC voltage down and the unbalanced RF voltage up during a transition period between the first period of time and the second period of time; and eject ions from the linear ion trap after the second period of time. 
     In various embodiments of the first aspect, the ions can enter the trap during the first period of time. 
     In various embodiments of the first aspect, a kinetic energy spread of ions before ejection from the linear ion trap can be less than about 5.0 eV, such as less than about 2.5 eV, such as less than about 0.5 eV, even less than about 0.2 eV. 
     In various embodiments of the first aspect, an electric field on a centerline of the linear ion trap can be near zero during the first period of time. 
     In various embodiments of the first aspect, the AC voltage can be in a frequency range of between about 100 kHz and about 600 kHz. 
     In various embodiments of the first aspect, the AC voltage can be less than about 400 V 0-P , such as less than about 200 V 0-P . 
     In various embodiments of the first aspect, the RF voltage can be in a frequency range of between about 750 kHz and about 1500 kHz. 
     In various embodiments of the first aspect, during the transition period, a ramp down time for the AC voltage can be less than about 1.5 ms and a ramp up time for the RF voltage can be between about 0.8 ms and about 2.5 ms. 
     In a second aspect, a method for identifying components of a sample can include supplying ions to a mass selective linear ion trap, the ion trap including a plurality of trap electrodes spaced apart from each other and surrounding a trap interior, the trap electrodes configured for generating a quadrupolar trapping field in the trap interior; trapping the ions within a balanced trapping field; transitioning between a balanced trapping field to an unbalanced trapping field; and maintaining the unbalanced trapping field while selectively ejecting ions from the trap interior based on their mass using an auxiliary RF voltage. 
     In various embodiments of the second aspect, a kinetic energy spread of ions before ejection from the linear ion trap can be less than about 5.0 eV, such as less than about 2.5 eV, such as less than about 0.5 eV, even less than about 0.2 eV. 
     In various embodiments of the second aspect, an electric field on a centerline of the linear ion trap can be near zero when trapping the ions within the balanced trapping field. 
     In various embodiments of the second aspect, the balanced trapping field can be generated using an AC voltage in a frequency range of between about 100 kHz and about 600 kHz. 
     In various embodiments of the second aspect, the balanced trapping field can be generated using an AC voltage of less than about 400 V 0-P , such as less than about 200 V 0-P . 
     In various embodiments of the second aspect, the unbalanced trapping field can be generated using an RF voltage in a frequency range of between about 750 kHz and about 1500 kHz. 
     In various embodiments of the second aspect, transitioning can include ramping down time the AC voltage over less than about 1.5 ms and ramping up the RF voltage over between about 0.8 ms and about 2.5 ms. 
     In a third aspect, a mass selective ion trapping device can include a linear ion trap and an RF control circuitry. The linear ion trap can include a plurality of trap electrodes spaced apart from each other and surrounding a trap interior. The plurality of trap electrodes can include a first pair of trap electrodes and a second pair of trap electrodes. At least a first trap electrode of the first pair of trap electrodes can include a trap exit comprising an aperture. The trap electrodes can be configured to generate a quadrupolar trapping field in the trap interior and for mass selective ejection of ions from the trap interior. The RF control circuitry can be configured to generate a first quadrupolar trapping field having a near zero electric field on the centerline of the linear ion trap using a AC voltage during injection of ions; generate a second quadupolar trapping field during ejection of ions from the trap using a RF voltage such that ions have a kinetic energy spread of less than about 5.0 eV before ejection from the linear ion trap; and transition between the AC voltage and the RF voltage by ramping down the AC voltage and ramping up the RF voltage after injection of the ions and before ejection of the ions. 
     In various embodiments of the third aspect, the RF voltage can be applied in an unbalanced mode such that an RF voltage applied to the second trap electrodes is greater than an RF voltage applied to the first trap electrodes. 
     In various embodiments of the third aspect, the RF voltage can be in a frequency range of between about 750 kHz and about 1500 kHz. 
     In various embodiments of the third aspect, the AC voltage can be applied in a balanced mode such that the first trap electrodes receive an AC voltage of equivalent magnitude but opposite sign to the AC voltage received by the second trap electrodes. 
