BACKGROUND 
     The present invention relates to methods for the analysis of samples by mass spectrometry. The apparatus and methods for ion transport and analysis described herein are enhancements of the techniques referred to in the literature relating to mass spectrometry—an important tool in the analysis of a wide range of chemical compounds. Specifically, mass spectrometers can be used to determine the molecular weight of sample compounds. The analysis of samples by mass spectrometry consists of three main steps—formation of gas phase ions from sample material, mass analysis of the ions to separate the ions from one another according to ion mass, and detection of the ions. A variety of means and methods exist in the field of mass spectrometry to perform each of these three functions. The particular combination of the means and methods used in a given mass spectrometer determine the characteristics of that instrument. 
     To mass analyze ions, for example, one might use magnetic (B) or electrostatic (E) analysis, wherein ions passing through a magnetic or electrostatic field will follow a curved path. In a magnetic field, the curvature of the path will be indicative of the momentum-to-charge ratio of the ion. In an electrostatic field, the curvature of the path will be indicative of the energy-to-charge ratio of the ion. If magnetic and electrostatic analyzers are used consecutively, then both the momentum-to-charge and energy-to-charge ratios of the ions will be known and the mass of the ion will thereby be determined. Other mass analyzers are the quadrupole (Q), the ion cyclotron resonance (ICR), the time-of-flight (TOF), the Orbitrap, and the quadrupole ion trap analyzers. The analyzer used in conjunction with the method described here may be any of a variety of these. 
     Before mass analysis can begin, gas phase ions must be formed from a sample material. If the sample material is sufficiently volatile, ions may be formed by electron ionization (EI) or chemical ionization (CI) of the gas phase sample molecules. Alternatively, for solid samples (e.g., semiconductors, or crystallized materials), ions can be formed by desorption and ionization of sample molecules by bombardment with high energy particles. Further, Secondary Ion Mass Spectrometry (SIMS), for example, uses keV ions to desorb and ionize sample material. In the SIMS process a large amount of energy is deposited in the analyte molecules, resulting in the fragmentation of fragile molecules. This fragmentation is undesirable in that information regarding the original composition of the sample (e.g., the molecular weight of sample molecules) will be lost. 
     For more labile, fragile molecules, other ionization methods now exist. The plasma desorption (PD) technique was introduced by Macfarlane et al. (D. F. Torgerson, R. P. Skowronski, and R. D. Macfarlane,  Biochem. Biophys. Res Commoun.  60 (1974) 616)(“McFarlane”). Macfarlane discovered that the impact of high energy (MeV) ions on a surface, like SIMS would cause desorption and ionization of small analyte molecules. However, unlike SIMS, the PD process also results in the desorption of larger, more labile species (e.g., insulin and other protein molecules). 
     Additionally, lasers have been used in a similar manner to induce desorption of biological or other labile molecules. See, for example, Cotter et al. (R. B. VanBreeman, M. Snow, R. J. Cotter,  Int. J. Mass Spectrom. Ion Phys.  49 (1983) 35; Tabet, J. C.; Cotter, R. J., Tabet, J. C.,  Anal. Chem.  56 (1984) 1662; or R. J. Cotter et al.,  Anal. Instrument.  16 (1987) 93). Cotter modified a CVC 2000 time-of-flight mass spectrometer for infrared laser desorption of non-volatile biomolecules, using a Tachisto (Needham, Mass.) model 215G pulsed carbon dioxide laser. The plasma or laser desorption and ionization of labile molecules relies on the deposition of little or no energy in the analyte molecules of interest. 
     The use of lasers to desorb and ionize labile molecules intact was enhanced by the introduction of matrix assisted laser desorption ionization (MALDI) (K. Tanaka, H. Waki, Y. Ido, S. Akita, Y. Yoshida, T. Yoshica,  Rapid Commun. Mass Spectrom.  2 (1988) 151 and M. Karas, F. Hillenkamp,  Anal. Chem.  60 (1988) 2299). In the MALDI process, an analyte is dissolved in a solid, organic matrix. Laser light of a wavelength that is absorbed by the solid matrix but not by the analyte is used to excite the sample. Thus, the matrix is excited directly by the laser, and the excited matrix sublimes into the gas phase carrying with it the analyte molecules. The analyte molecules are then ionized by proton, electron, or cation transfer from the matrix molecules to the analyte molecules. This process (i.e., MALDI) is typically used in conjunction with time-of-flight mass spectrometry (TOFMS) and can be used to measure the molecular weights of proteins in excess of 100,000 Daltons. 
     Further, Atmospheric Pressure Ionization (API) includes a number of ion production means and methods. Typically, analyte ions are produced from liquid solution at atmospheric pressure. One of the more widely used methods, known as electrospray ionization (ESI), was first suggested by Dole et al. (M. Dole, L. L. Mack, R. L. Hines, R. C. Mobley, L. D. Ferguson, M. B. Alice,  J. Chem. Phys.  49, 2240, 1968). In the electrospray technique, analyte is dissolved in a liquid solution and sprayed from a needle. The spray is induced by the application of a potential difference between the needle and a counter electrode. The spray results in the formation of fine, charged droplets of solution containing analyte molecules. In the gas phase, the solvent evaporates leaving behind charged, gas phase, analyte ions. This method allows for very large ions to be formed. Ions as large as 1 MDa have been detected by ESI in conjunction with mass spectrometry (ESMS). 
     In addition to ESI, many other ion production methods might be used at atmospheric or elevated pressure. For example, MALDI has recently been adapted by Laiko et al. to work at atmospheric pressure (Victor Laiko and Alma Burlingame, “Atmospheric Pressure Matrix Assisted Laser Desorption”, U.S. Pat. No. 5,965,884, and Atmospheric Pressure Matrix Assisted Laser Desorption Ionization, poster #1121, 4 th  International Symposium on Mass Spectrometry in the Health and Life Sciences, San Francisco, Aug. 25-29, 1998) and by Standing et al. at elevated pressures (Time of Flight Mass Spectrometry of Biomolecules with Orthogonal Injection+Collisional Cooling, poster #1272, 4 th  International Symposium on Mass Spectrometry in the Health and Life Sciences, San Francisco, Aug. 25-29, 1998; and Orthogonal Injection TOFMS  Anal. Chem.  71(13), 452A (1999)). The benefit of adapting ion sources in this manner is that the ion optics (i.e., the electrode structure and operation) in the mass analyzer and mass spectral results obtained are largely independent of the ion production method used. 
     Many different types of analyzers have been used to mass analyze sample ions. One important type of mass analyzer is the quadrupole mass analyzer. There are also several types of quadrupole analyzers. Among them are the quadrupole filter, the quadrupole trap—a.k.a. the Paul trap—the cylindrical ion trap, linear ion trap, and the rectilinear ion trap. 
     The conventional quadrupole filter consists of four rods equally spaced at a predetermined radius around a central axis. A radio frequency (RF)—e.g. a 1 MHz sine wave—potential is applied between the rods. The potential on adjacent rods is 180° out of phase. Rods on opposite sides of the quadrupole axis are electrically connected—i.e. the quadrupole is formed as two pairs of rods. The quadrupole has an entrance end and an exit end. Ions to be filtered are injected into the entrance end of the quadrupole. These ions travel along the axis of the quadrupole to the exit end. The RF potential applied between the rods will tend to confine the ions radially. Applying a DC as well as an RF potential between the pairs of rods will cause ions of only a limited mass range to be transmitted through the quadrupole. Ions outside this mass range will be filtered away and will not reach the exit end. 
     In a quadrupole mass analyzer, ions transmitted through the quadrupole are detected as ion signals via a channeltron detector. To produce a mass spectrum the quadrupole parameters are “scanned” and the ion signals are recorded as a function of the scan parameters. In the so-called “mass-selective stability” mode of operation the amplitudes of RF and DC voltages applied to the quadrupole rods are ramped at a constant RF/DC ratio. At each point in the ramp, ions of nominally a single m/z have a stable trajectory and are transmitted. Recording the ion signal as a function of the ramp thus yields a mass spectrum. 
     The Paul ion trap (a.k.a. quadrupole ion trap) is based on a similar principle and construction as the quadrupole filter, however, as the name implies, ions are trapped in the Paul trap before they are mass analyzed. Also unlike the quadrupole filter, the Paul trap is cylindrically symmetric. The Paul trap is constructed using three rotationally symmetric hyperbolic electrodes. Two “end cap” electrodes are placed one on either side of a central “ring electrode”. Applying an RF potential between the ring electrode and the end caps forms a quadrupolar pseudopotential well in the interior volume of the trap. In a typical analysis ions enter the trap through apertures in one of the end caps, lose kinetic energy via collisions with gas in the trap and thereby become trapped in the pseudopotential well. 
     The quadrupole ion trap is typically operated in one of two modes—the mass selective instability mode or the resonance ejection mode. The mass selective instability mode differs from the mass selective stability mode described above in that ions are detected when their trajectories become unstable. Initially, a group of analyte ions is trapped near the center of the quadrupole ion trap. The ions will oscillate about the center of the trap with a frequency related to the m/z of the ion. When performing a mass selective instability scan, the amplitude of the RF potential applied to the ring electrode is ramped to higher values. At each point in the RF ramp, ions below a given m/z have unstable trajectory and are ejected from the trap. The given “cutoff” m/z is a linear function of the RF amplitude. Thus, recording the ion signal as a function of the ramp yields a mass spectrum. 
