PATENT ABSTRACT
Apparatus and methods are provided for trapping, manipulation and transferring ions along RF and DC potential surfaces and through RF ion guides. Potential wells are formed near RF-field generating surfaces due to the overlap of the radio-frequency (RF) fields and electrostatic fields created by static potentials applied to surrounding electrodes. Ions can be constrained and accumulated over time in such wells. During confinement, ions may be subjected to various processes, such as accumulation, fragmentation, collisional cooling, focusing, mass-to-charge filtering, spatial separation ion mobility and chemical interactions, leading to improved performance in subsequent processing and analysis steps, such as mass analysis. Alternatively, the motion of ions may be better manipulated during confinement to improve the efficiency of their transport to specific locations, such as an entrance aperture into vacuum from atmospheric pressure or into a subsequent vacuum stage.

PATENT DESCRIPTION
CROSS-REFERENCE TO RELATED APPLICATION  
       [0001]     This application claims priority to U.S. Provisional Application No. 60/573,667, filed on May 21, 2004, the disclosure of which is incorporated herein by reference in its entirety. 
     
    
     FIELD OF THE INVENTION  
       [0002]     The present invention relates to mass spectrometry and in particular to apparatus and methods for temporary storage, manipulation and transport of ions using a combination of radio-frequency fields and electrostatic fields in mass spectrometric analysis.  
       BACKGROUND OF THE INVENTION  
       [0003]     The application of mass spectrometry to the chemical analysis of sample substances has grown in recent years due in large part to advances in instrumentation and methods. Such advances include improved ionization sources, more efficient ion transport devices, more sophisticated ion processing, manipulation and separation methods, and mass-to-charge (m/z) analyzers with greater performance. However, while much progress has been made in these areas, there remains the potential for substantial improvements.  
         [0004]     In particular, compromises must often be made in order to maximize a particular performance characteristic or enable a particular functionality. For example, orthogonal pulse-acceleration has evolved as a preferred solution to the problem of coupling continuous ionization sources to a time-of-flight mass-to-charge analyzer (TOF MS), which require a well-defined pulsed introduction of ions. This approach has been refined to the point that mass-to-charge resolving power greater than 10,000 full-width-at-half-maximum (FWHM) can now be routinely achieved with such configurations. However, there is often a trade-off between sensitivity and resolving power, for example, when portions of the angular and/or spatial distributions of the sampled ion population must be sacrificed in order to achieve high resolving power. There may also be trade-offs between duty cycle directly related to sensitivity and m/z range, due to the reduction in repetition rate that is often required in order to accommodate the long flight times of high-m/z ions. Typically, a relatively small portion of the sample ion population from a continuous ion beam may be analyzed at a time, resulting in relatively low duty cycle efficiency. One approach to address such problems was described by Dresch, et al. in U.S. Pat. No. 5,689,111. Essentially, a multipole ion guide, used to transport ions generated in an ion source to a time-of-flight mass analyzer, was configured with an electrode at the exit end, to which potentials could be rapidly applied that either trap ions in the ion guide to store them between time-of-flight analyses, or release them into the time-of-flight pulsing region for analysis. A substantial improvement in duty cycle efficiency was realized, which approached 100%, but only over a limited m/z range, depending on the relative timing of the release of ions from the ion guide and the pulsing of ions into the TOF analyzer. For ion m/z values outside the selected high duty cycle m/z range, this approach introduces a reduction in duty cycle due to the m/z separation that accompanies the transfer of ions released from the ion guide into the orthogonal pulse-acceleration region of the time-of-flight mass-to-charge analyzer. Hence, as the duty cycle efficiency is increased for a selected range of m/z values, the duty cycle decreases for m/z values outside the selected range. Nevertheless, enhancement of the duty cycle for a selective m/z range can be advantageous for some analytical applications, particularly in targeted analysis. For other analytical applications, however, a high duty cycle and sensitivity is required over a wider m/z range than could be achieved with the teaching of Dresch &#39;111. The present invention improves the sensitivity of MS analysis, particularly TOF MS, over a wider range of m/z values.  
         [0005]     There have been other ion storage approaches to address the inherently poor duty cycle efficiency of TOF analyzers. For example, Lubman, et. al., in Anal. Chem. 66, 1630 (1994), and references therein, describe a configuration which incorporates a Paul three-dimensional RF-quadrupole ion trap as the TOF pulsing region for externally-generated ions. Ions can be accumulated prior to pulsing them out of the trap and into the TOF drift region. However, the continuous transfer of externally-generated ions into such a three-dimensional RF-quadrupole ion trap is problematic because ions with energies low enough to be trapped will only be able to overcome the RF fields and enter the trap during a relatively short segment of the RF cycle time, resulting in a relatively low duty cycle. Another disadvantage is that such an electrode geometry produces pulsed TOF acceleration fields that are generally not optimum for achieving maximum TOF mass resolving power.  
         [0006]     Also, Enke, et. al., J. Amer. Soc. Mass Spec. 7, 1009 (1996) describe a three-dimensional planar electrode ion trap configured as the pulsing region of a TOF mass spectrometer. Sample molecules are internally ionized by electron impact ionization and accumulated in the trap, before pulsing them into the TOF drift region for mass analysis. Relatively poor performance resulted from difficulties in efficient trapping of ions due to the non-ideal trapping fields, as well as from scattering of ions by the sample gas and by the gas introduced to collisionally cool the ions in the trap, which degrades TOF mass resolution and sensitivity. Grix, et. al., had previously described a more direct approach in Int. J. Mass Spectrom. Ion Processes 93, 323 (1989) in which an electron beam is directed to pass through the TOF pulsing region to ionize sample gas molecules. The electron beam is sufficiently intense so that the local potential well produced by the electrons traps a substantial number of ions, until they are pulsed into the TOF drift region for mass analysis. Disadvantages of this approach, as well as that of Enke, et al., include: 1) sample gas is introduced directly into the TOF optics, degrading the vacuum and causing ion scattering; 2) electron impact ionization results in substantial fragmentation which renders this ionization method impractical for mass analysis of many types of samples, such as large biomolecules; and 3) the sample needs to be introduced into the TOF as a gas, which makes this approach incompatible with non-volatile samples; and 4) the ionization efficiency is relatively small given the poor overlap between the neutral sample molecules and the electron beam.  
         [0007]     More recently, Whitehouse et al., describe in U.S. Pat. Nos. 6,683,301 B2 and 6,872,941 another type of ion trapping configuration incorporated into the pulsing region of a TOF analyzer. Essentially, the pulsing electrode in this region is configured as an array of small electrodes arranged along a surface, typically a planar surface. Opposite phases of an RF waveform are applied to neighboring electrodes, thereby generating an RF field highly localized above the array, and conforming to the array surface, as taught by Franzen in U.S. Pat. No. 5,572,035. Such a field acts to repel ions that come close to the array surface, so that, in conjunction with DC potentials applied to additional surrounding electrodes, an effective so-called ‘pseudopotential’ well is formed immediately above the electrode array surface, that is, the ‘RF surface’, in which ions may be trapped. Because the RF fields are highly localized at the RF array surface, ions may be readily transferred into the pulsing region, away from the influence of the RF field during the transfer, with high efficiency. Consequently, Whitehouse &#39;301 and &#39;941 teach that ions may be accumulated in such a trap between TOF introduction pulses, resulting in TOF performance improvements, including reduced m/z discrimination, increased duty cycle efficiency, and improved resolving power.  
         [0008]     However, the inventions disclosed by Whitehouse &#39;301 and &#39;941 require that the RF fields generated by an RF surface be sufficiently intense that ions are not able to come close enough to the RF surface to be trapped in the local potential wells between the RF electrodes. Ions are trapped within essentially a one-dimensional well normal to the RF surface, but are free to move in directions parallel to the RF surface, being trapped in these directions only by voltages applied to electrodes at the boundaries of the pulsing region, resulting in a contained two-dimensional ion ‘gas’, more or less. While such configurations lead to improved TOF performance, nevertheless, the relatively poor localization of trapped ions parallel to the RF surface precludes additional possible improvements and functionalities. For example, fragmentation of trapped ions by photon-induced dissociation via a focused, pulsed laser beam is relatively inefficient because the laser beam pulse is able to intersect only a small fraction of the trapped ion population with each pulse. Further, any interaction between trapped ions and other reagent species, such as electron transfer dissociation (ETD) ions, is relatively inefficient without better spatial localization of the reactant species. Even further, any opportunity to manipulate the spatial distribution of trapped ions is severaly limited, such as the ability to control the separation of the trapped ion population into sub-populations which are then directed to different TOF detectors, thereby providing better dynamic range, as described by Whitehouse, et al., in U.S. Application Publication No. 20020175292. The present invention provides such local three-dimensional trapping, thereby enabling these, and additional, TOF performance and functionality improvements.  