     In various embodiments of the third aspect, the AC voltage can be in a frequency range of between about 100 kHz and about 600 kHz. 
     In various embodiments of the third aspect, the AC voltage can be less than about 400 V 0-P , such as less than about 200 V 0-P . 
     In various embodiments of the third aspect, during the transition period, a ramp down time for the AC voltage can be less than about 1.5 ms and a ramp up time for the RF voltage can be between about 0.8 ms and 2.5 ms. 
    
    
     
       DRAWINGS 
       For a more complete understanding of the principles disclosed herein, and the advantages thereof, reference is now made to the following descriptions taken in conjunction with the accompanying drawings, in which: 
         FIG.  1    is a block diagram of an exemplary mass spectrometry system, in accordance with various embodiments. 
         FIG.  2    is a perspective view illustrating the basic design of a two-dimensional linear ion trap, in accordance with various embodiments. 
         FIGS.  3 ,  4 , and  5    illustrate the electrical fields in a linear ion trap, in accordance with various embodiments. 
         FIG.  6    is a flow diagram illustrating an exemplary method for operating a linear ion trap, in accordance with various embodiments. 
         FIG.  7    is a timing diagram illustrating an exemplary voltage scheme applied to a linear ion trap, in accordance with various embodiments. 
         FIG.  8    is a diagram illustrating an exemplary voltage supply circuitry, in accordance with various embodiments. 
         FIG.  9    is a block diagram illustrating an exemplary data analysis system, in accordance with various embodiments. 
         FIGS.  10 A,  10 B,  11 A,  11 B,  12 A,  12 B,  13 A,  13 B,  14 A,  14 B,  15 A,  15 B  are graphics illustrating simulation results of ions after transitioning from balanced mode to unbalance mode and after cooling. 
         FIG.  16    is a graph illustrating the voltage needed in imbalanced mode as a function of q and ion mass. 
         FIG.  17    is a graph illustrating ion losses for low mass ions (400 amu) as a function of q. 
         FIGS.  18 A,  18 B,  19 A, and  19 B  are graphics illustrating simulation results showing ion containment during injection at various frequencies of the balanced AC voltage. 
     
    
    
     It is to be understood that the figures are not necessarily drawn to scale, nor are the objects in the figures necessarily drawn to scale in relationship to one another. The figures are depictions that are intended to bring clarity and understanding to various embodiments of apparatuses, systems, and methods disclosed herein. Wherever possible, the same reference numbers will be used throughout the drawings to refer to the same or like parts. Moreover, it should be appreciated that the drawings are not intended to limit the scope of the present teachings in any way. 
     DESCRIPTION OF VARIOUS EMBODIMENTS 
     Embodiments of systems and methods for ion separation are described herein. 
     The section headings used herein are for organizational purposes only and are not to be construed as limiting the described subject matter in any way. 
     In this detailed description of the various embodiments, for purposes of explanation, numerous specific details are set forth to provide a thorough understanding of the embodiments disclosed. One skilled in the art will appreciate, however, that these various embodiments may be practiced with or without these specific details. In other instances, structures and devices are shown in block diagram form. Furthermore, one skilled in the art can readily appreciate that the specific sequences in which methods are presented and performed are illustrative and it is contemplated that the sequences can be varied and still remain within the spirit and scope of the various embodiments disclosed herein. 
     All literature and similar materials cited in this application, including but not limited to, patents, patent applications, articles, books, treatises, and internet web pages are expressly incorporated by reference in their entirety for any purpose. Unless described otherwise, all technical and scientific terms used herein have a meaning as is commonly understood by one of ordinary skill in the art to which the various embodiments described herein belongs. 
     It will be appreciated that there is an implied “about” prior to the temperatures, concentrations, times, pressures, flow rates, cross-sectional areas, etc. discussed in the present teachings, such that slight and insubstantial deviations are within the scope of the present teachings. In this application, the use of the singular includes the plural unless specifically stated otherwise. Also, the use of “comprise”, “comprises”, “comprising”, “contain”, “contains”, “containing”, “include”, “includes”, and “including” are not intended to be limiting. It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the present teachings. 