     A similar principle is applied when operating in the resonance ejection mode. However, in resonance ejection mode, an additional AC potential is applied between the end cap electrodes. The ions are excited not only by the RF as in selected ion instability mode but also by the supplemental AC. Therefore the ions are ejected more quickly from the trap—i.e. earlier in the ramp. Because ions are ejected from the trap at lower RF amplitudes, experiments using resonance ejection can be used to analyze higher m/z ions than can be achieved in mass selective instability experiments. 
     Many additional methods of manipulating ions in traps are know from the prior art including ion trapping, precursor isolation, CID, tandem mass spectrometry, ion-ion reactions, etc. Such methods may be applied, not only to the Paul trap as described above, but also to the other prior art trapping devices described below and to the present invention. 
     The cylindrical ion trap (CIT) is a simplified form of the Paul trap described above. The cylindrical ion trap is formed by a central cylinder instead of a hyperbolic ring electrode, and two flat plates instead of hyperbolic end caps. Due the simplified geometry of these electrodes, the CIT has a lower resolution than conventional Paul traps of similar inner diameter. However, because of its simplified construction—i.e. flat end caps and cylindrical ring electrode instead of hyperbolic surfaces—the CIT can more readily be miniaturized. 
     Yet another type of ion trap is the “linear ion trap”. In principle, any type of multipole in which ions are trapped may be considered a linear ion trap, however, the device now commonly referred to as a linear ion trap can be used not only to trap ions but also to analyze them. As described by Schwartz et al. (J. C. Schwartz, M. W. Senko, and J. E. P. Syka,  J. Am. Soc. Mass Spectrom.  13, 659 (2002)) a linear ion trap includes two pairs of electrodes or rods, which contain ions by utilizing an RF quadrupole trapping field in two dimensions, while a non-quadrupole DC trapping field is used in the third dimension. Simple plate lenses at the ends of a quadrupole structure can provide the DC trapping field. This approach, however, allows ions which enter the region close to the plate lenses to be exposed to substantial fringe fields due to the ending of the RF quadrupole field. These non-linear fringe fields can cause radial or axial excitation which can result in loss of ions. In addition, the fringe fields can cause shifting of the ions frequency of motion in both the radial and axial dimensions. 
     An improved electrode structure of a linear quadrupole ion trap  11 , which is known from the prior art, is shown in  FIG. 1 . The quadrupole structure includes two pairs of opposing electrodes or rods, the rods having a hyperbolic profile to substantially match the equipotential contours of the quadrupole RF fields desired within the structure. Each of the rods is cut into a main or central section and front and back sections. The two end sections differ in DC potential from the central section to form a “potential well” in the center to constrain ions axially. An aperture or slot  12  allows trapped ions to be selectively resonantly ejected in a direction orthogonal to the axis in response to AC dipolar or quadrupolar electric fields applied to the rod pair containing the slotted electrode. In this figure, as per convention, the rod pairs are aligned with the x and y axes and are therefore denoted as the X and Y rod pairs. 
     In prior art according to Song et al. (Y. Song, G. Wu, Q. Song, R. G. Cooks and Z. Ouyang, J Am. Soc Mass Spectrom. 17, 631 (2006) and U.S. Pat. No. 6,838,666 which is incorporated herein by reference), the hyperbolic rods of the conventional 2D linear ion trap were replaced by rectangular electrodes. This design (shown in  FIG. 2 ) is now known as a rectilinear ion trap (RIT). According to Song et al. the trapping volume is defined by x and y pairs of spaced flat or plate RF electrodes  15 ,  16  and  13 ,  14  in the zx and zy planes. Ions are trapped in the z direction by DC voltages applied to spaced flat or plate end electrodes (not shown) in the xy plane disposed at the ends of the volume defined by the x, y pair of plates, or by DC voltages applied together with RF in sections  18  and  19  each comprising pairs of flat or plate electrodes  15   a ,  16   a  and  13   a ,  13   b . In addition to the RF sections flat or plate end electrodes can be added. The ions are trapped in the x, y direction by the quadrupolar RF fields generated by the RF voltages applied to the plates. Ions can be ejected along the z axis through apertures formed in the end electrodes or along the x or y axis through apertures formed in the x or y electrodes. The ion trap is generally operated with the assistance of a buffer gas. Thus, when ions are injected into the ion trap they lose kinetic energy by collision with the buffer gas and are trapped by the DC potential well. While the ions are trapped by the application of RF trapping voltages AC and other waveforms can be applied to the electrodes to facilitate isolation or excitation of ions in a mass selective fashion. To perform an axial ejection scan the RF amplitude is scanned while an AC voltage is applied to the end plates. Axial ejection depends on the same principles that control axial ejection from a linear trap with round rod electrodes (U.S. Pat. No. 6,177,668). In order to perform an orthogonal ion ejection scan, the RF amplitude is scanned and the AC voltage is applied on the set of electrodes which include an aperture. The AC amplitude can be scanned to facilitate ejection. Circuits for applying and controlling the RF, AC and DC voltages are well known. 
     The addition of the two end RF sections  18  and  19  to the RIT also helps to generate a uniform RF field for the center section. The DC voltages applied on the three sections establish the DC trapping potential and the ions are trapped in the center section, where various processes are performed on the ions in the center section. 
     The most significant advantage of the RIT over the LIT is that of fabrication. The electrodes composing the RIT, being flat surfaces, are much easier to produce, with precision, than the hyperbolic surfaces of the LIT. As a result, the RIT can be more readily miniaturized than the LIT and can be more readily incorporated into portable instruments. 
     In order to determine the structure of an original analyte molecule it is often helpful to dissociate molecular ions into fragments. Typically, the fragment ions are then mass analyzed. The masses and mass differences between the fragment ions can be used then to determine the original molecule&#39;s structure. There are many means of fragmenting precursor analyte ions—collision induced dissociation (CID), infrared multi photon dissociation (IRMPD), surface induced dissociation (SID), etc. The production of identifiable fragment ions is an important measure of the success of a dissociation method. 
     Collision induced dissociation (CID) is a widely used prior art method used in tandem mass spectrometry experiments. During CID, the internal energy of precursor ions is increased via collisions between the precursor ion and collision gas. The increased internal energy of the ion causes it to dissociate into one or more fragment ions. Collisional activation of precursor ions is achieved by accelerating the ion via an electric field. In instruments using quadrupole filters, the accelerating electric field is typically applied between adjacent multipoles. That is, analyte ions enter the quadrupole filter. In the filter, ions of the mass of interest—i.e. precursor ions—are selected. The selected precursor ions exit the quadrupole filter and are accelerated by an electric field into a collision cell. The collision cell includes another RF multipole used to confine the ions as they undergo activation and fragmentation. The resulting precursor and fragment ions pass through and out of the collision cell multipole and to downstream optics and/or detectors. 
     In a multipole trap, activation toward dissociation may be accomplished by resonant excitation of the precursor. In a resonant excitation experiment, the electric field used to accelerate the ions is an RF potential applied between the trapping electrodes at the secular frequency of the precursor. In a conventional Paul trap the excitation electric field, for example, might take the form of a 150 mVp-p sine wave applied between the endcap electrodes for a period of tens of milliseconds. Alternatively, a higher amplitude electric field (˜1 Vpp) might be applied for a shorter time (˜2 ms). Further, as described in the prior art of Glish et al. (C. Cunningham Jr., G. L. Glish, and D. J. Burinsky,  J Am Soc Mass Spectrom  17, 81 (2006)) and Schwartz et al. in U.S. Pat. No. 7,102,129, the amplitude of the RF potential confining the ions in the trap may be reduced after collisional activation so that fragment ions of low m/z can be observed. 
     Another fragmentation method used in tandem mass spectrometry experiments is electron capture dissociation (ECD). The prior art method of ECD (K. Vekey, A. G. Brenton, et al.,  Int J Mass Spectrom Ion Process  70, 277 (1986); F. W. McLafferty,  Mass Spectrometry in the Analysis of Large Molecules , C. J. McNeal, Ed., John Wiley, New York, 1986, pp 107-120; and N. C. Polfer et al.,  Rapid Commun Mass Spectrom  16, 936 (2002)) activates multiply charged positive precursor ions toward fragmentation by partial neutralization of the ion using low kinetic energy electrons. The energy associated with neutralization is often sufficient to produce prompt fragmentation. 
     Electron transfer dissociation (ETD) and electron capture dissociation (ECD) tandem mass spectrometry techniques have been shown to be useful for the characterization of peptides and proteins (e.g. top-down analysis). Both techniques produce c- and z-type fragment ions, which are complementary to the b- and y-type fragment ions produced in collision induced dissociation (CID). Additionally ETD and ECD provide more extensive fragmentation than CID, resulting in richer product ion spectra and better sequence coverage. Moreover, ETD and ECD are processes which tend to preserve weakly bound post-translational modifications (PTMs) thereby enabling a means of identification and localization of PTMs by mass spectrometry. Neutral loss scans (in a triple quadrupole or ion trap) in conjunction with CID can be used to look for the loss of PTMs, however, this scanning method is an indirect measurement and not always efficient at identifying all PTMs. The reason why ETD and ECD preserve PTMs is highly debated, and whether the processes are ergodic or non-ergodic does not change the utility of the techniques. The combination of the complementary information to CID, richer sequence coverage, and the identification of PTMs make ETD and ECD powerful analytical proteomics tools. 