         [0009]     Another area in which progress has been made in recent years, but for which the potential for substantial improvement remains, is the transport of ions from atmospheric pressure ionization (API) sources to a mass-to-charge analyzer in vacuum. Generally, ions produced at atmospheric pressure are transported through an atmospheric-pressure/vacuum interface, and then typically through a series of vacuum pumping stages to a mass-to-charge analyzer under vacuum. A major challenge with such interfaces is to direct as many of the ions produced at atmospheric pressure through one or more small orifices comprising the API interface. This is generally accomplished by a combination of electrostatic electric fields and gas flow dynamics. Focusing ions toward the orifice into vacuum in an API source is typically conducted by applying a DC voltage gradient between the first API interface orifice electrode and the surrounding electrodes. The motion of ions through atmospheric pressure is strongly damped by collisions with background gas, so ion motion is determined by a combination of electric field and gas flow forces. While the applied electrostatic field is effective at drawing the ions in close to the orifice, the same electric field lines terminating on the face or edge of the orifice into vacuum direct the ions onto the conductive surface or edge where they are lost. A portion of the ions directed near the orifice into vacuum are swept through the orifice by the gas expanding into vacuum. The opposing requirements of high electric fields for ion focusing, and low electric fields for ion transport driven by gas dynamics, has resulted in inefficient transport of ions produced at or near atmospheric pressure into vacuum. The present invention provides improvements in the efficiency of ion transport from atmosphere through an orifice into vacuum by mitigating the impact of these competing requirements.  
         [0010]     Another challenge has been to transport ions efficiently through multiple vacuum pumping stages. Generally, multiple vacuum regions separated by vacuum partitions are employed to achieve good vacuum in a downstream vacuum pumping stage, which may, for example, contain a mass-to-charge analyzer. RF multipole ion guides have long been used to transport ions through an individual vacuum stage, and ions have been transported from one stage to the next by focusing them through a vacuum orifice in the vacuum partition between the stages. A significant improvement in the transmission efficiency of ions between vacuum stages was realized with the development of RF multipole ion guides that extend continuously through the vacuum partition between vacuum pumping stages, while also effectively limiting gas flow between the stages, similar to the effect of a vacuum partition orifice, as taught by Whitehouse, et al., in U.S. Pat. Nos. 5,652,427; 5,962,851; 6,188,066; and 6,403,953. Nevertheless, there remain compromises in these configurations between maximizing ion transport efficiency and minimizing gas flow between vacuum pumping stages. The inventions disclosed herein provide improvements over prior art for ion transport, while simultaneously reducing gas flow, between vacuum stages.  
         [0011]     The aforementioned deficiencies in the art are addressed and improvements are provided by the inventions disclosed herein,  
       SUMMARY OF THE INVENTION  
       [0012]     Ions in RF multipole ion guides experience alternating attractive and repulsive forces, due to the alternating electric voltages applied to adjacent electrodes. Integrated over time, the RF surface operates as an ion repulsive surface. A surface of multipole tips approaches the behavior of an RF surface with an infinitely large number of poles, producing a wide field free region bordering on very steep repulsive walls. The ion interaction with the RF field is very short range. As discussed by Dehmelt, in Adv. At. Mol. Physics, 3, 59 (1963), this integrated repelling force field is often called a “pseudo force field, described by a “pseudo potential distribution”. For a single electrode tip, this pseudo potential is proportional to the square of the RF-field strength and decays as a function of distance r from the tip with a 1/r 4  dependence. Additionally, the pseudo potential is inversely proportional to both the particle mass m and the square of the angular RF frequency □ 2 , where ω=2Πf with f equal to the RF frequency. For an array of RF electrode tips, such as will be described in detail below, the pseudo potential near the surface is stronger than that of a single tip and decays even more rapidly as a function of distance from the surface formed by the tip array. In a distance that is large compared to the distance between neighboring electrode tips, the RF-field is negligible. The net effect is the formation of a steep pseudo potential barrier localized very near the multiple electrode surface with low penetration into the space above the surface for ions of moderate kinetic energies. Similar pseudo potential distributions can be formed above surfaces that are composed of alternative electrode array geometries, such as the combination of electrode tips and a grid mesh formed around the tips. The tips and the mesh have opposite RF phases applied or an array of closely-spaced parallel electrodes, where every other electrode has the opposite RF phase applied relative to neighboring electrodes. An alternative RF surface electrode geometry comprises parallel rod electrodes extending the length of the RF surface with opposite phase RF applied to adjacent RF rod electrodes. The minimum number of RF tip electrodes comprising an RF surface is four arranged in a quadrupole configuration with a single ion trapping region or energy well located at the center of the four electrodes. Alternatively an RF surface configured according to the invention may comprise an array of more than four RF electrodes forming multiple ion trapping regions.  
         [0013]     As described by Whitehouse et. al. in U.S. Pat. No. 6,683,301 B2, an electrostatic potential can be applied to a counter electrode positioned above or across from a surface of RF electrodes (RF surface). The counter electrode electrostatic potential can be set relative to the DC offset potential applied to the RF surface electrodes to move ions toward or away from the RF surface. Ions approaching the RF surface are prevented from hitting the RF electrode surfaces by the repelling “pseudo force field” formed by the RF voltage. A “pseudo potential well” is created capable of trapping ions of moderate translational energy over a wide range of mass-to-charge values between the counter electrode and the RF surface. Ions directed toward the RF surface by an increased electrical potential applied to a counter electrode tend to move back and forth in the pseudo energy well that forms in the center of RF electrode sets. To control the position of ions trapped in these pseudo energy wells and to facilitate movement of ions along an RF surface, an RF surface configured according to the present invention comprises electrodes positioned behind the RF surface electrodes and on the sides of the RF surface electrode array in addition to the counter electrode. DC voltages are applied to such back and side electrodes during operation. The RF surface, configured according to the invention, comprises multiple DC back and side electrodes positioned to control trapped ion positions above or below the RF surface plane or to move ions along the RF surface when appropriate DC voltages are applied. Repelling electrostatic potentials are applied to the back electrodes relative to the local RF offset potential to move ions trapped in local energy wells above the RF trapping surface. The distance that the repelling DC potentials applied to back electrodes penetrate between the RF electrodes is a function of the RF electrode tip shape and spacing geometry as well as the relative electrostatic potentials applied to the back electrodes, side electrodes, the RF electrode offset and the counter electrode. As the repelling potential from the back electrodes is increased the energy well depth between RF electrode sets decreases allowing ions to move more freely along the RF surface during operation. In some cases it is advantageous to preferably repel ions at some positions along the RF surface and attract them at others. For example, the back electrodes can be segmented to provide an attractive potential in a region in space where it is desirable to encourage ions to leak through the gaps in the electrodes, and to provide a retarding potential in regions of space to discourage ions from leaking through the gaps.  
         [0014]     In one preferred embodiment of the invention, the RF electrodes comprising the RF surface are configured in a repeating quadrupole pattern with separate concentric shaped back electrostatic electrodes positioned between each row of RF electrodes starting at the center quadrupole electrode set and extending in larger electrode concentric patterns in the radial direction. In one embodiment of the invention, this RF surface is configured in a TOF MS pulsing region and is operated to effect trapping and release ions during the pulsing cycle of a Time-Of-Flight (TOF) mass to charge analyzer. Voltages can be applied to the DC and RF electrodes comprising the RF surface assembly to concentrate trapped ions at the center of the RF surface, spread trapped ions out along the RF surface or concentrate trapped ions in specific locations on the RF surface prior to pulsing the trapped ions into the TOF mass analyzer flight tube for mass to charge analysis. A pulsed packet of ions or a continuous ion beam entering the gap between the RF surface and the counter electrode in the TOF pulsing region is directed toward the RF surface and trapped by the combined RF and DC fields formed by the back, side, counter and RF electrodes. Trapped ions are pulsed into the TOF flight tube by rapidly switching the voltage applied to the counter electrode to pull ions away from the RF surface and accelerate the ions down the TOF flight tube for mass to charge analysis.  