     As used herein, “a” or “an” also may refer to “at least one” or “one or more.” Also, the use of “or” is inclusive, such that the phrase “A or B” is true when “A” is true, “B” is true, or both “A” and “B” are true. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. 
     A “system” sets forth a set of components, real or abstract, comprising a whole where each component interacts with or is related to at least one other component within the whole. 
     Mass Spectrometry Platforms 
     Various embodiments of mass spectrometry platform  100  can include components as displayed in the block diagram of  FIG.  1   . In various embodiments, elements of  FIG.  1    can be incorporated into mass spectrometry platform  100 . According to various embodiments, mass spectrometer  100  can include an ion source  102 , a mass analyzer  104 , an ion detector  106 , and a controller  108 . 
     In various embodiments, the ion source  102  generates a plurality of ions from a sample. The ion source can include, but is not limited to, a matrix assisted laser desorption/ionization (MALDI) source, electrospray ionization (ESI) source, atmospheric pressure chemical ionization (APCI) source, atmospheric pressure photoionization source (APPI), inductively coupled plasma (ICP) source, electron ionization source, chemical ionization source, photoionization source, glow discharge ionization source, thermospray ionization source, and the like. 
     In various embodiments, the mass analyzer  104  can separate ions based on a mass-to-charge ratio of the ions. For example, the mass analyzer  104  can include a quadrupole mass filter analyzer, a quadrupole ion trap analyzer, a time-of-flight (TOF) analyzer, an electrostatic trap (e.g., Orbitrap) mass analyzer, Fourier transform ion cyclotron resonance (FT-ICR) mass analyzer, and the like. In various embodiments, the mass analyzer  104  can also be configured to fragment the ions using collision induced dissociation (CID) electron transfer dissociation (ETD), electron capture dissociation (ECD), photo induced dissociation (PID), surface induced dissociation (SID), and the like, and further separate the fragmented ions based on the mass-to-charge ratio. 
     In various embodiments, the ion detector  106  can detect ions. For example, the ion detector  106  can include an electron multiplier, a Faraday cup, and the like. Ions leaving the mass analyzer can be detected by the ion detector. In various embodiments, the ion detector can be quantitative, such that an accurate count of the ions can be determined. 
     In various embodiments, the controller  108  can communicate with the ion source  102 , the mass analyzer  104 , and the ion detector  106 . For example, the controller  108  can configure the ion source or enable/disable the ion source. Additionally, the controller  108  can configure the mass analyzer  104  to select a particular mass range to detect. Further, the controller  108  can adjust the sensitivity of the ion detector  106 , such as by adjusting the gain. Additionally, the controller  108  can adjust the polarity of the ion detector  106  based on the polarity of the ions being detected. For example, the ion detector  106  can be configured to detect positive ions or be configured to detected negative ions. 
     Linear Ion Trap 
       FIG.  2    illustrates a quadrupole electrode/rod structure of a linear or two-dimensional (2D) quadrupole ion trap  200 . The quadrupole structure includes two sets of opposing electrodes including rods that define an elongated internal volume having a central axis along a z direction of a coordinate system. An X set of opposing electrodes includes rods  215  and  220  arranged along the x axis of the coordinate system, and a Y set of opposing electrodes includes rods  205  and  210  arranged along the y axis of the coordinate system. As illustrated, each of the rods  205 ,  210 ,  215 ,  220  is cut into a main or center section  230  and front and back sections  235 ,  240 . 
     The ions are radially contained by the RF quadrupole trapping potentials applied to the X and Y electrode/rod sets under the control of a controller  290 . A Radio Frequency (RF) voltage is applied to the rods with one phase applied to the X set, while the opposite phase is applied to the Y set. This establishes a RF quadrupole containment field in the x and y directions and will cause ions to be trapped in these directions. 
     To constrain ions axially (in the z direction), the controller  290  can be configured to apply or vary a DC voltage to the electrodes in the center segment  230  that is different from that in the front and back segments  235 ,  240 . Thus a DC “potential well” is formed in the z direction in addition to the radial containment of the quadrupole field resulting in containment of ions in all three dimensions. 