     Prior art instruments primarily combine ETD with conventional Paul ion traps (3-D ion traps), linear ion traps (2-D ion traps), and hybrid quadrupole time of flight mass analyzers (qTOF). For trap analyzers, which have a fixed line width across the mass range, it is necessary to perform charge manipulation techniques to reduce the charge of the ions if complex ion populations are to be resolved. Reducing the number of charges on an ion results in a larger spacing between the isotopes and also shifts the ion m/z to a region of the mass spectrum that allows the isotopes to be resolved and the actual charge state and molecular mass determined. 
     In performing ETD experiments in a 2-D or 3-D ion trap, the spatial overlap between reagent and analyte ions is inherent to the operation of the device. Because the pressure is relatively high, both positive and negative ions are collisionally cooled to the center of the storage device. As a result the reagent and analyte ions occupy nearly the same volume. This strong spatial overlap, of course, tends to promote the ETD reaction. This spatial overlap between the reagent and analyte ions can be optimized but does not change from experiment to experiment. The efficiency of ETD in the 3-D traps suggests that it may be possible to generate ETD data without the need to average multiple mass spectra. In addition the time necessary for the accumulation and reaction for an ETD experiment are typically amenable to on-line separations. 
     Xia et al. demonstrated an experimental setup in which ions were trapped in a linear quadrupole ion trap using only RF potentials (Xia, Y.; Chrisman, P. A.; Erickson, D. E.; Liu, J.; Liang, X. R.; Londry, F. A.; Yang, M. J.; McLuckey, S. A.  Anal. Chem.  2006, 78, 4146-54). Once trapped, the analyte ions were reacted with ETD reagent ions. Product ions and remaining analyte ions were transferred from the quadrupole trap to an orthogonal time-of-flight (OTOF) mass analyzer for mass analysis. 
     Postactivation—i.e. ion activation following the ETD reaction—is an important issue in ETD experiments. Swaney et al. (D. L. Swaney, G. C. McAlister, M. Wirtala, J. C. Scwartz, J. E. P. Syka, and J. Coon,  Anal. Chem.  79, 477 (2007).) have shown that postactivation can substantially improve the fragmentation efficiency of ETD experiments. In ETD experiments an electron is transferred from the reagent ion to the analyte ion. In many cases, the energy from the resulting charge neutralization can fragment the analyte ion. However, in some cases a charge reduced nondissociated precursor ion is produced. In such cases additional energy is required to form fragment ions. The additional energy can be provided by accelerating the ions to a few eV of kinetic energy and then allowing the ions to collide with gas molecules in the trapping device. In a quadrupole trap this can be done by introducing a supplemental excitation waveform. 
     In the course of performing ion-ion reaction experiments such as ETD, it is often useful to trap a first reactant ion type in a first ion trap and a second reactant ion type in a second ion trap. The ions can then be allowed to mix and react for a well controlled, predetermined time. 
     When performing tandem mass spectrometry experiments in prior art traps, typically all analyte ions except for a single type of selected precursor ion are ejected from the trap. As a result, all ions except for the selected precursor are lost. Fragment ions may be formed from the selected precursor ion and these fragment ions may be further mass analyzed or fragmented, however, all other ions of potential interest originally stored in the trap are lost in the initial precursor isolation and are therefore unavailable for further analysis. 
     This is equally true of fragment ions when performing multiple step tandem mass spectrometry experiments. That is, if a precursor is selected, and if fragment ions are formed from the precursor, and then a single type of fragment ion is isolated for further fragmentation, then all the original ions except for the precursors will be lost and all the first generation fragment ions except for those isolated for further analysis will be lost. 
     As discussed below, the stacked well ion trap according to the present invention overcomes many of the limitations of prior art ion traps discussed above. The traps disclosed herein provides a unique combination of attributes making it especially suitable for use in the mass analysis of complex samples containing more than one type of analyte ion. 
     SUMMARY 
     In accordance with one embodiment of the invention, an apparatus and method are provided for containing and manipulating ions in a multitude of pseudopotential wells. According to this embodiment, the apparatus has no electrodes separating the pseudopotential wells. Rather, there are no barriers between the pseudopotential wells except the electrodynamic potentials represented by the pseudopotential wells themselves. Unlike prior art devices, ions can be transmitted from one pseudopotential well to another without losses due to collisions of the ions with electrodes or other ion optical elements. In further alternate embodiments, interstitial electrodes may cover part of the gap between adjacent pseudopotential wells. 
     According to another embodiment, an apparatus and method are provided for containing and manipulating ions in a multitude of quadrupolar pseudopotential wells. According to this embodiment, the apparatus has no electrodes separating the pseudopotential wells. Rather, there are no barriers between the pseudopotential wells except the electrodynamic potentials represented by the pseudopotential wells themselves. Unlike prior art devices, ions can be transmitted from one pseudopotential well to another without losses due to collisions of the ions with electrodes or other ion optical elements. Prior art quadrupole methods of mass selective stability, mass selective instability, and resonance ejection can be performed within or between pseudopotential wells. In one embodiment, resonance ejection is used to eject ions of a selected type from a first pseudopotential well into a second pseudopotential well while maintaining ions of substantially all other types in the first pseudopotential well. Any other know prior art quadrupole method including ion isolation methods, excitation methods, dissociation methods, and ion-ion, ion-neutral, or ion-electron reaction methods, may be used in conjunction with the present invention. In further alternate embodiments, interstitial electrodes may cover part of the gap between adjacent pseudopotential wells. 
     According to another embodiment, an apparatus and method are provided for containing and manipulating ions in a multitude of quadrupolar pseudopotential wells using substantially planar electrodes to form substantially rectilinear fields. According to this embodiment, the apparatus has no electrodes separating the pseudopotential wells. Rather, there are no barriers between the pseudopotential wells except the electrodynamic potentials represented by the pseudopotential wells themselves. Unlike prior art devices, ions can be transmitted from one pseudopotential well to another without losses due to collisions of the ions with electrodes or other ion optical elements. Prior art quadrupole methods of mass selective stability, mass selective instability, and resonance ejection can be performed within or between pseudopotential wells. In one embodiment, resonance ejection is used to eject ions of a selected type from a first pseudopotential well into a second pseudopotential well while maintaining ions of substantially all other types in the first pseudopotential well. Any other know prior art quadrupole method including ion isolation methods, excitation methods, dissociation methods, and ion-ion, ion-neutral, or ion-electron reaction methods, may be used in conjunction with the present invention. In further alternate embodiments, interstitial electrodes may cover part of the gap between adjacent pseudopotential wells. 
     According to another embodiment, an apparatus and method are provided for containing and manipulating ions in a multitude of quadrupolar pseudopotential wells formed using cylindrically symmetric electrodes. According to this embodiment, the apparatus has no electrodes separating the pseudopotential wells. Rather, there are no barriers between the pseudopotential wells except the electrodynamic potentials represented by the pseudopotential wells themselves. Unlike prior art devices, ions can be transmitted from one pseudopotential well to another without losses due to collisions of the ions with electrodes or other ion optical elements. Prior art quadrupole methods of mass selective stability, mass selective instability, and resonance ejection can be performed within or between pseudopotential wells. In one embodiment, resonance ejection is used to eject ions of a selected type from a first pseudopotential well into a second pseudopotential well while maintaining ions of substantially all other types in the first pseudopotential well. Any other know prior art quadrupole method including ion isolation methods, excitation methods, dissociation methods, and ion-ion, ion-neutral, or ion-electron reaction methods, may be used in conjunction with the present invention. In further alternate embodiments, interstitial electrodes may cover part of the gap between adjacent pseudopotential wells. 
     In accordance with the present invention, ions of a selected type may be resonantly ejected from a first pseudopotential well into a second pseudopotential well while maintaining ions of substantially all other types in the first pseudopotential well. The selected ions may be caused to dissociate, for example by CAD, ETD, IRMPD, or any other known method of dissociation. The fragment ions may then be analyzed by a resonance ejection scan out of the second pseudopotential well into a detector. 
     Alternatively, the fragment ions may be mass inselectively transmitted to another analyzer for mass analysis or further manipulations. Once ions associated with the first selected type have cleared the second pseudopotential well, a second type of ions may be resonantly ejected from the first pseudopotential well into the second pseudopotential well, dissociated, and analyzed. This process may be repeated any number of times until all ions of interest from the first pseudopotential well have been fully analyzed. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       For a more complete understanding of the present invention, reference is now made to the following drawings in which: 
         FIG. 1  depicts a prior art linear ion trap according to Schwartz et al.; 
         FIG. 2  depicts a prior art rectilinear ion trap according to Ouyang et al.; 
         FIG. 3  depicts a rectilinear ion trap according to the present invention having two pseudopotential wells; 
         FIG. 4  is a plot of the equipotential lines in the rectilinear ion trap of  FIG. 3  when potentials are applied to the electrodes according to the preferred method; 
         FIG. 5A  depicts a rectilinear ion trap according to the present invention including interstitial electrodes between adjacent pseudopotential wells; 
         FIG. 5B  is a cross sectional view of the rectilinear ion trap of  FIG. 5A . 
         FIG. 6  depicts a rectilinear ion trap according to the present invention incorporated into a mass spectrometer; 
         FIG. 7  depicts an alternate embodiment mass spectrometer incorporating a rectilinear ion trap according to the present invention; 
         FIG. 8A  is an end view of a cylindrical ion trap according to the present invention having two adjacent pseudopotential wells; 
         FIG. 8B  is a side view of a cylindrical ion trap according to the present invention having two adjacent pseudopotential wells; 
         FIG. 8C  is a cross sectional view of a cylindrical ion trap according to the present invention having two adjacent pseudopotential wells; 
         FIG. 9  depicts a cylindrical ion trap having four adjacent pseudopotential wells; and 
         FIG. 10  is a cross sectional view of a hexapolar linear ion trap having two adjacent pseudopotential wells. 