         [0015]     Prior to pulsing trapped ions into the TOF fight tube, a sequence of RF and DC voltage changes and collisional cooling of ion kinetic energy can be applied to improve or expand TOF analytical performance. In one operating sequence according to the invention, the spatial spread of trapped ions can be compressed by applying a rapid change of RF voltages and electrostatic potentials to the RF, back, side and counter electrodes just prior to pulsing the spatially compressed trapped ions into the TOF flight tube for mass to charge analysis. The spatial ion compression improves TOF resolving power in mass to charge analysis by allowing more effective correction of initial ion energy spread in the TOF flight tube ion reflector. The back electrodes configured with an RF surface may be shaped as concentric rings and/or segmented. In some cases it is advantageous to repel ions at some positions along the RF surface and attract them at others. In one embodiment of the invention, an ion population entering the TOF pulsing region is collected and trapped at two separated positions along the RF surface. Both sets of trapped ions are pulsed simultaneously into the TOF flight tube and hit two different detectors operating at different gain. Higher concentration ion packets hitting the higher gain detector may saturate the detector output while the second lower gain detector output will fall below its saturation level. Two analog to digital data acquisition systems record both TOF spectra simultaneously. The simultaneously acquired spectra are added with the appropriate gain corrections to form a combined mass spectrum with improved dynamic range and improved low signal amplitude resolution. The RF surface separation of ion packets with simultaneous pulsing of separated ion packets to two detectors operating at different gain improves TOF mass analyzer dynamic range while preserving accurate quantitative mass measurement capability.  
         [0016]     The translational energy of trapped ions may be collisionally cooled by the continuous or pulsed addition of neutral gas molecules into the TOF pulsing region. Neutral gas can be introduced near the RF surface during ion trapping to cause collisional damping of ion translational energy prior to pulsing into the TOF flight tube for mass to charge analysis. Neutral gas may be introduced into the TOF pulsing region from upstream vacuum pumping stages or pulsed into the TOF pulsing region synchronized with the TOF puling cycle. In one embodiment of the invention, the TOF pulsing region comprising an RF surface is configured to maximize local neutral gas pressure at the RF surface while minimizing the gas load into the TOF flight tube. Damping of ion translational motion near the RF surface, decreases ion energy and spatial spread prior to pulsing into the TOF flight tube. Damping of trapped ion kinetic energy effectively decouples energy spread of the trapped ion population caused by upstream events from the subsequent TOF pulsing and mass to charge analysis events. Reduced ion translational energy and spatial spread improves TOF resolving power and mass measurement accuracy.  
         [0017]     Ions trapped at the RF surface may be subjected to ion-molecule reactions or laser dissociation fragmentation in the TOF pulsing region. Reactant gas may be pulsed into the TOF pulsing region to react with ions trapped at the RF surface. The reaction time between the neutral gas molecules and the trapped ions can be set by varying the time between the introduction of reagent gas and the pulsing of stored ions into the TOF flight tube. Alternatively, the reagent gas can be continuously added to the TOF pulsing region and ion packets may be directed into the TOF pulsing region stored for a period of time and pulsed into the TOF flight tube. Ion molecule reaction times can be controlled precisely by manipulation of ion populations through accurately timed ion storage and pulse cycles using the RF surface configured in a TOF pulsing region. Simultaneously or alternatively, a laser can be pulsed in a direction parallel to the RF surface to induce fragmentation of ions trapped by the RF surface. Trapped ions can be subjected to multiple laser pulses focused locally or broadly along the RF surface. The resulting population of parent and fragment ions may be trapped and subsequently pulsed into the TOF flight tube for mass to charge analysis.  
         [0018]     In another embodiment of the invention, an RF surface configured in the pulsing region of a TOF mass spectrometer can be operated to trap ion populations at different locations on the RF surface. Ions trapped in one location on the RF surface follow a different trajectory traversing a TOF flight tube when compared with ions pulsed from a second location on the RF surface. In one example, the first trajectory ions may pass once through one ion reflector before impinging on the TOF detector. The second trajectory ions may pass through a two ion reflector flight path, improving TOF resolving power. Alternatively, ions trapped in local energy wells along the RF surface can be steered as point sources to follow different ion trajectories when pulsed down the TOF flight tube. The steering of ions accelerated from the RF surface traps can be achieved by applying asymmetric DC voltages to the local RF electrodes surrounding the pseudo potential well while simultaneously turning off the RF voltage and applying an accelerating potential to the counter electrode. Ions leaving the RF surface can be steered to pass through single or multiple ion reflectors to improve TOF resolving power or to impinge on different detectors operating at different gain to improve TOF dynamic range as described above.  
         [0019]     In an alternative embodiment of the invention a multipole ion guide is incorporated into an RF surface or such ion guide is configured to serve the dual functions or an RF surface as well as an ion guide. Such a hybrid RF surface can be run in multiple operating modes to capture, manipulate and transfer ions in a mass spectrometer apparatus. Ions approaching the RF surface directed by DC fields are prevented from hitting the RF electrodes due to the RF voltage applied. The DC voltages applied to back, side and counter electrodes direct ions into an ion guide integrated into the RF surface. Ions passing into the ion guide center channel, driven by electric fields and gas dynamics, are directed to the ion guide centerline through collisional damping with neutral gas molecules with radial trapping of ions due to the RF field. RF surfaces with integrated ion guides can be operated in background pressures ranging from atmospheric pressure where rapid collisional cooling of kinetic energy occurs to vacuum levels where minimal collisions occur between ions and neutral background gas. RF surfaces with integrated ion guides operating at or near atmospheric pressure direct captured or trapped ions into an orifice into vacuum improving ion transmission efficiency into vacuum. Aspects of multiple ion guide apparatus and operations to improve ion transmission efficiency from API sources into vacuum are described by Whitehouse, C. M., in U.S. Pat. No. 6,707,037 B2 incorporated herein by reference. Multipole ion guide embodiments configured according to the current invention to improve ion transmission from atmospheric pressure ion sources into vacuum are incorporated into RF surfaces or stand alone operating simultaneously as an RF surface and an ion guide. The multipole ion guide assembly is configured at atmospheric pressure with counter and back electrostatic lenses to aid in focusing and directing ions into the center channel of the multipole ion guide. The atmospheric pressure ion (API) source orifice into vacuum is configured as the ion guide electrostatic exit lens. The ion guide embodiments configured according to the invention include elements that constrain gas flow to pass longitudinally through the ion guide length from the entrance end to the exit end. All gas flow through the orifice into vacuum first passes through the ion guide center channel volume moving the radially trapped ions through the ion guide length. The dual purpose RF surface and multipole ion guide effectively reduces ion loss to the API orifice into vacuum improving the sensitivity of atmospheric pressure ion sources coupled to mass spectrometers.  
         [0020]     In an alternative embodiment of the invention, multipole ion guides incorporated into RF surfaces or serving the dual function of RF surface and ion guide are configured in vacuum pressure regions. In one embodiment of the invention, multipole ion guides integrated into RF surfaces are configured to transfer ions through one or more vacuum pumping stages. Multipole ion guides that transfer ions through multiple vacuum stages have been described by Whitehouse, C. M. and Gulcicek, E. in U.S. Pat. Nos. 5,652,427, 5,962,851 and 6,188,066 incorporated herein by reference. In the present invention, the multipole ion guide operates as an RF surface or is incorporated into a multiple pseudo energy well RF surface extending from the ion guide electrodes. The fringing fields at the entrance of multipole ion guides prevent ions approaching the ion guide entrance, through background gas imposing strong collisional damping of ion kinetic energy, from hitting the ion guide electrodes. Ions move into and through multipole ion guides configured according to the invention driven by dynamic and electrostatic fields and by gas dynamics. The ion guide assemblies are configured to extend though vacuum stage partitions transporting ions into and through one or more vacuum pumping stages.  