     An aperture  245  is defined in at least one of the center sections  230  of one of the rods  205 ,  210 ,  215 ,  220 . Through the aperture  245 , the controller  290  can further facilitate trapped ions can be selectively expelled based on their mass-to-charge ratios in a direction orthogonal to the central axis by causing an additional AC dipolar electric field to be applied or varied in this direction. In this example, the apertures and the applied dipole electric field are on the X rod set. Other appropriate methods may be used to cause the ions to be expelled, for example, the ions may be ejected between the rods. 
     One method for obtaining a mass spectrum of the contained ions is to change the trapping parameters so that trapped ions of increasing values of mass-to-charge ratio become unstable. Effectively, the kinetic energies of the ions are excited in a manner that causes them to become unstable. These unstable ions develop trajectories that exceed the boundaries of the trapping structure and leave the quadrupolar field through an aperture or series of apertures in the electrode structure. 
     The sequentially expelled ions typically strike a dynode and secondary particles emanating therefrom are emitted to the subsequent elements of the detector arrangement. The placement and type of detector arrangement may vary, the detector arrangement for example extending along the length of the ion trap. Throughout this description, the dynode is considered to be part of the detector arrangement, the other elements being elements such as electron multipliers, pre-amplifiers, and other such devices. 
     It should be recognized that different arrangements for the mass analyzing system may be used, as is well known by the art. For example, analyzing device may be configured such that ions are expelled axially from the ion trap rather than radially. The available axial direction could be used to couple the linear ion trap to another mass analyzer such as a Fourier Transform RF Quadrupole Analyzer, Time of Flight Analyzer, three-dimensional ion trap, ORBITRAP Mass Analyzer or other type of mass analyzer in a hybrid configuration. 
     Combined balanced AC/unbalanced RF operation of the RF system can allow for optimized injection and ejection events. The ions are injected into the LIT in the balanced AC mode. This AC-supported injection does not require the resonance circuit. A transition event can be initiated with AC phasing out and unbalanced RF phasing in. The balanced AC can be ramped down and the unbalanced RF (high frequency) can be ramped up. The timing of both ramping events and AC/RF levels can be optimized to avoid ion losses during transition. After the AC is off, the ion trap can work in unbalanced RF mode until the ions are scanned-out. The combined mode can allow for near-optimum operation conditions both for ions&#39; injection and ejection and can provide grounds for highly efficient usage of the LIT in DIA applications. 
     A well-balanced RF applied to opposite pairs of RF rods in the LIT can provide optimum conditions for ion trapping during injection.  FIG.  3    illustrates the electrical field within an ion trap operated in a balanced mode. For illustrative purposes, the e-field is shown at the point in time where there is a positive 500V potential on the X electrodes  302  and a negative 500V potential on the Y electrodes  304 . The potentials create a near zero e-potential at points equidistant between an X electrode  302  and a Y electrode  304 , as shown by line  306 . This creates a near-zero e-field region  308  near the centerline of the LIT that can be ideal for capturing and retaining of ions. 
     In DIA applications, ions can be scanned out from the LIT to be processed in post-ejection event. It can be important to contain the kinetic energy distribution (KED) in a narrow range. Preferably the KED width should be within tens of electron-volts or less. In normal LIT operation, the KED width can vary between hundreds and thousands of eV. Using an unbalanced RF mode for ion ejection can improve the KED by removing the negative effect of post ejection KE modulation by an RF voltage applied to the slotted RF rod (X electrode) the ion pass through. However, the unbalanced RF mode is inferior for ion injection because of non-zero e-field on the centerline of ion injection. 
       FIGS.  4  and  5    illustrate the electrical field within an ion trap operated in an unbalanced mode. In unbalanced mode, the same difference between the Y electrodes  304  and the X electrodes  302  can be required to maintain the trapping potential within the LIT. However, the X electrodes  302  are held at a near 0V potential while the RF is applied entirely to the Y electrodes  304 . For illustrative purposes,  FIG.  4    shows the e-field at the point in time where there is a positive 1000V potential on the Y electrodes  304 , while  FIG.  5    shows the e-field at a point in time where there is a negative 1000V potential on the Y electrodes  304 . The potentials create a significant e-field (approximately half the voltage applied to the Y electrodes  304 ) at points equidistant between an X electrode  302  and a Y electrode  304 , as shown by line  306 . The region  308  near the centerline of the LIT can experience drastic swings in the potential from a positive 500V in  FIG.  4    to a negative 500V in  FIG.  5   . Such significant variability in the centerline potential can make it difficult to efficiently trap incoming ions. However, once inside the LIT, ions are effected primarily by the difference between the X electrodes  302  and the Y electrodes  304  rather than the absolute magnitude of the centerline. 