     
    
    
     DETAILED DESCRIPTION 
     While the invention has been shown and described with reference to a number of embodiments thereof, it will be recognized by those skilled in the art that various changes in form and detail may be made herein without departing from the spirit and scope of the invention as defined by the appended claims. 
     As discussed above, the present invention relates generally to the mass spectroscopic analysis of chemical samples and more particularly to mass spectrometry. Specifically, a method is described for the mass spectrometric analysis of a sample. Reference is herein made to the figures, wherein the numerals representing particular parts are consistently used throughout the figures and accompanying discussion. 
       FIG. 3  depicts dual rectilinear ion trap (DRIT)  20  according to a preferred embodiment of the present invention. Ion trap  20  consists of center section  24 , front section  22 , and back section  26 . Each section,  22 ,  24 , and  26  consist of six electrodes arranged symmetrically about two axes,  48  and  50 . Front section  22  consists of electrodes  30   a ,  32   a ,  34   a ,  36   a ,  38   a , and  40   a . Center section  24  consists of electrodes  30 ,  32 ,  34 ,  36 ,  38 , and  40  and back section  26  consists of electrodes  30   b ,  32   b ,  34   b ,  36   b ,  38   b , and  40   b . All the above referenced electrodes forming trap  20  are planar. The dimensions and placement of the above referenced electrodes may be any desired dimensions and placement, however, as an example, all the electrodes forming trap  20  are 10 mm wide and 2 mm thick. As shown in  FIG. 3 , electrodes having the same numerical designation—e.g.  30   a ,  30 , and  30   b —are adjacently aligned and in the same plane. Electrodes  30   a  and  30  and electrodes  30  and  30   b  are separated from each other by 1 mm along the z-axis. Other electrodes are separated similarly from one another along the z-axis. Electrodes  38  and  40  are separated from one another along the x-axis by 2 mm. Similarly, electrodes  30  and  32  are separated from one another along the x-axis by 2 mm. Electrodes  32  and  40  and electrodes  30  and  38  are separated from one another by 12 mm along the y-axis. Electrodes  34  and  36  are separated from each other along the x-axis by 24 mm. The length of the electrodes composing front section  22  and back section  26  is 15 mm. The length of the electrodes composing center section  24  is 40 mm. 
     In alternate embodiments, trap  20  may be “stretched” in one or more dimensions. In the embodiment described above with reference to  FIG. 3 , the interior dimension of trap  20  along the x-axis (24 mm) is twice that along the y-axis (12 mm). In alternate embodiments, the width of electrodes  38 ,  40 ,  30  and  32  along the x-axis may be increased to 13 mm. This increases the inner dimension of trap  20  to 30 mm along the x-axis. As described in the prior art (Z. Ouyang, et al.,  Anal. Chem.  76, 4595 (2004).) stretching a RIT can improve its performance. In a similar manner stretching a DRIT in accordance with the present invention can also improve its performance. 
     In order to establish pseudopotential wells about axes  48  and  50  (shown in  FIG. 4 ) and thereby laterally (i.e. in the x-y plane) that confine ions in trap  20 , an RF potential is applied between the electrodes of trap  20 . In the preferred method of operation, the RF potential has two phases separated by 180°. Both phases have the same amplitude and frequency. The function, amplitude, and frequency of the RF potential may be any desired function, amplitude, and frequency, however, as an example, the RF potential may be sinusoidal having an amplitude of 1 kV pp , and a frequency of 1 MHz. Electrodes having the same numerical designation—e.g.  30   a ,  30 , and  30   b —will have the same phase and amplitude RF applied to them. Electrodes  30   a ,  30 ,  30   b ,  38   a ,  38 , and  38   b  have a first phase of the RF potential applied to them whereas electrodes  32   a ,  32 ,  32   b ,  40   a ,  40 , and  40   b  have a second phase—i.e. 180° away from the first phase—of the RF potential applied to them. Electrodes  34   a ,  34 ,  34   b ,  36   a ,  36 , and  36   b  are held at ground potential. 
     Applying RF potentials as described above produces an electric field in trap  20  as depicted in  FIG. 4 .  FIG. 4  is the result of a calculation of the potential as a function of position inside trap  20  at an instant in time when the RF potential on electrodes  30  and  38  is +100V and the potential on electrodes  32  and  40  is −100V. The potential on electrodes  34  and  36  is 0V. Equipotential lines  46  show clearly that the electric field is quadrupolar near both axes  48  and  50 . That is, if the origin of a Cartesian coordinate system is taken to be on one of axes  48  or  50 , then the potential near that axis will take the form A(x 2 -y 2 )+B, where A and B are constants. Notice that the potential at center plane  49  is 0V even though there is no electrode at this position. Each of the quadrupolar field regions are thus bound on two sides by a ground plane and on two sides by RF electrodes. 
     The RF potential applied to trap  20  establishes a pseudopotential well about axes  48  and  50  such that ions in trap  20  are laterally confined about axes  48  and  50 . To confine ions along axes  48  and  50 , a DC potential may be applied between sections  22 ,  26  and  24 . Any desired DC potential difference may be applied between sections  22 ,  24  and  26 , however, as an example, section  24  may be held at a DC (i.e. time averaged) potential of 0V whereas the potential on sections  22  and  26  may be held at a DC potential of 5V. In such a case positively charged ions will be repelled from sections  22  and  26  and attracted to section  24 . Thus, positively charged ions would be trapped laterally by the RF potential and axially by the DC potential. 
     Trap  20  is operated at a pressure such that ions in trap  20  may be cooled via collisions with gas. Any pressure of any type of gas may be used in conjunction with trap  20 , however, as an example, trap  20  may be maintained at a pressure of greater than about 5E-4 mbar and less than about 1E-2 mbar of nitrogen. 
     Ions may be formed in trap  20  by, for example, laser ionization of analyte gas introduced into trap  20 . Alternatively, analyte ions may be injected into trap  20  from an external ion source. Electrodes  34  and  36  include slots  37  and  39  (see cross sectional view of  FIG. 5B ) respectively through which ions may enter and exit trap  20 . Slots  37  and  39  may be of any desired dimensions, however, as an example, slots  37  and  39  are each 30 mm long and 1 mm high. Ions from an external ion source are accelerated to a kinetic energy sufficient to overcome the pseudopotential barrier formed by the above mentioned RF potential. The ions then pass through slot  37  and into the pseudopotential well around axis  50 . In order to be trapped in the pseudopotential well, the kinetic energy of the ions must then be reduced via collisions with the gas in trap  20 . The gas in trap  20  is therefore ideally maintained at a pressure high enough that the ions have a high probability of undergoing at least one collision in the time necessary for the ion to pass laterally through the pseudopotential well. As discussed above, this is typically a pressure of 5E-4 mbar or higher. 
     Ions may alternatively enter trap  20  via slit  39  in electrode  36 . In such a case the ions would first encounter the pseudopotential well about axis  48 . Ions entering trap  20  through slit  39  will undergo collisions with the gas in trap  20 . With each collision, the ions will lose kinetic energy. If the ions have enough collisions in their first passage between slit  39  and center plane  49 , they will have insufficient energy to overcome the pseudopotential barrier between axis  48  and  50  and will be trapped in the well about axis  48 . Alternatively, if the kinetic energy of ions entering through slit  39  is high or if the pressure of gas in the trap  20  is relatively low, then the ions may not lose enough energy in their first pass between slit  39  and plane  49  and may therefore pass into the well centered on axis  50 . In such a case analyte ions may be distributed between and trapped in both the pseudopotential well centered on axis  48  and that centered on axis  50 . 
     In alternate methods of operation, ions may enter and exit trap  20  along axes  48  and  50  via sections  22  and  26 . As discussed above a DC potential may be applied between sections  22 ,  26 , and  24  in order to trap ions axially within trap  20 . The RF potentials applied as discussed above will also create a pseudopotential barrier along axes  48  and  50  that will tend to prevent ions from entering and exiting trap  20  along axes  48  and  50 . To be injected into trap  20  along axes  48  and  50 , ions must have sufficient kinetic energy and preferably should be injected at the optimum phase in the RF. The injection of ions over the pseudopotentially barrier along axes  48  or  50  or through slots  37  or  39  is similar to the injection of ions into prior art Paul traps. Methods of ion injection known in the prior art with respect to Paul may be used in conjunction with the present invention. Ions may be directed from outside trap  20  with a high velocity along axis  48  into section  22 . The source of ions may have a DC potential higher than that on trap section  22  such that ions are accelerated into section  22 . Once over the RF pseudopotential barrier, the ions may lose energy via collisions with gas and thereby be trapped in section  24 . 
     In alternate embodiments entrance and exit gate electrodes may be placed on either end of trap  20 . Such gate electrodes may, for example, be apertured planar conducting electrodes placed with the apertures on axes  48  and  50  and with the plane occupied by the electrode perpendicular to axes  48  and  50 . Alternate embodiments may include four gate electrodes, a first gate electrode at one end of trap  20  having an aperture aligned with axis  48 , a second gate electrode at the opposite end of trap  20  having an aperture aligned with axis  48 , a third gate electrode at one end of trap  20  having an aperture aligned with axis  50 , and a fourth gate electrode at the opposite end of trap  20  having an aperture aligned with axis  50 . In alternate embodiments, ions may enter trap  20  via the apertures in the gate electrodes. In alternate embodiments, RF and DC potentials may be applied to the gate electrodes so as to prevent and, at other times, allow the ions to pass into or out of trap  20  via the apertures in the gate electrodes. 