         [0021]     Ion guides configured according to the invention may be operated to trap and release ions, mass to charge select ions, fragment ions through collision induced dissociation with background molecules and/or separate species in ion populations through ion mobility. Ion guides can be incorporated into hybrid mass to charge analyzers including but not limited to TOF, quadrupole, three dimensional ion trap, linear ion trap, magnetic sector, Fourier Transform Ion Cyclotron Resonance (FTICR) and Orbitrap mass analyzers. Such ion guide functions and hybrid combinations configured with multipole ion guides extending through one or more vacuum stages are described by Dresch, T., Gulcicek, E. E., and Whitehouse, C. M. in U.S. Pat. Nos. 5,689,111 and 6,020,586 and Whitehouse, C. M., Dresch, T. and Andrien, B. in U.S. Pat. No. 6,011,259 all incorporated herein by reference. Ion guides configured according to the present invention have extended lengths that serve as ion transport conduits or tunnel regions between vacuum stages. Portions of the guide assemblies form longitudinal extended sections in which gas is prevented from passing out of the ion guide interior through gaps between the multipole ion guide electrodes. Other regions along the ion guide length are configured to allow neutral gas to be pumped out through the gaps between ion guide electrodes. Neutral gas flowing from one vacuum pumping stage into a subsequent vacuum stage is constrained to pass through the center channel or internal bore region of the multiple vacuum stage multipole ion guide. The multipole ion guide, serving as the ion and neutral gas conduit or tunnel between vacuum pumping stages, minimizes the neutral gas conductance while maximizing ion transmission. Neutral gas conductance through vacuum stages is constrained by the inner cross section opening area of the multipole ion guide and by the resistance to neutral molecule flow created by the increased length to diameter ratio of the ion guide conduit between vacuum stages. The length to diameter ratio of the multipole ion guide can be extended in the conduit region between vacuum pumping stages to reduce neutral gas conductance without compromising ion transmission efficiency. Larger cross section ion guides can be configured for the same vacuum pumping speed to increase ion current or ion trapping capacity. Alternatively, vacuum pumping speed and cost can be reduced considerably for the same multipole ion guide cross section by increasing the ion conduit length to diameter ratio between vacuum pumping stages.  
         [0022]     Ion guides can be configured as quadrupoles, hexapoles, octopoles or with a higher number of poles. The cross section shape of multipole ion guide electrodes may be round, hyperbolic, flat or other shapes as known in the art. The multipole ion guide mounting hardware, configured according to the invention, serves the multiple functions of holding the multipole ion guide electrodes in position, preventing neutral gas from exiting the multipole ion guide through gaps between the ion guide poles along portions of the ion guide length, serve as vacuum partitions between vacuum stages and electrically insulate the RF electrodes from surrounding conductive elements. The conduit portions of the multipole ion guides formed between vacuum pumping stages create a pressure drop longitudinally along the conduit sections of the ion guide length. Multipole ion guides extending into multiple vacuum stages may be segmented along the ion guide length allowing the application of different DC electrical offset potentials to different ion guide segments. Ions can be accelerated from one multipole ion guide segment to another with sufficient energy to cause collision induced dissociation (CID) by application of the appropriate relative offset potentials between ion guide segments. RF/DC or resonant frequency excitation and mass to charge selection may be conducted in quadrupole ion guides configured according to the invention. Single or multiple RF/DC or resonant frequency mass to charge selection and fragmentation steps may be conducted combined with linear acceleration CID fragmentation. MS/MS n  mass to charge selection and fragmentation may be conducted in single or multiple segment multipole ion guides operated as a linear ion trap. Single or multiple segment ion guide configured and operated according to the invention can be incorporated into hybrid mass spectrometers with mass analyzer types as listed above.  
         [0023]     Multipole ion guides configured according to the invention to serve as conduits through multiple vacuum pumping stages may comprise one or more sections where the ion guide electrodes are curved in the longitudinal direction. When incorporated into hybrid mass spectrometers, straight or curved multipole ion guides configured as ion and neutral gas conduits between vacuum pumping stages can be interfaced to ion guides of different types and different cross sections that are connected to different RF power supplies. When a multipole ion guide configured according to the invention is interfaced to a second multipole ion guide comprising a different number of poles or a different cross section no electrostatic electrode may be included between the exit end of one ion guide and the entrance end of the second ion guide. With no electrostatic electrode included in the interface junction between the two ion guides, less contamination buildup occurs on the electrode during operation. Minimizing contamination buildup along the ion path increases the mass spectrometer reliability and consistency of performance over longer time periods.  
         [0024]     In an alternative embodiment of the RF surface, a magnetic field of strength &gt;0.05 Tesla is applied in conjunction with the RF trapping potentials to spatially confine the ions above the RF surface or to direct the ion trajectories along the RF surface. In this embodiment of the invention, ions are trapped by the combination of interacting RF and DC electric fields and magnetic fields. Different ion manipulation functions can be conducted by applying magnetic fields along different axes of the RF surface. Ion trajectories near the RF surface can be varied by controlling ion velocity, RF and DC voltages and magnetic field strength. The applied magnetic field can increase the trapping efficiency for less favorable phase space conditions on the RF surface. In one embodiment of the invention, the magnetic field is applied perpendicular to the plane of the RF surface. When operating this embodiment of the RF surface, ion translational motion occurs in the rotational direction around the magnetic field axis just above the RF surface. A population of ions form a sheet of rotating ions that in specific operating modes separate radially according to mass to charge. The radial mass to charge separation can be used to conduct mass to charge analysis of multiple species ion populations.  
         [0025]     In another embodiment of the invention, the RF field-generating surface can be configured as at least one electrode assembly in an ICR cell. Ions entering the ICR cell can be captured and trapped along one or more RF field-generating surfaces and selectively directed into the center of the FTMS cell for FTMS analysis. Ions can be introduced into the ICR cell through an ion guide integrated into one RF surface assembly. In one embodiment of the invention, an ICR cell comprises two RF surface end electrode assemblies. Back electrode and RF electrode voltages are applied in the FTMS magnetic field such that ions rotate around the magnetic field axis in a sheet that is parallel to two RF surfaces. When operating this embodiment of the invention, rotating ions in the ICR cell experience minimum electric field gradients along the center axis of the FTMS cell, resulting in improved resolving power during mass to charge analysis.  
         [0026]     The invention can be configured with a wide range of vacuum ion sources including but not limited to, Electron Ionization (EI), Chemical Ionization (Cl), Laser Desorption (LD), Matrix Assisted Laser Desorption (MALDI), Fast Atom Bombardment (FAB), and Secondary Ion Mass Spectrometry (SIMS), intermediate vacuum pressure ion sources including but not limited to Glow Discharge (GD) and intermediate pressure Matrix Assisted Laser Desorption (IP MALDI) and atmospheric pressure ion sources including but not limited to Electrospray (ES), Atmospheric Pressure Chemical Ionization (APCI) and Pyrolysis MS, Inductively Coupled Plasma (ICP). Hybrid mass spectrometers comprising RF surfaces and ion guides configured according to the invention may comprise quadrupole, three dimensional ion traps, linear ion traps, TOF, magnetic sector or Orbitrap mass to charge analyzers. 
     
    
     BRIEF DESCRIPTION OF THE DRAWINGS  
       [0027]      FIG. 1  is a top view diagram of one embodiment of an RF surface configured with spherical RF electrodes and concentric rings of backing electrostatic electrodes and positioned in the pulsing region of a TOF mass analyzer.  
         [0028]      FIG. 2  is a side diagram view of RF surface shown in  FIG. 1  comprising spherical RF electrodes.  
         [0029]      FIG. 3  is a top view diagram of the backing electrode circuit board configured in the RF surface diagrammed in  FIG. 1 .  
         [0030]      FIG. 4A  is a top view of the RF surface similar to that diagrammed in  FIG. 1  showing a calculated trajectory of ion motion along the surface for the same potential applied to all backing electrodes.  
         [0031]      FIG. 4B  is a magnified top view of the ion trajectory shown in  FIG. 4A .  
         [0032]      FIG. 4C  is a magnified top view of the trapping region of the ion trajectory shown in  FIG. 4A .  
         [0033]      FIG. 4D  is a side view of the ion trajectory simulation shown in  FIG. 4C .  
         [0034]      FIG. 5  is a diagram of an orthogonal pulsing TOF mass analyzer configured with the RF surface assembly shown in  FIG. 1 .  
         [0035]      FIGS. 6A through 6D  are cross section diagrams of an orthogonal TOF pulsing region comprising an ion trapping RF surface sequentially showing a TOF pulsing region ion trap and pulse sequence.  
         [0036]      FIG. 7  is a timing diagram of a TOF pulsing sequence followed in  FIGS. 6A through 6D .  
         [0037]      FIG. 8  is a diagram of one embodiment of the power supply connections and switches providing electrical potentials to an RF surfaced configured in an orthogonal pulsing TOF mass analyzer.  
         [0038]      FIG. 9  is a top view diagram of an RF surface configured with linear backing electrodes and with linear RF electrodes oriented perpendicular to the primary ion beam in an orthogonal TOF pulsing region.  
         [0039]      FIG. 10A  is an isometric view of the RF surface diagrammed in  FIG. 9  showing a calculated ion trajectory along the RF surface.  
         [0040]      FIG. 10B  is a side view of the calculated ion trajectory shown in  FIG. 10A .  
         [0041]      FIG. 11  is a top view diagram of an RF surface configured with linear backing electrodes and with linear RF electrodes oriented parallel to the primary ion beam in an orthogonal TOF pulsing region.  