     Combining balanced AC mode operation during ion injection into the LIT and unbalanced RF mode operation for ion ejection can provide optimal trapping during injection and minimal KED during ejection.  FIG.  6    illustrates a method for operating the LIT. At  602 , a balanced trapping field can be applied, and at  604 , ions can be supplied to the ion trap. At  606 , the ions can be trapped within the ion trap. At  608 , the ion trap can transition to an unbalanced trapping field, and, after the transition is complete, the ions can be selectively ejected from the ion trap while an unbalanced trapping field is applied. In various embodiments, the ions can be selectively ejected from the ion trap using an excitation waveform that is targeted to ions having a particular mass-to-charge ratio. 
       FIG.  7    is a timing diagram illustrating the potentials applied to the electrodes on the LIT. During injection, the LIT is operated in balanced mode with an AC frequency waveform applied to both the X and Y electrodes. The AC frequency waveform applied to the Y electrodes is phase shifted 180 degree from the AC frequency waveform applied to the X electrodes. In various embodiments, the AC voltage can be in a frequency range of between about 100 kHz and about 600 kHz, such as between about 200 kHz and about 300 kHz. In other embodiments, the AC voltage can be in frequency range of between about 300 kHz and about 400 kHz or between about 400 kHz and about 500 kHz or between about 500 kHz and about 600 kHz. In various embodiments, the AC voltage can be less than about 400 V 0-P , such as less than about 200 V 0-P . Once injection is complete, the LIT transitions from balanced mode to unbalanced mode. The AC frequency waveform is ramped down while an RF frequency waveform is ramped up on the Y electrodes. In various embodiments, the RF voltage can be in a frequency range of between about 750 kHz and about 1500 kHz. The unbalanced mode can be maintained while cooling the ions to reduce their kinetic energy and while ejecting ions. In various embodiments, the ions can be cooled such that the kinetic energy spread of ions before ejection from the linear ion trap can be less than about 5.0 eV, such as less than about 2.5 eV, such as less than about 0.5 eV, even less than about 0.2 eV. 
     In various embodiments, the AC frequency waveform can be applied an analog waveform, such as a sine wave. Alternatively, the AC frequency waveform can be applied as a digital waveform of the same frequency and amplitude. 
     The LIT can be switched back to balanced mode prior to the next injection (not shown). However, since trapping of ions is not important when switching back to balanced mode, there is no need to ramp the waveforms and the transition can be relatively abrupt by turning the RF frequency waveform off and turning the AC frequency waveform on. 
     Use of balanced AC for ion injection instead of balanced RF has additional benefits. An AC frequency used for the injection event can be significantly lower than RF frequency required for analytical operation of the LIT in ion isolation and scan-out event. This can reduce the need for a second resonance-based system to provide RF frequency potentials to the X electrodes. Instead the trapping AC can be applied in a non-resonant mode. 
     The efficiency of ion injection can be controlled by choosing optimal range of q factors. Its value is proportional to RF voltage on rods and inversely proportional to m/z and square of frequency. Dropping the frequency by a factor of 2-5 allows a reduction in voltage on electrodes by a factor of 4-25 keeping the value of q-factor. That frequency range is typically referred to as the AC range. Operating with AC voltages on electrodes at or below 400 V 0-p , such as less than about 200 V 0-P , allows for usage of non-resonant circuits to generate the AC. This, in turn, can give good control on turning on, linear ramp and switching off the AC independent of RF circuit operation. There can be a lower total dissipated RF power as well. 