     Once ions are trapped in a pseudopotential well they may be manipulated in various previously unavailable, sophisticated ways. Importantly, ions can be transferred without losses, in a selective or an unselective manner, back and forth between the pseudopotential wells. Notice in  FIG. 3  that there is no physical obstruction between the pseudopotential wells centered on axes  48  and  50 . That is, there is nothing between the wells for the ions to collide with. 
     Any type of experiment known in the prior art that can be performed in an ion trap can be performed in conjunction with the present invention. Such experiments include but are not limited to mass analysis by a resonance ejection scan or a mass selective instability scan, resonance excitation, isolation, CID, IRMPD, ETD, and any other fragmentation experiments, ion-molecule reactions, ion-ion reactions, and tandem MS experiments. 
     As with prior art traps, a mass selective instability scan is performed by ramping the RF amplitude applied to electrodes  30 ,  32 ,  38 , and  40  and detecting ions that exit one or both of slots  37  and  39  as a function of RF amplitude. As with prior art traps, the RF is ramped from low to high amplitude and the ions detected are initially of low m/z and are higher m/z as the RF amplitude is increased. The same principles of physics, equations of motion, calibration function, etc. used with prior art traps may be applied to the present invention. 
     A resonance ejection scan in conjunction with the present invention is also performed in much the same manner as with a prior art trap. As the RF amplitude is increased an AC potential is applied between electrodes  34  and  36  in much the same manner as the AC potential is applied to the end caps of a prior art Paul trap. The AC potential is applied at a fixed frequency such that as the RF amplitude is increased, ions of successively higher m/z come into resonance with the AC potential. When the ions come into resonance with the AC potential they pick up energy from the AC potential and are ejected from trap  20  through slots  37  and/or  39 . 
     For the purpose of isolation, mass selective stability experiments may be performed. By applying an appropriate RF and DC to the elements of trap  20 , ion of all but a selected m/z or m/z range can be ejected from trap  20 . A mass selective stability experiment may be performed, for example, by applying the appropriate RF and DC potentials between electrodes  30 ,  32 ,  38 , and  40 . As described above, a first phase of RF is applied to electrodes  30  and  38  whereas a second phase separated from the first by 180° is applied to electrodes  32  and  40 . In a mass selective stability experiment, the DC is applied in a similar manner—i.e. a DC potential of a first polarity is applied to electrodes  30  and  38  and a DC potential of the opposite polarity but the same magnitude is applied to electrodes  32  and  40 . The required RF amplitude and DC potentials can be predicted in the same manner and using the same equations as in prior art traps. 
     Notice that if all analyte ions start in a single pseudopotential well, then the selected analyte ions will remain in that well after the mass selective stability experiment. All other ions will be ejected from trap  20 —i.e. they will reside in neither pseudopotential well. In alternative experiments, selected ions may be transferred from one pseudopotential well to another. In a resonance ejection experiment, for example, assuming all analyte ions start in one pseudopotential well, selected ions can be ejected from one well into the other well of trap  20  by applying the AC potential to only one of electrodes  34  or  36 . In this experiment, a fixed RF amplitude is applied to trap  20 . Assuming all ions start in the pseudopotential well centered on axis  48 , an AC potential is applied to electrode  36 . The frequency of the AC potential is chosen to be in resonance with the secular frequency of the ion of interest and of an amplitude sufficient to eject the ions of interest before collisional cooling can occur. The AC potential amplitude should also be chosen to be as low as possible so that the selectivity of the ejection is as high a possible. Ions of interest will be ejected from the pseudopotential well centered on axis  48 . Some of these ions will be ejected towards the pseudopotential well around axis  50 . Some of these ions will undergo collisions with gas, lose energy, and become trapped in the well centered on axis  50 . The fraction of ions ejected towards the pseudopotential well around axis  50  can be increased by applying a repelling DC potential to electrode  36 . Ions not excited by the AC potential will remain in the well centered on axis  48  and may be subjected to further manipulations and experiments. 
     The selected ions that are transferred by resonance excitation to the pseudopotential well around axis  50  may be further manipulated, fragmented, reacted, and otherwise analyzed. To perform a CID experiment on the selected analyte ions, for example, a low amplitude AC potential may be applied to electrode  34 . The AC potential is applied at the resonant frequency of the ion of interest such that the ions gain kinetic energy from the AC potential. An RF amplitude corresponding to a q of greater than about 0.6 can be beneficial during the CID experiment, because it allows for the trapping of more highly excited precursor ions. Through collisions with gas while under the influence of the AC potential, the selected ions are activated towards dissociation. Some of the dissociation products are ionized and can be further analyzed. These fragment ions can be mass analyzed directly by, for example, a resonance ejection scan in trap  20 . Alternatively, the fragment and remaining precursor ions can be mass inselectively transferred to another mass analyzer for mass analysis there. Alternatively, a selected fragment ion may be isolated by, for example, mass selective stability and then further fragmented as in the course of an MS 3  or MS n  experiment. 
     Once the ions of interested have been fully analyzed and ejected from trap  20 , one or more of the ion types remaining in the pseudopotential well about axis  48  may be selected by resonance ejection and thereby transferred to the well about axis  50 . The above set of experiments may then be performed on this second set of ions of interest. This process may be repeated as many times as desired or until all of the original set of analyte ions trapped in the well about axis  48  have been consumed. 
     To perform a resonance ejection scan of the fragment and remaining precursor ions in the well about axis  50  without disturbing the ions remaining in the well about axis  48 . The AC potential is applied to electrode  34  at a frequency corresponding to a relatively low q. As the RF amplitude is increased, ions will be ejected from the well around axis  50  but not from the well around axis  48  because the ions in the well around axis  48  do not experience the AC potential applied to electrode  34 . The frequency of the AC potential is chosen such that the fragment ions of interest are ejected before the ions in the well about axis  48  become unstable due to the RF ramp. 
     To perform the mass unselective transfer mentioned above the DC potential difference between sections  26  and the downstream optics adjacent to trap  20  is increased so as to push the ions over the above mentioned axial pseudopotential barrier. In the case where gate electrodes are used, the potential on the gate electrode centered on axis  50  and adjacent to section  26  is made sufficiently attractive to pull the ions out through the axial pseudopotential. 
     As alternatives to CID other fragmentation may be used to form fragment ions from precursor ions of interest. Such methods include IR multiphoton dissociation (IRMPD), electron capture dissociation (ECD), electron transfer dissociation (ETD), or any other known method of fragmenting ions. To perform ETD, for example, one need only introduce ETD reagent ions into the well about axis  50  with the ions of interest. The axial and radial pseudopotential barriers will simultaneously hold both the positively charged analyte ions of interest and the negatively charged ETD reagent ions in the well about axis  50 . As the analyte and reagent ions mix, they will react and form fragments from the analyte ions. ETD reagent ions can be introduced into trap  20  through slits  37  or  39  or along axes  48  or  50  in the same manner as described above with respect to the introduction of analyte ions. 
     In an alternative experiment, one might inject multiply charged positive analyte ions into the pseudopotential well about axis  48  and negatively charged reagent ions in the well about axis  50 . Once the wells are filled with a selected number of ions, the reagent ions are transferred to the analyte well. The transfer may be achieved by resonance ejection from the well about axis  50  or a repulsive DC potential might be applied to electrodes  32 ,  34 , and  40  sufficient to push the reagent ions out of the well about axis  50 . Once mixed, the analyte and reagent ions will react to form product ions. Products of the ion-ion reaction can be analyzed directly in DRIT  20  or the products may be transferred mass unselectively to a downstream analyzer. The downstream mass analyzer may be of any known type including FTICR, TOF, or quadrupole mass analyzer. Alternatively, all analyte component ions are trapped in a first well and reagent ions in a second. Then, as described above, only selected analyte precursor ions are resonantly ejected from the first well into the second, while all remaining analyte ions are retained in the first well. 
     Turning next to  FIG. 5A , an alternate embodiment of trap  52  according to the present invention is shown which has interstitial electrodes  42 ,  44 ,  42   a ,  44   a ,  42   b , and  44   b  positioned on central plane  49  between RF electrodes  30 ,  32 ,  38 , and  40 .  FIG. 5B  shows a cross sectional view of trap  52  through center section  24 . Interstitial electrodes  42  and  44  are positioned to leave gap  43  between them. Electrodes  42  and  44  are positioned such that ions may pass from the well about axis  48  to the well about axis  50  via gap  43 . The dimensions and placement of electrodes may be any dimension and placement, however, as an example, the thickness of electrodes  42  and  44  is 0.5 mm and gap  43  between electrodes  42  and  44  is 3 mm. In alternate embodiments, thinner interstitial electrodes may be beneficial in that thinner electrodes would distort the electric field less. In further alternate embodiments, interstitial electrodes  42  and  44  may be replaced by an electrically conducting mesh which covers the entire central plane  49  within trap  52 . 