         [0042]      FIG. 12  is a diagram of an alternative embodiment of the RF surface comprising a layered structure configured in the pulsing region of a TOF mass to charge analyzer.  
         [0043]      FIG. 13  is a diagram of an orthogonal pulsing TOF mass analyzer configured with a dual RF surface in the TOF pulsing region and dual multichannel plate detectors.  
         [0044]      FIGS. 14A  through F show are calculated ion trajectories of ions trapped above an RF surface in the presence of a cross magnetic field.  
         [0045]      FIG. 15  is side view diagram of an RF surface embodiment configured in a cross magnetic field mass to charge analyzer.  
         [0046]      FIG. 16  is a front end view diagram of the RF surface cross magnetic field mass to charge analyzer diagrammed in  FIG. 15   
         [0047]      FIG. 17  is a side view diagram of an FTICR MS cell comprising RF surface assemblies.  
         [0048]      FIG. 18  is cross section diagram of an RF surface comprising an ion guide and multiple electrostatic electrodes in an atmospheric pressure ion source.  
         [0049]      FIG. 19  is a cross section diagram of an RF surface comprising an ion guide in an atmospheric pressure MALDI ion source.  
         [0050]      FIG. 20  is a top view of the RF surface with ion guide as shown in  FIG. 18 .  
         [0051]      FIG. 21  is a top view of the backing electrode circuit board configured in the RF surface shown in  FIGS. 18 and 19 .  
         [0052]      FIG. 22  is a cross section side view of a spherical electrode RF surface comprising a multipole ion guide and an ion tunnel section extending from a first vacuum pumping stage into a second vacuum pumping stage.  
         [0053]      FIG. 23  is a cross section side view of a four electrode RF surface comprising a multipole ion guide and an ion tunnel section extending from a first vacuum pumping stage into a second vacuum pumping stage.  
         [0054]      FIG. 24  is a cross section side view diagram of an Electrospray ion source interfaced to a mass to charge analyzer comprising multiple RF surfaces incorporating a multipole ion guides configured in the ion path from atmospheric pressure through multiple vacuum stages.  
         [0055]      FIG. 25  is a cross section side view diagram of an Electrospray ion source and an intermediate MALDI source interfaced to a mass to charge analyzer comprising multiple RF surfaces incorporating ion guides.  
         [0056]      FIG. 26  is a cross section side view diagram of a multipole ion guide extending into four vacuum pumping stages comprising an RF surface, three ion tunnel or conduit sections and two open vacuum pumping sections configured in a mass to charge analyzer.  
         [0057]      FIG. 27A  is an end view section of a quadrupole ion guide conduit region configured with hyperbolic ion guide electrodes.  
         [0058]      FIG. 27B  is an end view section of a hexapole ion guide conduit region configured with round ion guide electrodes.  
         [0059]      FIG. 27C  is an end view section of a quadrupole multiple ion guide conduit region configured with flat ion guide electrodes.  
         [0060]      FIG. 28  is a die view cross section of an RF disk electrode multipole ion guide configured as an ion tunnel or conduit between two vacuum pumping stages.  
         [0061]      FIG. 29  is a cross section side view of a segmented multipole ion guide configured with two conduit sections interfaced to a larger cross section ion guide.  
         [0062]      FIG. 30  is a cross section side view of a segmented multipole ion guide configured in an orthogonal pulsing TOF mass analyzer.  
         [0063]      FIG. 31  is a cross section side view of a segmented multipole ion guide comprising a curved section configured in a quadrupole mass to charge analyzer. 
     
    
     DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS  
       [0064]     A series of electrodes spaced in a grid pattern, to which RF of opposite phase and appropriate voltage is applied to adjacent RF electrodes, generates a field that reflects ions away from the surface. In the absence of a retarding field above the surface, ions of appropriate m/z and kinetic energy are reflected. As described by Whitehouse and Welkie in U.S. Pat. No. 6,683,301 B2, incorporated herein by reference, ions can be confined to a volume of space directly above the RF surface when an electrostatic retarding field is maintained above the surface, trapped by the RF pseudo potential wells. In one aspect of the present invention, the shape and size of the electrode tips, and the spacing between them, are adjusted such that an ion population is confined to localized volumes of space above gaps between the electrodes during ion trapping operation. Multiple Electrostatic electrodes configured behind and to the sides the RF surface, in the present invention, improve trapping efficiency, provide control of ion motion along the RF surface and provide control of the position of trapped ions in the pseudo potential wells along the RF surface. Different DC offset potentials can be applied to sets of RF electrodes to provide additional control of ion motion along the RF surface and to provide steering or focusing of ions as they are accelerated away from the RF surface. Neutral collision gas can be added to provide collisional cooling of ion kinetic energy for ions trapped at the RF surface.  
         [0065]     RF surfaces, configured according the invention, are incorporated into the pulsing region of TOF mass to charge analyzers. RF surfaces configured into TOF MS pulsing regions can be run in multiple operating modes providing multiple functions. Ion trapping and pulsing functions of the RF surface operated in the pulsing region of a TOF mass spectrometer increases TOF MS duty cycle and resolving power. Additional improvement in TOF MS resolving power can be achieved by compression of trapped ion spatial spread in the TOF pulsing region prior to pulsing ions into the TOF flight tube. Compression of trapped ion spatial spread is achieved by application of the appropriate RF and electrostatic voltages during timing sequences in the TOF pulsing cycle. Pulsed or accelerated ion trajectories through the TOF flight tube can be steered at the RF surface by adjusting the relative electrostatic or DC potentials applied to RF surface electrodes during the TOF pulsing cycle. Ions trapped in pseudo potential wells along the RF surface are effectively accelerated into the TOF flight tube from point sources. Steering ion trajectories from multiple RF surface point sources, minimizes ion beam distortion compared with steering of a broader ion beam using steering electrodes after pulsing ions into the TOF flight tube. Ion trajectories can be steered to single or multiple ion reflectors or to multiple detectors in the TOF flight tube during mass to charge analysis. Ions trapped along the RF surface in the TOF pulsing region can be subjected to laser cooling of ion kinetic energy or laser induced dissociation fragmentation prior to pulsing the trapped ion population into the TOF flight tube. The applied RF amplitude or frequency can be changed or ramped during ion trapping to eliminate ion m/z values that fall outside the RF trapping stability window.  
         [0066]     One embodiment of the invention comprising spherical RF electrodes is diagrammed in  FIGS. 1 and 2 .  FIG. 1  is a top view and  FIG. 2  is a side view of RF surface assembly  1  comprising spherical RF electrodes  2 A and  2 B, side surface electrostatic electrodes  5 ,  6 ,  7  and  8 , entrance side electrode  11 , side electrode  12 , back electrodes  13  through  18  and front electrode  20  with grid section  21 . All spherical RF electrodes comprising RF surface assembly  1 , including spherical RF electrodes  2 ,  3  and  4  are held in position and electrically isolated by RF electrode insulator  34 . Insulator  34  comprises dielectric material including but not limited to ceramic or alumina, silica, plastic or glass. Ceramic materials may be molded, machined or laser cut green and fired, silica may be etched or laser cut, and plastic or glass may be machined or molded or other material forming known in the art may be applied to produce the required configuration for RF electrode insulator  34 . Adjacent RF electrodes are electrically insulated from each other and from surrounding electrostatic electrodes. In the embodiment shown in  FIGS. 1 and 2 , RF spherical electrodes are connected to reduced diameter electrode posts that pass through holes in insulator  34 . For example posts  40  and  41 , connected to RF spherical electrodes  3 A and  3 B respectively, pass through holes in insulator  34  holding spherical electrodes  3 A and  3 B in position and providing electrical connection with RF and DC power supply  47 . Sine wave alternating current or AC in the Radio Frequency or RF frequency range is applied to all spherical electrodes comprising RF surface assembly  1 . Such RF electrical potentials are applied with an AC frequency typically in the range between one hundred kilohertz to several megahertz. Opposite or approximately opposite phase RF voltage is applied to adjacent RF spherical electrodes as indicated by crosshatch and clear spheres shown in  FIGS. 1 and 2 .  