     To successfully transition from balanced mode to unbalanced mode while maintaining the ions in the LIT requires ramping down the AC synchronously with ramping up the RF voltage keeping the total e-field strong enough to retain ions but not too strong to eject ions. These two ramps start together but their time lengths may be different. In various embodiments, a ramp down time for the AC voltage can be less than about 1.5 ms and a ramp up time for the RF voltage can be between about 0.8 ms and about 2.5 ms. 
       FIG.  8    is an electrical diagram of an exemplary voltage supply  800  to supply the necessary voltages to ion trap  200 . The voltage supply  800  can include RF amplifier  802 , DC offset source  804 , AC source  806 , AC source  808 , and auxiliary supply  810 . 
     DC offset source  804  can provide a DC offset on the Y rods between the front  235 , center  230 , and back  240  portions of the ion trap  200 . In various embodiments, it can be desirable to have an elevated DC voltage for the front  235  and back  240  portions and a relatively lower DC voltage for the center  230  portion to create a well to trap ions in the z direction. 
     During balanced mode operation, AC source  806  can provide the AC voltage to the Y rods  205  and  210  and AC Source  808  can provide the AC voltage to the x rods  215  and  220 . 
     During unbalanced mode operation, main RF amplified  802  can provide the RF voltage to Y rods  205  and  210 . 
     During ejection, auxiliary supply  810  can provide the excitation waveform to the X rods  215  and  220  to selectively eject ions from the trap. 
     Voltage supply  800  can further include low pass filter  812  to reduce noise on the main RF circuit, filter  814  to block RF on the DC offset circuit, and filter choke and step-up transformers  816 ,  818 , and  820  to reduce noise and increase the voltage of the balanced AC circuits and the auxiliary circuit. 
     Voltage supply  800  can further include transformers  822 ,  824 , and  826  to couple the sources to ion trap  200 . Transformer  824  couples AC supply  806  to the front  235 , center  230 , and back  240  sections of Y rods  205  and  210 . Transformer  822  couples the RF amplifier  802  to lines from the DC offset source  804  and AC source  806 . Transformer  826  couples AC source  808  and auxiliary source  820  to the X rods  215  and 
     Voltage supply  800  also includes capacitors  828  and  830  so the capacitance of each circuit can be matched. 
     Computer-Implemented System 
       FIG.  9    is a block diagram that illustrates a computer system  900 , upon which embodiments of the present teachings may be implemented as which may incorporate or communicate with a system controller, for example controller  110  shown in  FIG.  1   , such that the operation of components of the associated mass spectrometer may be adjusted in accordance with calculations or determinations made by computer system  900 . In various embodiments, computer system  900  can include a bus  902  or other communication mechanism for communicating information, and a processor  904  coupled with bus  902  for processing information. In various embodiments, computer system  900  can also include a memory  906 , which can be a random access memory (RAM) or other dynamic storage device, coupled to bus  902 , and instructions to be executed by processor  904 . Memory  906  also can be used for storing temporary variables or other intermediate information during execution of instructions to be executed by processor  904 . In various embodiments, computer system  900  can further include a read only memory (ROM)  908  or other static storage device coupled to bus  902  for storing static information and instructions for processor  904 . A storage device  910 , such as a magnetic disk or optical disk, can be provided and coupled to bus  902  for storing information and instructions. 
     In various embodiments, computer system  900  can be coupled via bus  902  to a display  912 , such as a cathode ray tube (CRT) or liquid crystal display (LCD), for displaying information to a computer user. An input device  914 , including alphanumeric and other keys, can be coupled to bus  902  for communicating information and command selections to processor  904 . Another type of user input device is a cursor control  916 , such as a mouse, a trackball or cursor direction keys for communicating direction information and command selections to processor  904  and for controlling cursor movement on display  912 . This input device typically has two degrees of freedom in two axes, a first axis (i.e., x) and a second axis (i.e., y), that allows the device to specify positions in a plane. 
     A computer system  900  can perform the present teachings. Consistent with certain implementations of the present teachings, results can be provided by computer system  900  in response to processor  904  executing one or more sequences of one or more instructions contained in memory  906 . Such instructions can be read into memory  906  from another computer-readable medium, such as storage device  910 . Execution of the sequences of instructions contained in memory  906  can cause processor  904  to perform the processes described herein. In various embodiments, instructions in the memory can sequence the use of various combinations of logic gates available within the processor to perform the processes describe herein. Alternatively hard-wired circuitry can be used in place of or in combination with software instructions to implement the present teachings. In various embodiments, the hard-wired circuitry can include the necessary logic gates, operated in the necessary sequence to perform the processes described herein. Thus, implementations of the present teachings are not limited to any specific combination of hardware circuitry and software. 