     Any desired potential may be applied to interstitial electrodes  42  and  44 , however, as an example, during ion trapping, interstitial electrodes  42  and  44  have no RF applied to them and are at the same DC potential as electrodes  34  and  36 . The main benefit of interstitial electrodes  42  and  44  is to electrically isolate the regions around axis  48  and axis  50  during ion manipulations such as resonant ejection or excitation. When performing experiments in which ions in both pseudopotential wells are to be excited, an AC potential may be applied between interstitial electrodes  42  and  44  and electrode  34  and between interstitial electrodes  42  and  44  and electrode  36 . However, when it is desired that only ions in the pseudopotential well about axis  48  be excited, then an AC potential may be applied only between interstitial electrodes  42  and  44  and electrode  36 . Alternatively, to mass unselectively eject all ions from the well about axis  48  into that about axis  50 , repulsive DC potentials may be applied to electrodes  30 ,  36 , and  38 . The DC electric field thus produced does not penetrate as far into the region about axis  50  as it would if interstitial electrodes  42  and  44  were not present. Thus, the presence of interstitial electrodes  42  and  44  reduces the influence of field about one axis on ions near the other axis. 
     In alternate methods of operation, RF is applied also to interstitial electrodes  42  and  44 . In one such method, the above mentioned first phase of RF is applied to electrodes  38 ,  40 ,  30 , and  32  and a second phase of RF separated from the first phase by 180° is applied to electrodes  36 ,  37 , and interstitial electrodes  42  and  44 . By applying the RF potentials in this manner, the axial pseudopotential barrier discussed above can be reduced or eliminated. The reduction or elimination of the axial pseudopotential barrier depends on the dimensions and placement of interstitial electrodes  42  and  44 . If gap  43  is made to be smaller then the axial pseudopotential barrier will also tend to be smaller. Also, the asymmetric placement of the surfaces of interstitial electrodes  42  and  44  in trap  52  can be used to reduce the axial pseudopotential. In  FIG. 5B  notice that the plane occupied by the surface of electrodes  42  and  44  nearest axis  48  is 0.25 mm nearer axis  48  than the inner surface of electrode  36 . Also notice that interstitial electrodes  42  and  44  extend vertically further than electrodes  36  and  34 . Both the asymmetric placement and further vertical extension of electrodes  42  and  44  will tend to compensate for the presence of gap  43  in the present mode of operation. That is, the presence of slots  37 , and  39  and gap  43  lead to asymmetries in the electric fields around axes  48  and  50  as well as an axial pseudopotential. The asymmetric placement and vertical extension of electrodes  42  and  44  can be used to partially bring the electric fields back into symmetry and to reduce the axial pseudopotential barrier. 
     In further alternate embodiments, electrodes  42   a  and  44   a  may be replaced by a single electrode extending vertically through trap  52  on center plane  49  in section  22 . Similarly electrodes  42   b  and  44   b  may be replaced by a single electrode extending vertically through trap  52  on center plane  49  in section  26 . Finally, electrodes  42  and  44  may be replaced by a single electrode extending vertically through trap  52  on center plane  49  in section  24 . Such a contiguous interstitial electrode in center section  24  would include a slot of similar dimensions as slots  37  and  39  such that ions can pass through the slot so as to be moved from one pseudopotential well to another. Alternatively the contiguous interstitial electrode in center section  24  may be composed of an electrically conducting mesh such that ions can pass between the wires of the mesh when moving from one pseudopotential well to the other. 
     Turning next to  FIG. 6 , a mass spectrometer incorporating DRIT  52  is depicted. The instrument depicted in  FIG. 6  includes ion source  60 , quadrupole  54 , DRIT  52 , ion detector  62 , hexapole collision cell  68 , and mass analyzer  58 . Each of these components may occupy separate chambers in the instrument&#39;s vacuum system and may be operated at independent pressures. As an example, quadrupole  54  may be operated at a pressure of about 1E-5 mbar of nitrogen, DRIT  52  may be operated at a pressure of about 1E-3 mbar of helium, collision cell  68  may be operated at a pressure of about 1E-3 mbar of argon, analyzer  58  may be operated at a pressure of 1E-10 mbar of residual gas, and detector  62  may be operated at a pressure of 1E-5 mbar of residual gas. 
     Analyte ions are produced from sample material in ion source  60 . Ion source  60  may be any ion source including, but not limited to, electrospray (ESI), matrix assisted laser desorption ionization (MALDI), atmospheric pressure chemical ionization (APCI), chemical ionization (CI), electron ionization (EI), fast atom bombardment (FAB), and any other known source of ions. The particulars of ion sources and their operation is well known in the prior art. A potential difference is maintained between ion source  60  and quadrupole filter  54  such that ions are accelerated from source  60  into quadrupole  54 . 
     Under the influence of an electric field, analyte ions from ion source  60  follow path  64  into quadrupole filter  54 . Because quadrupole  54  is maintained at a relatively low pressure, the ions undergo collisions with the gas only rarely. Thus, the ions retain a kinetic energy equal to the potential difference between source  60  and quadrupole  54  as they pass through quadrupole  54 . Substantially all ions entering quadrupole  54  via path  64  may be allowed to exit quadrupole  54  along path  66  if the quadrupole  54  is operated in RF-only (i.e. transmission) mode. Alternatively, quadrupole  54  may be operated in isolation mode. In isolation mode, ions of a selected m/z or m/z range may pass through quadrupole  54  to the exclusion of ions of all other m/z values. The particulars of quadrupole filters, and their design and operation are well know in the prior art. 
     A potential difference is maintained between quadrupole  54  and DRIT  52  such that ions are further accelerated from quadrupole  54  into DRIT  52 . Under the influence of the electric field, selected ions pass out of quadrupole  54  along path  66  into DRIT  52 . Ions enter DRIT  52  via an aperture in a gate electrode centered on axis  48 . As discussed above the ions become trapped through a combination of collisions with gas that cause the selected ions to lose kinetic energy, the pseudopotential that confines the ions radially about axis  48  and DC potentials between sections  22 ,  24  and  26 . 
     Ions of interest are transferred from the pseudopotential well about axis  48  to the well about axis  50  via resonant ejection as described above. As further discussed above, the ions of interest may be caused to fragment by CID, IRMPD, ETD, or any other known fragmentation method while trapped in the well about axis  50 . Alternatively, the ions may be caused to undergo ion-molecule or ion-ion reactions as described above and in the prior art. The product ions and remaining precursor ions of such manipulations can be analyzed by a resonance ejection scan into detector  60  or they can be mass unselectively ejected via path  70  into hexapole collision cell  68 . 
     The mass unselective ejection of ions along path  70  may be accomplished by making the DC potential applied to section  26  more attractive to the ions while simultaneously making that on section  22  more repulsive. Also, the gate electrode centered on axis  50  adjacent to section  26  and collision hexapole  68  are successively more attractive still. As a result the product and remaining precursor ions are accelerated by the DC electric fields along axis  50  and path  70  into hexapole collision cell  68 . 
     The potential difference between section  24  and collision cell  68  defines the kinetic energy the ions will have as they enter collision cell  68 . If the potential difference is high enough, then the kinetic energy of the ions will be sufficient to cause CID. In alternative experiments, a product ion of interest—e.g. a fragment ion—may be selected, for example by mass selective stability, while still in section  24  of DRIT  52 . The CID product ions formed in collision cell  68  would then be second generation fragment ions. The end result of such an experiment would be an MS 3  spectrum. 
     Collision cell  68  includes a hexapole composed of six rods to which an RF potential is applied. Ions are confined radially in the hexapole via the RF field. Ions are confined axially by the application of DC potentials applied to entrance and exit electrodes (not shown). The construction and operation of hexapoles and collision cells is well known in the prior art. In alternate embodiments the collision cell may be composed of a multipole of any number of rods—i.e. quadrupole, octapole, etc. 
     During the injection of ions into collision cell  68 , the exit electrode is held at a trapping DC potential—that is the electrode between the hexapole of collision cell  68  and analyzer  58  is held at a DC potential substantially more repulsive to the ions than that applied to the hexpole of collision cell  68 . After injection into collision cell  68 , the ions lose kinetic energy via collisions with gas in collision cell  68  and may form fragment ions or other product ions. 
     The ions are then ejected from collision cell  68  into analyzer  58  along path  72 . To eject the ions from collision cell  68 , the DC potential on the exit electrode is made more attractive to the ions than that on the hexapole of collision cell  68 . The potential on collision cell  68  is also held at a more repulsive potential than that on the entrance of analyzer  58 . The potential difference between collision cell  68  and analyzer  58  accelerates the ions along path  72  into analyzer  58 . In analyzer  58 , the ions are mass analyzed and detected so as to form a mass spectrum. Mass analyzer  58  may be any known type of mass analyzer including but not limited to a Fourier transform ion cyclotron (FTICR) mass analyzer, a time of flight (TOF) mass analyzer, a quadrupole mass analyzer, a magnetic or electric sector mass analyzer, a Paul trap, or an Orbitrap. 
     In an alternate embodiment instrument as depicted in  FIG. 7 , source  60  and quadrupole  54  are oriented orthogonal to DRIT  52 . The operation of the instrument of  FIG. 7  is similar to that of the instrument of  FIG. 6 , except that ions follow path  74  between quadrupole  54  and DRIT  52  and enter DRIT  52  via slot  39 . As described above ions are injected into trap  52  via slot  39  with enough kinetic energy to overcome the pseudopotential barrier at slot  39 . The ions undergo collisions with gas in trap  52 , lose kinetic energy, and become trapped in the pseudopotential well about axis  48 . As discussed above selected ions are transferred along path  76  into the pseudopotential well about axis  50 , manipulated according to the desired experiment, transferred to collision cell  68 , and finally to analyzer  58 . 