         [0067]     One or more DC offset potentials are applied to sets of spherical Electrodes. Different DC offset potentials may be applied to sets of RF electrodes through appropriate capacitor and resistor elements, as is known in the art, to provide one means of controlling ion motion along the RF surface. In the embodiment shown in  FIG. 2 , all RF electrodes are connected to a common offset potential through RF and DC power supply  47 . The RF surface embodiment shown in  FIGS. 1 and 2  comprises RF electrodes arranged in repeating patterns of four electrodes forming quadrupole electrode sets. For example, four RF electrodes  3 A,  3 B,  3 C and  3 D define a four RF electrode set that creates a pseudo potential well and trapping region  24  between them during ion trapping operation. As a second example, electrodes  4 A,  4 B,  4 C and  4 D define a four RF electrode set creating pseudo potential well and trapping region  25  between them during ion trapping operation. In the embodiment shown in  FIGS. 1 and 2 , all spherical RF electrodes including  2 A,  2 B,  3 A through  3 D and  4 A through  4 D form a planar surface. Alternatively the RF electrodes may be configured to form different shaped surfaces including but not limited to curved, curved spherical, parabolic or hyperbolic shapes or angled in a cone or terraced shape. In addition to RF electrodes, RF surface assembly  1  comprises multiple surrounding electrostatic electrodes to provide additional control of ion trajectories, trapping and manipulation along the RF surface.  
         [0068]     RF surface assembly  1  comprises four separate planar electrostatic side electrodes  5 ,  6 ,  7  and  8  configured on the top side of circuit board  22 . Figure Electrostatic electrodes  13 ,  14 ,  15 ,  16 ,  17  and  18  are configured in concentric square shapes centered at RF electrode set  3 A,  3 B,  3 C and  3 D. Entrance side electrode  11  and side electrode  12  are configured outside and to the sides of RF surface assembly  1 . Electrostatic electrodes  20  and  45  with grid portions  21  and  46  respectively are positioned above and parallel to plane  51  formed by RF surface assembly  1 . Direct Current (DC) or electrostatic electrical potentials are applied to the electrostatic electrodes to control ion motion and trapping near RF surface  51  and to control ion motion during the acceleration, focusing and steering of ions accelerated away from RF surface assembly  1  during TOF pulsing cycles. In one embodiment of the invention, circuit board  22  is fabricated with separate electrostatic electrodes  5 ,  6 ,  7  and  8  configured on its top surface as diagrammed in  FIGS. 1, 2  and  3 .  FIG. 3  is a top view diagram of circuit board  22  mounted on the top face of circuit board  30  as a subassembly in RF surface assembly  1 . Circuit board  30  comprises through holes  54  drilled to provide clearance for insulator  34  posts to protrude through circuit board  22  as shown in  FIG. 2 . Electrical conductive traces such as  38  configured on the back side of circuit board  30  connects with front electrode  16  by electrical connections or vias such as via  37  through circuit board  30 . Concentric ring front electrodes  13  through  18  are electrically insulated from each other by gaps in circuit board conductive traces such as  31  and  53  between back electrodes  17  and  18  and  15  and  16  respectively. Individual voltages are applied to back electrodes  13 ,  14 ,  15 ,  16 ,  17  and  18  through connections to multiple output power supply  61 . Planar side electrodes  5 ,  6 ,  7  and  8  are connected to power supplies  55 ,  56 ,  57  and  58  respectively during ion trapping and manipulation. The supply of voltages applied to planar electrodes  5  through  8  from DC power supplies  55  through  58  respectively during ion trapping is rapidly switched to power supply  59  through switch  60  during a TOF pulsing cycle to accelerate ions into the TOF flight tube. Voltages applied to back electrodes  13  through  18  remain constant or are switched through power supply  61  during a TOF pulsing cycle. Power supplies  55  through  59 , power supply  61  and switch  60  are controlled through logic unit  62  during a TOF pulsing cycle.  
         [0069]     Pulsed or continuous neutral gas  27  can be added through side electrode  12  from gas flow controller  26  to provide collisional damping of ion kinetic energy during ion trapping along RF surface  51 . Alternatively, neutral gas can be introduced along with ions  23  through opening  52  in electrode  11  from upstream vacuum pumping stages during operation of RF surface assembly  1 . Laser or light source  28  is configured to direct photons  29  along surface  51  of RF surface assembly  1  to cool or fragment trapped ions. Laser or light source  28  may focus light beam  29  at specific locations or raster beam  29  across RF surface  51 . Photo dissociation of trapped ions occurs when ions absorb sufficient energy from photons to undergo fragmentation. RF surface assembly  1  as diagrammed in  FIGS. 1 and 2  is configured in orthogonal pulsing region  54  of a TOF mass spectrometer. An example of one TOF ion pulsing cycle operated according to the invention will be described below to illustrate one embodiment of the RF surface assembly ion trapping and release functions. TOF pulsing region  54  can be configured to provide poor neutral molecule pumping conductance from gap  50  to maximize gas pressure at RF surface  51  for collisional cooling while minimizing the gas and vacuum pressure in the TOF tube. For example, if the local background pressure in gap  50  were maintained at approximately 5×10 −5  torr due to gas conductance from upstream vacuum stages, ions trapped at RF surface  51  would be subject to collisional cooling but would experience little or no collisions when accelerated into the TOF flight tube. The TOF flight tube vacuum pressure can be maintained in the low 10 −7  torr range with modest size vacuum pumps and restricted neutral molecule conductance from the TOF pulsing region. In one embodiment of the invention, TOF pulsing region  54  is configured with a surrounding structure that prevents loss of neutral gas. In addition, electrodes  20  and  45  with grids  21  and  46  respectively are mounted in an electrically insulated tunnel as diagrammed in  FIG. 5  to reduce neutral gas conductance into TOF flight tube  105 .  
         [0070]     In one embodiment of the invention, RF surface assembly  1  is configured to trap ions having an initial trajectory approximately parallel to RF surface  51 . The tops of RF spherical electrodes  2 ,  3  and  4  and planar DC electrodes  5 ,  6 ,  7  and  8  define the plane of RF surface  51  in RF surface assembly  1 . Ion beam or gated ion packet  23  enters gap  50  between RF surface  51  and front or counter electrode  20  with grid  21  in a trajectory substantially parallel to RF surface  51 . RF and DC offset potentials are applied to all RF electrodes comprising RF surface assembly  1 . Electrostatic potentials are applied to front electrode  20  with grid  21  and planar side electrodes  5 ,  6 ,  7  and  8  relative to the RF electrode offset potential, to form a DC electric field that directs ions  23  toward RF surface  51  as they traverse gap  50 . The potentials applied to side electrodes  11  and  12 , and planar side electrodes  5 ,  6 ,  7  and  8  are set higher in amplitude than the RF electrode offset potential, forming a DC energy well with the RF electrode surface positioned at the bottom of the DC energy well. The electrostatic voltages applied to electrodes  6 ,  7  and  8  are set above the kinetic energy of the ions  23  entering gap  50  of TOF pulsing region  54  to retard the forward ion motion and direct the ions toward the center region of RF surface  51 . Electrostatic repelling potentials are applied to backing electrodes  13  through  18 . As ions  23  move toward RF surface  51  directed by the DC far field in gap  50 , they are prevented from hitting the RF electrodes by near field repelling force formed by the applied RF voltage. Ions move along RF surface  51  losing kinetic energy through collisions with neutral background gas and are eventually trapped in pseudo potential wells between electrode sets. The back electrode DC repelling field penetrating through gaps between RF electrodes prevents ions trapped in pseudo potential wells from moving through and below RF surface  51  and hitting back DC electrodes  13  through  18 . The DC voltage values applied to back electrodes  13  through  18  and forward electrode  20  with grid  21  relative to the applied RF electrode DC offset potential determine the position of trapped ions relative to RF surface plane  51 . Increasing the voltage amplitude applied to back electrodes  13  through  18  will move trapped ions to a position above RF surface  51  allowing the ions to skate across RF surface  51 . Reducing back electrode voltage will move trapped ions into or slightly below RF surface  51  in the center region between RF electrode sets.  