     While the present teachings are described in conjunction with various embodiments, it is not intended that the present teachings be limited to such embodiments. On the contrary, the present teachings encompass various alternatives, modifications, and equivalents, as will be appreciated by those of skill in the art. 
     Further, in describing various embodiments, the specification may have presented a method and/or process as a particular sequence of steps. However, to the extent that the method or process does not rely on the particular order of steps set forth herein, the method or process should not be limited to the particular sequence of steps described. As one of ordinary skill in the art would appreciate, other sequences of steps may be possible. Therefore, the particular order of the steps set forth in the specification should not be construed as limitations on the claims. In addition, the claims directed to the method and/or process should not be limited to the performance of their steps in the order written, and one skilled in the art can readily appreciate that the sequences may be varied and still remain within the spirit and scope of the various embodiments. 
     Results 
     Typical mass range of precursor ions in bottom-up Proteomics can be 400-850 amu. A more extended range can be 400-1200 amu.  FIGS.  10 A,  10 B,  11 A,  11 B,  12 A,  12 B,  13 A,  13 B,  14 A,  14 B,  15 A, and  15 B  show x-y the simulation results (SIMION) on efficiency of ion trapping after injection of various size ions within the range of 400-1200 amu. The timing is as follows: injection for 500 us, transition period when AC is ramped down for 500 us and RF is ramped up 1200 us. At the end of ramp-up event, RF remained constant. Total time with the final cool-down event—2500 us. AC frequencies are 160 kHz. The corresponding AC voltages were calculated based on injection q for ion masses of interest. RF frequency was kept at 1.1 MHz in all simulations.  FIGS.  10 A and  10 B  show the results for ions of 400 amu.  FIGS.  11 A and  11 B  show the results for ions of 550 amu.  FIGS.  12 A and  12 B  show the results for ions of 700 amu.  FIGS.  13 A and  13 B  show the results for ions of 850 amu.  FIGS.  14 A and  14 B  show the results for ions of 1000 amu.  FIGS.  15 A and  15 B  show the results for ions of 1200 amu. 
     One of practical considerations is available AC voltage for balanced AC for a frequency range 100-600 kHz.  FIG.  16    is a graph of the voltage (V 0-p ) needed for trapping ions using a balanced AC waveform. 110 V 0-p  is used as a benchmark based on the available AC voltage on commercially available mass spectrometer systems with a LIT. A supplementary AC system capable of providing 110 V 0-p  can work across the mass range 400-850 amu at frequencies up to 300 kHz, q from 0.3 to 0.6. For the extended mass range (up to 1200 amu) the upper q value would be ˜0.55 at frequency 300 kHz. For higher frequency, 0.4 MHz, the normal mass range up to 850 amu allows operating at q up to 0.45 and for the extended mass range q limit will be 0.3. Alternatively, increasing the available AC voltage could achieve a broader operating range. For example, at 200 V 0-p , the normal mass range up to 850 amu allows operating at q up to 0.55 and for the extended mass range q limit will be 0.4 at frequencies of up to 500 kHz. At 400 V 0-9 , the extended mass range allows operating at a q limit above 0.6 at frequencies of up to 500 kHz. 
       FIG.  17    illustrates the trapping efficiency at the low end of the mass range (400 amu) at a frequency of 0.16 Mhz. Below a q of about 0.4, there can be significant losses of low mass ions, with almost no loss occurring at q greater than about 0.45. 
     Benefits of increasing the AC frequency is clear from  FIGS.  18 A,  18 B,  19 A, and  19 C . Both 400 amu and 1200 amu ions are much better contained to the center of the trap when higher frequency (0.3 or 0.24 MHz) is used during injection vs. at low frequencies (0.16 or 0.2 MHz). This reduces cooling time before ejection. That time factor can be important for high-throughput applications.