       FIG. 8  depicts a dual cylindrical ion trap (DCIT) according to the present invention.  FIG. 8A  is an end view of the DCIT.  FIG. 8B  is a side view of the DCIT. And  FIG. 8C  is a cross sectional view of the DCIT according to the present invention taken at line A-A in  FIG. 8A . As depicted in  FIG. 8 , DCIT  80  consists of two adjacent identical cylinders  82  and  84  and two endplate electrodes  86  and  88 . All elements  82 ,  84 ,  86 , and  88  are electrically conducting, cylindrically symmetric, and positioned on a common axis. Endplate electrodes  86  and  88  include apertures  90  and  92  through which ions may pass so as to enter or exit trap  80 . The gap between adjacent cylinder electrodes  82  and  84  is twice the gap between cylinders  82  and  84  and adjacent endplate electrodes  86  and  88  respectively. In alternate embodiments the gap between adjacent electrodes  82 ,  84 ,  86 , and  88  may be any suitable distance. 
     Electrodes of any desired dimension and placement may be used to construct DCIT  80 , however, as an example, the inner diameter and outer diameter of electrodes  82  and  84  is 10 mm and 19 mm respectively. The length of electrodes  82  and  84  along their axis of symmetry is 7.4 mm. The gap between electrodes  82  and  84  is 3.2 mm. The gap between electrodes  82  and  86  and between  84  and  88  is 1.6 mm. The thickness of electrodes  86  and  88  is 0.5 mm. And the diameter of apertures  90  and  92  is 1 mm. In alternate embodiments, cylindrical electrodes  82  and  84  may have curved inner surfaces that may approximate round or hyperbolic surfaces. 
     In order to establish pseudopotential wells about the center of cylinders  82  and  84  and thereby confine ions in trap  80 , an RF potential is applied between electrodes  82  and  84 . In the preferred method of operation, the RF potential has two phases separated by 180°. Both phases have the same amplitude and frequency. The function, amplitude, and frequency of the RF potential may be any desired function, amplitude, and frequency, however, as an example, the RF potential may be sinusoidal having an amplitude of 1 kV pp , and a frequency of 1 MHz. Electrode  82  has a first phase of the RF potential applied to it whereas electrode  84  has a second phase—i.e. 180° away from the first phase—of the RF potential applied to it. Electrodes  86  and  88  are held at ground potential. 
     Applying RF potentials as described above produces an electric field in trap  80  that is quadrupolar near the center of both electrodes  82  and  84 . That is, if the origin of a Cartesian coordinate system is taken to be at the center of one of electrodes  82  or  84 , then the potential near that point will take the form A(r 2 -2z 2 )+B, where A and B are constants, z is along the axis of symmetry and r is the distance from the axis of symmetry. Notice that the potential at center plane  89  is 0V even though there is no electrode at this position. Each of the quadrupolar field regions are thus bound on two sides by a ground plane and on two sides by RF electrodes. 
     Trap  80  is operated at a pressure such that ions in trap  80  may be cooled via collisions with gas. Any pressure of any type of gas may be used in conjunction with trap  80 , however, as an example, trap  80  may be maintained at a pressure of greater than about 5E-4 mbar and less than about 1E-2 mbar of nitrogen. 
     Ions may be formed in trap  80  by, for example, laser ionization of analyte gas introduced into trap  80 . Alternatively, analyte ions may be injected into trap  80  from an external ion source. Electrodes  86  and  88  include apertures  90  and  92  (see cross sectional view of  FIG. 8C ) respectively through which ions may enter and exit trap  80 . Ions from an external ion source are accelerated to a kinetic energy sufficient to overcome the pseudopotential barrier formed by the above mentioned RF potential. The ions then pass through aperture  90  and into the pseudopotential well around the center of electrode  82 . In order to be trapped in the pseudopotential well, the kinetic energy of the ions must then be reduced via collisions with the gas in trap  80 . The gas in trap  80  is therefore ideally maintained at a pressure high enough that the ions have a high probability of undergoing at least one collision in the time necessary for the ion to pass through the pseudopotential well along the z axis. As discussed above, this is typically a pressure of 5E-4 mbar or higher. 
     Ions may alternatively enter trap  80  via aperture  92  in electrode  88 . In such a case the ions would first encounter the pseudopotential well about the center of electrode  84 . Ions entering trap  80  through aperture  92  will undergo collisions with the gas in trap  80 . With each collision, the ions will lose kinetic energy. If the ions have enough collisions in their first passage between aperture  92  and center plane  89 , they will have insufficient energy to overcome the pseudopotential barrier between the center of electrode  82  and  84  and will be trapped in the well about the center of electrode  84 . Alternatively, if the kinetic energy of ions entering through aperture  92  is high or if the pressure of gas in the trap  80  is relatively low, then the ions may not lose enough energy in their first pass between aperture  92  and plane  89  and may therefore pass into the well about the center of electrode  82 . In such a case analyte ions may be distributed between and trapped in both the pseudopotential well about the center of electrode  82  and that about the center of electrode  84 . 
     Once ions are trapped in a pseudopotential well, they may be manipulated in various previously unavailable, sophisticated ways. Importantly, ions can be transferred without losses, in a selective or unselective manner, back and forth between the pseudopotential wells. Notice in  FIG. 8  that there is no physical obstruction between the pseudopotential wells about the centers of electrodes  82  and  84 . That is, there is nothing between the wells for the ions to collide with. 
     Any type of experiment known in the prior art that can be performed in an ion trap can also be performed in conjunction with the present invention. Such experiments include but are not limited to mass analysis by a resonance ejection scan or a mass selective instability scan, resonance excitation, isolation, CID, IRMPD, ETD, and any other fragmentation experiments, ion-molecule reactions, ion-ion reactions, and tandem MS experiments. 
     As with prior art traps, a mass selective instability scan is performed by ramping the RF amplitude applied to electrodes  82  and  84  and detecting ions that exit one or both of apertures  86  and  88  as a function of RF amplitude. As with prior art traps, the RF is ramped from low to high amplitude and the ions detected are initially of low m/z and are higher m/z as the RF amplitude is increased. The same principles of physics, equations of motion, calibration function, etc. used with prior art cylindrical ion traps may be applied to the present invention. 
     A resonance ejection scan in conjunction with the present invention is also performed in much the same manner as with a prior art trap. As the RF amplitude is increased an AC potential is applied between electrodes  86  and  88  in much the same manner as the AC potential is applied to the end caps of a prior art Paul trap. The AC potential is applied at a fixed frequency such that as the RF amplitude is increased, ions of successively higher m/z come into resonance with the AC potential. When the ions come into resonance with the AC potential they pick up energy from the AC potential and are ejected from trap  80  through apertures  90  and/or  92 . 
     For the purpose of isolation, mass selective stability experiments may be performed. By applying an appropriate RF and DC potentials to the elements of trap  80 , ions of all but a selected m/z or m/z range can be ejected from trap  80 . A mass selective stability experiment may be performed, for example, by applying the appropriate RF and DC potentials between electrodes  82  and  84 . As described above a first phase of RF is applied to electrode  82  whereas a second phase separated from the first by 180° is applied to electrode  84 . In a mass selective stability experiment, the DC is applied in a similar manner—i.e. a DC potential of a first polarity is applied to electrode  82  and a DC potential of the opposite polarity but the same magnitude is applied to electrode  84 . The required RF amplitude and DC potentials can be predicted in the same manner and using the same equations as in prior art traps. 
     Notice that if all analyte ions start in a single pseudopotential well, then the selected analyte ions will remain in that well after the mass selective stability experiment. All other ions will be ejected from trap  80 —i.e. they will reside in neither pseudopotential well. In alternative experiments, selected ions may be transferred from one pseudopotential well to another. In a resonance ejection experiment, for example, assuming all analyte ions start in one pseudopotential well, selected ions can be ejected from one well into the other well of trap  80  by applying the AC potential to only one of electrodes  86  or  88 . In this experiment, a fixed RF amplitude is applied to trap  80 . Assuming all ions start in the pseudopotential well about the center of electrode  82 , an AC potential is applied to electrode  86 . The frequency of the AC potential is chosen to be in resonance with the secular frequency of the ion of interest and of an amplitude sufficient to eject the ions of interest before collisional cooling can occur. The AC potential amplitude should also be chosen to be as low as possible so that the selectivity of the ejection is as high a possible. Ions of interest will be ejected from the pseudopotential well about the center of electrode  82 . Some of these ions will be ejected towards the pseudopotential well around the center of electrode  84 . Some of these ions will undergo collisions with gas, lose energy, and become trapped in the well around the center of electrode  84 . The fraction of ions ejected towards the pseudopotential well around the center of electrode  84  can be increased by applying a repelling DC potential to electrode  86 . Ions not excited by the AC potential will remain in the well around the center of electrode  82  and may be subjected to further manipulations and experiments. 
     The selected ions that are transferred by resonance excitation to the pseudopotential well around the center of electrode  84  may be further manipulated, fragmented, reacted, and otherwise analyzed. To perform a CID experiment on the selected analyte ions, for example, a low amplitude AC potential may be applied to electrode  88 . The AC potential is applied at the resonant frequency of the ion of interest such that the ions gain kinetic energy from the AC potential. An RF amplitude corresponding to a q of greater than about 0.6 can be beneficial during the CID experiment, because it allows for the trapping of more highly excited precursor ions. Through collisions with gas while under the influence of the AC potential, the selected ions are activated towards dissociation. Some of the dissociation products are ionized and can be further analyzed. These fragment ions can be mass analyzed directly by, for example, a resonance ejection scan in trap  80 . 