         [0071]      FIGS. 4A, 4B ,  4 C and  4 D show a calculated ion trajectory along RF surface  70  with spherical RF electrodes configured in a pattern as described for RF surface assembly  1 . The ion trajectory calculation was run using the software program SIMION 7.0 (David A. Dahl 43ed ASMS 1995, pg. 717) with factors added to emulate ion collisions with neutral background gas.  FIG. 4A  shows a top view of RF surface  70  comprising spherical RF electrodes  71  each configured with a 1 millimeter (mm) diameter. The diameter of a circle drawn inside of each set of four spherical electrodes just touching each of the four electrodes in a set, such as that formed by the inscribed diameter of RF electrodes  72 A,  72 B,  72 C and  72 D, equals 1.128 mm. Planar side electrode  73  is electrically connected to the forward electrode not shown in  FIG. 4A . Single back electrode  75  is maintained at a uniform DC potential behind the RF electrode surface. The RF voltage applied to RF electrodes  71  was set at 400 volts peak to peak (Vptp) with a frequency of 5 MHz. The RF electrode offset potential was set to zero volts. The DC electrical potential applied to back electrode  75  was set to +100 Volts (V). The electrostatic or DC potential applied to side  73  and front electrode was set to +11 V. Ion  74  enters the gap above RF surface  70  with a translational energy of 10 electron volts (ev) and moves toward RF surface  70  due to the front electrode voltage directing ion  74  toward RF surface  70 . As ion  74  moves above RF surface  70  with trajectory  77 , as shown in  FIG. 4A , it loses kinetic energy due to collisions with neutral background gas. Eventually ion  74  is trapped in a pseudo potential well at position  78  between RF electrodes  80 A,  80 B,  80 C and  80 D. Magnified top view of trapped ion  74  trajectory  81  is shown in  FIGS. 4B and 4C . Ion collisions with neutral background gas reduces the kinetic energy of trapped ion  74 , effectively collapsing the trajectory of ion  74  towards the bottom of the pseudo potential well at the center of RF electrode set  80 A,  80 B,  80 C and  80 D.  FIG. 4D  is a magnified side view of spherical electrodes  80  C and  80 D showing the trajectory of kinetic energy damped ion  74 . As the kinetic energy of ion  74  cools through collisions with background neutral molecules, the ion movement collapses to a small volume centered between RF electrodes  80 A,  80 B,  80 C and  80 D sitting just above RF surface plane  82 .  
         [0072]     The ion trapping trajectory calculation shown in  FIGS. 4A through 4D  illustrates the compression of ion trajectories in the direction of TOF tube axis  48  or  83  by trapping ions on RF surface  51  or  70  prior to pulsing ions into a TOF flight tube for mass to charge analysis. Reducing the spatial spread of an ion population prior to pulsing the population of ions into the TOF flight tube, increases TOF resolving power and mass measurement accuracy. Typically ion beam  23  enters TOF orthogonal pulsing region  54  gap  50  having a width of 1 to 3 mm with non parallel ion trajectories due to inevitable imperfections in upstream ion beam focusing. The non parallel trajectories of ions  23  moving across gap  50  contribute to random ion energies in the direction of TOF axis  83  or  48  uncorrelated to spatial spread when ions are pulsed into the TOF flight tube. As is known in the art, ion reflectors configured in TOF flight tubes can be tuned to reduce the effects of ion energy spread or ion spatial spread but not both if ion energy and spatial spread are uncorrelated. Correlated ion energy and spatial spread occurs in orthogonal TOF pulsing when a parallel trajectory ion beam  23  traverses gap  50  parallel to RF surface  51  and front electrode grid  21 . This ideal case is rarely achieved in practice. By trapping ions in pseudo potential wells formed between RF electrode sets along RF surface  70  or  51 , the spatial and energy spread of an ion population can be reduced prior to pulsing the ion population into the TOF flight tube. As shown in  FIGS. 4A through 4D , ion beam  23  entering gap  50  with a cross section of 2 mm can be trapped in multiple pseudo potential wells and subjected to collisional cooling prior to pulsing into the TOF flight tube. Ion spatial spread in the TOF flight tube axis direction can be reduced to a few tenths of a millimeter prior to pulsing into the TOF tube. With reduced spatial spread, initial ion energy spread in the TOF axis direction can be focused at the TOF detector surface using ion reflectors in the TOF flight tube, increasing resolving power and mass measurement accuracy. As will be described below, additional spatial compression can be achieved by applying a transient increase in relative electrode potentials to briefly compress the trapped ion trajectories prior to pulsing ions into the TOF flight tube.  
         [0073]     Ions trapped in pseudo potential wells are pulsed into the TOF flight tube by simultaneously turning off the RF voltage applied to the RF electrodes, switching planar electrode potentials close to the RF electrode offset potential and rapidly reversing the voltage applied to forward electrode  20  with grid  21  and electrode  45  with gird  46  to accelerate ions away from RF surface  51  and into the TOF flight tube. To accelerate positive polarity ions into the TOF flight tube with zero volts applied to the offset potential to the RF electrodes, negative polarity voltages are rapidly switched to electrodes and grids  20 / 21  and  45 / 46 . Conversely, positive voltage polarity is applied to electrodes and grids  20 / 21  and  45 / 46  to accelerate negative polarity ions into the TOF flight tube. Voltages applied to back electrodes  13  through  18  and planar side electrodes  5  through  8  can be switched synchronized with the TOF ion acceleration pulse to optimize the accelerated ion trajectory down the TOF flight tube. Alternatively, the offset potential applied to RF electrodes comprising RF surface  51  can be rapidly increased to accelerate trapped ions into the TOF flight tube. For positive ion acceleration into the TOF flight tube, positive polarity offset potential is rapidly switched to the RF electrodes while the RF voltage is turned off. Negative polarity offset voltage is switched to the RF electrodes to accelerate negative polarity ions into the TOF flight tube during a TOF pulsing cycle. Alternatively, opposite polarity DC voltages can be switched to the offset potential of RF electrodes and the forward electrodes with grids  20 / 21  and  45 / 46 . The acceleration of ions from gap  50  in pulsing region  54  into the TOF drift or flight tube can be described as pushing ions out of, pulling ion from or push pull of ions from pulsing region  54  gap  50  as ion acceleration voltages are applied to electrodes in TOF pulsing region  54 .  
         [0074]     One embodiment of a Time-Of-Flight mass to charge analyzer configured according to the invention is diagrammed in  FIG. 5 . Hybrid TOF mass spectrometer  100  comprises Electrospray (ES) ion source  101 , dielectric capillary  102 , multipole ion guide and ion trap  103 , RF surface assembly  104  configured in orthogonal pulsing region  115  of TOF flight tube  105 . Ions are generated in ES source  101  from sample solution sprayed, with or without pneumatic nebulization assist, from ES inlet probe  117 . The resulting ions produced from the Electrospray ionization in Electrospray ion source  101  are directed into capillary bore  120  of capillary  102 . The ions are swept though bore  120  of capillary  102  by the expanding neutral gas flow into vacuum and enter the first vacuum pumping stage  111 . The potential energy of the ions passing through capillary  102  changes from the entrance to exit end as described in U.S. Pat. No. 4,542,293 incorporated herein by reference. A portion of the ions exiting capillary  102  continue through skimmer orifice  123  in skimmer  124  and pass into multipole ion guide  103  where they are radially trapped as they traverse the length of ion guide  103 . Multipole ion guide  103  extends into second and third vacuum stages  112  and  113  respectively. Multipole ion guide  103  can be operated in RF only single pass or trapping and release mode, mass to charge selection mode or ion fragmentation mode as described in U.S. Pat. Nos. 5,652,427 and 5,689,111 and 6,011,259 incorporated herein by reference. Hybrid TOF  100  can be operated in MS or MS/MS” mode with ion mass to charge selection and gas phase collision induced dissociation (CID) functions occurring ion guide  103 . Ion guide  103  comprises ion tunnel or conduit sections  121  and  122  configured according to the present invention and described in more detail below.  
         [0075]     Ions exiting ion guide  103  pass through ion guide exit lens  125  and focusing lens  126  and are directed into pulsing region or first accelerating region  115  of Time-Of-Flight mass analyzer  130  with a trajectory that is substantially parallel to RF surface  131  and counter or front electrodes  127  and  128 . The planes described by RF surface  131  and front electrodes  127  and  128  are perpendicular to the axis of Time-Of-Flight drift or flight tube  105 . RF surface assembly  104  is configured as described for RF surface assembly  1  shown in  FIGS. 1 and 2 . Electrodes  127  and  128  are equivalent to electrodes  20  and  45  shown in  FIGS. 1 and 2  and described above. Electrical insulator  132  surrounding TOF pulsing region  133  forms a tunnel like structure to minimize gas conductance from pulsing region gap  115  into TOF flight tube  105 . Ion collisions with neutral gas molecules entering pulsing region gap  115  from upstream vacuum pumping stage  113  provide collisional cooling of ion kinetic energy for ions trapped along RF surface  131 . Ions entering gap  115  from guide  103  operating with a continuous or pulsed ion beam are directed to RF surface  131  where they are trapped. Trapped ions at RF surface  131  undergo cooling of translational energies due to collisions with neutral background gas. Ions accelerated from RF surface  131  pass through grids in electrodes  127 ,  128  and  135  and enter TOF drift or flight tube  105 . Ions can be steered using steering electrode set  134  in TOF flight tube  105  or can be steered directly from RF surface  131  as described above. As an example, ions following ion trajectory  137  in TOF flight tube  105  are steered by steering electrode set  134  to make a single pass through first ion reflector  106  before impacting on multichannel plate detector  110 . Alternatively, ions following ion trajectory  138  are steered from RF surface  131  to make a double reflection through first ion reflector  106  and second ion reflector  107  before impinging on detector  110 . Multiple ion reflections in TOF flight tube  105  improve TOF resolving power at some reduction in sensitivity due to ion loss on ion reflector entrance grids. Alternatively, ions can be accelerated into TOF flight tube  105  with no steering and impinge on linear flight path detector  108 . A description of the timing sequence of a TOF pulsing cycle conducted using TOF pulsing region  133  comprising RF surface assembly  104  is given below.  