     Once the ions of interested have been fully analyzed and ejected from trap  80 , one or more of the ion types remaining in the pseudopotential well about the center of electrode  82  may be selected by resonance ejection and thereby transferred to the well about the center of electrode  84 . The above set of experiments may then be performed on this second set of ions of interest. This process may be repeated as many times as desired or until all of the original set of analyte ions trapped in the well about the center of electrode  82  have been consumed. 
     To perform a resonance ejection scan of the fragment and remaining precursor ions in the well about the center of electrode  84  without disturbing the ions remaining in the well about the center of electrode  82 , the AC potential is applied to electrode  88  at a frequency corresponding to a relatively low q. As the RF amplitude increased, ions will be ejected from the well around the center of electrode  84  but not from the well around the center of electrode  82  because the ions in the well around the center of electrode  82  do not experience the AC potential applied to electrode  88 . The frequency of the AC potential is chosen such that the fragment ions of interest are ejected before the ions in the well about the center of electrode  82  become unstable due to the RF ramp. 
     As alternatives to CID other fragmentation may be used to form fragment ions from precursor ions of interest. Such methods include IR multiphoton dissociation (IRMPD), electron capture dissociation (ECD), electron transfer dissociation (ETD), or any other known method of fragmenting ions. To perform ETD, for example, one need only introduce ETD reagent ions into the well about the center of electrode  84  with the ions of interest. The pseudopotential barrier will simultaneously hold both the positively charged analyte ions of interest and the negatively charged ETD reagent ions in the well about the center of electrode  84 . As the analyte and reagent ions mix, they will react and form fragments from the analyte ions. ETD reagent ions can be introduced into trap  80  through apertures  90  or  92  in the same manner as described above with respect to the introduction of analyte ions. 
     In an alternative experiment, one might inject multiply charged positive analyte ions into the pseudopotential well about the center of electrode  82  and negatively charged reagent ions in the well about the center of electrode  84 . Once the wells are filled with a selected number of ions, the reagent ions are transferred to the analyte well. The transfer may be achieved by resonance ejection from the well about the center of electrode  84  or a repulsive DC potential might be applied to electrodes  84  and  88  sufficient to push the reagent ions out of the well about the center of electrode  84 . Products of the ion-ion reaction can be analyzed directly in DCIT  80  or the products may be transferred mass unselectively to a downstream analyzer. The downstream mass analyzer may be of any known type including FTICR, TOF, or quadrupole mass analyzer. Alternatively, all analyte component ions are trapped in a first well and reagent ions in a second. Then, as described above, only selected analyte precursor ions are resonantly ejected from the first well into the second, while all remaining analyte ions are retained in the first well. 
     In the alternate embodiment of  FIG. 9 , additional ring electrodes  94  and  96  have been added so as to form a trap capable of four pseudopotential wells. Electrodes  94  and  96  are substantially identical in dimension and composition to electrodes  82  and  84 . All electrodes  86 ,  82 ,  84 ,  94 ,  96 , and  88  are cylindrically symmetric and centered on a common axis. Electrodes  82 ,  84 ,  94 , and  96  are equally spaced along their common axis. 
     In alternate embodiments, electrodes of any desired dimension and placement may be used, however, as an example, the inner diameter and outer diameter of electrodes  82 ,  84 ,  94 , and  96  is 10 mm and 19 mm respectively. The length of electrodes  82 ,  84 ,  94 , and  96  along their axis of symmetry is 7.4 mm. The gap between adjacent electrodes  82 ,  84 ,  94 , and  96  is 3.2 mm. The gap between electrodes  82  and  86  and between  96  and  88  is 1.6 mm. The thickness of electrodes  86  and  88  is 0.5 mm. And the diameter of apertures  90  and  92  is 1 mm. In alternate embodiments cylindrical electrodes  82 ,  84 ,  94 , and  96  may have curved inner surfaces that may approximate round or hyperbolic surfaces. 
     In order to establish pseudopotential wells about the center of cylinders  82 ,  84 ,  94 , and  96  and thereby confine ions in trap  98 , an RF potential is applied between electrodes  82 ,  84 ,  94 , and  96 . In the preferred method of operation, the RF potential has two phases separated by 180°. Both phases have the same amplitude and frequency. The function, amplitude, and frequency of the RF potential may be any desired function, amplitude, and frequency, however, as an example, the RF potential may be sinusoidal having an amplitude of 1 kV pp , and a frequency of 1 MHz. Electrodes  82  and  94  have a first phase of the RF potential applied to them whereas electrodes  84  and  96  have a second phase—i.e. 180° away from the first phase—of the RF potential applied to them. Electrodes  86  and  88  are held at ground potential. 
     The operation of quadruple cylindrical ion trap  98  is substantially the same as described above with respect to trap  80 . However, as depicted in  FIG. 9 , cylindrical ion trap  98  consists of four cylindrical electrodes  82 ,  84 ,  94 , and  96 , each of which will have a pseudopotential well at its geometric center. Ions may be transferred between adjacent pseudopotential wells, manipulated, and mass analyzed as described above with respect to trap  80 . In alternate embodiments any number of cylindrical electrodes may be used in such a trapping arrangement to produce a trap having any desired number of pseudopotential wells. To drive the trap, the RF applied to any given cylindrical electrode is 180° out of phase with that applied to adjacent cylindrical electrodes. 
     In alternate embodiments interstitial electrodes may be placed between adjacent cylindrical electrodes. The interstitial electrodes would be held at a ground potential. The interstitial electrodes may be planar electrodes having apertures aligned with the axis of symmetry of the trap. Alternatively, the interstitial electrodes may be composed of electrically conducting mesh. 
     Similarly, in alternate embodiments, dual rectilinear ion traps  20  and  52  may be extended to include as many pseudopotential wells as desired. Additional electrodes having the same dimensions as electrodes  32  and  40  are spaced equally along the x-axis adjacent to and in the same plane as electrodes  32  and  40 . The RF applied to any given electrode is 180° out of phase with that applied to adjacent electrodes along the x-axis. The RF applied to any given electrode has the same phase as that applied to adjacent electrodes along the y-axis. Interstitial electrodes may also be placed between adjacent sets of RF electrodes and may be used in the manipulation of ions as described above. 
       FIG. 10  is a cross sectional view of a dual hexapole linear ion trap  100  according to the present invention. As depicted in  FIG. 10 , dual hexpole linear ion trap  100  consists of ten electrically conducting rods  102 ,  104 ,  106 ,  108 ,  110 ,  112 ,  114 ,  116 ,  118 , and  120  equally spaced, and symmetrically centered about two axes  124  and  126 . Similar to dual rectilinear ion trap  20 , rods  102 - 120  extend parallel to axes  124  and  126  into and out of the page. The surface of rods  102 - 120  facing axes  124  and  126  is planar and normal to a line extending from the axis about which they are centered. The distance between axis  124  and then inner surface of electrodes  114  is the same as the distance between axis  124  and central plane  122 . Similarly, the distance between axis  126  and the inner surface of electrodes  120  is the same as the distance between axis  126  and central plane  122 . 
     In alternate embodiments, electrodes of any desired dimension and placement may be used, however, as an example, the distance between axis  124  and the midpoint of the inner surface electrodes  102 ,  104 ,  110 ,  112 , and  114 —i.e. the inner radius of the hexapole formed around axis  124 —is 2.5 mm. Similarly, the distance between axis  126  and the midpoint of the inner surface electrodes  106 ,  108 ,  116 ,  118 , and  120 —i.e. the inner radius of the hexapole formed around axis  126 —is also 2.5 mm. The width of the inner surface of electrodes  102 - 120  is 2 mm and their length along axis  124  is 100 mm. 
     In order to establish pseudopotential wells about axes  124  and  126  and thereby confine ions in trap  100 , an RF potential is applied between electrodes  102 - 120 . In the preferred method of operation, the RF potential has two phases separated by 180°. Both phases have the same amplitude and frequency. The function, amplitude, and frequency of the RF potential may be any desired function, amplitude, and frequency, however, as an example, the RF potential may be sinusoidal having an amplitude of 600 V pp , and a frequency of 2 MHz. Electrodes  110 ,  112 , and  114  have a first phase of the RF potential applied to them whereas electrodes  116 ,  118 , and  120  have a second phase—i.e. 180° away from the first phase—of the RF potential applied to them. Electrodes  102 ,  104 ,  106 ,  108  are held at ground potential. In alternate embodiments interstitial electrodes may be placed at plane  122  in a similar manner as described above with respect to traps  52  and  80 . 
     In alternate embodiments the concepts presented above may be extended to higher order linear or cylindrical trapping devices—i.e. hexapole, octapole, dodecapole, etc. 
     While the present invention has been described with reference to one or more preferred and alternate embodiments, such embodiments are merely exemplary and are not intended to be limiting or represent an exhaustive enumeration of all aspects of the invention. The scope of the invention, therefore, shall be defined solely by the following claims. Further, it will be apparent to those of skill in the art that numerous changes may be made in such details without departing from the spirit and the principles of the invention. It should be appreciated that the present invention is capable of being embodied in other forms without departing from its essential characteristics.
In an apparatus for performing a mass spectrometric analysis of a sample, a plurality of electrodes are positioned and driven by RF potentials to form a plurality of adjacent pseudopotential wells. Ions may be manipulated, reacted, analyzed, and ejected from the apparatus in a manner similar to conventional ion traps. In addition, selected ions or groups of ions may be passed from one pseudopotential well to another pseudopotential well without ion losses due to physical obstructions. The apparatus may be used alone or in conjunction with other mass analyzers to produce mass spectra from analyte ions.