         [0076]      FIGS. 6A, 6B ,  6 C and  6 D show the TOF pulsing sequence of one embodiment of TOF pulsing region  133  operation.  FIG. 6A  shows TOF pulsing region  133  just after an ion pulse into TOF tube  105  has occurred. RF voltage is reapplied to the RF electrodes comprising RF surface  131  and all voltages applied to surrounding DC lenses are reset for trapping ions at RF surface  131 . Ions  140  are radially and longitudinally trapped in ion guide  103  by the RF voltage applied to the poles of ion guide  103  and by trapping DC voltages applied to skimmer  124  and ion guide exit electrode  125 . In  FIG. 6B  a DC voltage is applied to ion guide exit electrode  125  to release ions from the exit end of ion guide  103 . After a period of time, trapping voltage is again applied to ion guide exit electrode  125  to stop the release of ions from ion guide  103  and resume ion trapping of remaining ions in ion guide  103 . Ion packet  141  released from ion guide  103  moves into pulsing region gap  115 . Voltages applied to front electrode  127 , RF surface  131  and planar side electrodes  145  direct ion packet  141  toward RF surface  131  as shown in  FIG. 6B . Ions comprising ion packet  141  are trapped at RF surface  131  as shown in  FIG. 6C . Once ion packet  141  has entered pulsing region gap  115 , the voltage applied to front electrode  127  and planar side electrodes  145  can be increased above the initial ion energy value to improve ion trapping efficiency at RF surface  131  and to move ion motion toward the center of RF surface  131 . Trapped ion population  142  undergoes collisions with neutral background gas which reduce the trapped ion kinetic energy as shown in  FIG. 6C . The ion trajectories of kinetic energy cooled ion population  142  can be compressed by briefly increasing the voltage amplitude applied to front electrode  127 , back electrodes, planar side electrodes  145  and the RF electrodes comprising RF surface  131  just prior to accelerating ion population into TOF flight tube  105 . Spatially compressed ion packet  143  is accelerated into TOF flight tube  105  by switching off the RF voltage and rapidly switching the DC potential applied to front electrode  127  and planar side electrodes  145  as shown in  FIG. 6D . When spatially compressed ion packet  143  has entered TOF flight tube  105 , RF and DC voltages in TOF pulsing region  133  are reset to trap another ion packet released from ion guide  103 .  
         [0077]     Ions can be accelerated into TOF flight tube by different combinations of voltages applied or switched to electrodes surrounding gap  115  in TOF pulsing region  133 . When the offset potential applied to the RF electrodes comprising RF surface  131  is held constant, trapped ions  143  can be accelerated or pulled through the grid of electrode  127  by switching the voltage applied to electrode  127 . For example, if the offset potential applied to the RF surface electrodes equals ground or zero volts, the accelerating or pulling potential applied to electrode  127  comprises negative polarity for positive ions and positive polarity for negative ions. Electrode  135  is connected to TOF flight tube or drift region surrounding electrode  148  as diagrammed in  FIG. 5 . Connected electrodes  135  and  148  are maintained at negative or positive kilovolt potentials applied to during positive or negative ion mass to charge analysis respectively. For positive ion acceleration into TOF flight tube  105 , the potential applied to electrodes  127  and  128  is switched from a few volts positive, maintained during ion trapping, to a negative potential for ion acceleration into TOF drift region  105  maintained at negative kilovolt potentials. The reverse polarity case occurs for negative ion acceleration into TOF drift region  105 . Alternatively, the offset potential applied to the RF electrodes and the DC potentials applied to planar side electrodes  145  and RF surface back electrodes can be switched to a positive potential to accelerate positive polarity ions into TOF drift region  105  or negative polarity to accelerate negative polarity ions into TOF drift region  105 . Raising the potential applied to RF surface assembly  104  accelerates ions out of gap  115  through the grid of electrode  127  by effectively pushing them out. Alternatively, ion packet  143  ions can be accelerated from gap  115  by a simultaneous push and pull, achieved for positive ions by raising the voltage applied to RF surface assembly  104  electrodes in the positive polarity direction while applying a negative polarity accelerating potential to electrodes  127  and  128 . The relative DC voltage values applied to RF surface assembly  104  electrodes, electrodes  127 ,  128 ,  135 / 148 , the electrodes of ion reflectors  106  and  107  and detector  110  are set during ion acceleration and drift time to maximize TOF mass to charge analysis resolving power and sensitivity.  
         [0078]     Timing diagram  148  in  FIG. 7  shows one example of a TOF pulsing sequence, for positive polarity ion mass to charge analysis, operated according to the invention. Lines  163  through  171  represent the voltage amplitudes applied to ion guide  103  DC offset ( 163 ), ion guide exit electrode  125  ( 164 ), RF surface  131  RF electrodes DC offset ( 165 ), RF surface  131  RF electrodes RF voltage ( 166 ), RF surface assembly  104  back electrodes DC voltage ( 167 ), RF surface assembly  104  side planar electrodes  145  DC voltage ( 168 ), TOF pulsing region first front electrode  127  DC voltage ( 169 ), TOF pulsing region second front electrode  128  DC voltage ( 170 ) and TOF pulsing region third front electrode  135  or TOF flight tube DC voltage  148  ( 171 ). Timing diagram  148  begins at timing point  149  in the middle of a TOF acquisition pulsing cycle. At timing point  149  and along time period  156 , ions are traveling through TOF tube  105  and hitting detector  110  while ion population  142  is trapped at RF surface  131  and is undergoing collisional cooling of translation energy as shown in  FIG. 6C . At timing point  150  trapped ion population  142  is subjected to spatial compression by an increase in the voltage applied to DC electrodes surrounding RF surface  131 . The compression time lasts short time period  151 . At time point  172 , the RF voltage applied to the RF electrodes is switched off as shown at event  158  along RF voltage amplitude line  166 . Simultaneously, DC voltages on front electrodes  127  and  128  are switched low to accelerate positive polarity ions into TOF flight tube  105  while RF surface back, side and offset DC voltages are switched to provide an optimal DC field at RF surface  131  for accelerating ions uniformly into TOF flight tube  105 . Time point  172  is illustrated in  FIG. 6D .  
         [0079]     Ion acceleration voltages are held for time duration  152  which is sufficient time for the highest mass to charge value ion to pass through the grid in electrode  135 . At time point  173  a new TOF the RF voltage is turned on and the DC voltages in pulsing region  133  are set to allow ions to enter gap  115  and be directed to RF surface  131  as shown in  FIG. 6A . Simultaneously, the voltage applied to ion guide exit lens  125  is switched to allow the release of trapped ions  140  from ion guide  103  as shown at event  157  along DC voltage amplitude line  164 . After time period  153  has elapsed, the voltage applied to ion guide exit lens  125  is raised to trap remaining ions in ion guide  103  as shown in  FIG. 6B . Released ions comprising ion packet  141  enter gap  115  and are directed towards RF surface  131  while the previously pulsed ion packet  143  is traversing TOF flight tube  105  toward detector  110  separating in time by mass to charge value. Time period  154  is set to provide sufficient time for the highest m/z value ion to hit detector  110  completing the TOF spectrum acquisition for the TOF pulse starting at time period  172 . While the previous pulsed packet is traversing TOF flight tube  105 , the translational energies of ions in ion packet  142  trapped at RF surface  131  are being cooled due to collisions with background gas. At time point  174  the amplitude of DC voltages applied to DC electrodes surrounding RF surface  131  are increased to spatially compress trapped ion packet  142  for the short time period  160 . This begins a new pulsing cycle. The new spatially compressed ion packet  143  is pulsed into TOF flight tube  105  beginning at time point  161  analogous to time point  172  of the previous TOF pulse. Ion accelerating potentials applied to electrodes are maintained up to time point  162  as the TOF pulsing cycle is repeated. TOF spectra acquired for each TOF pulse cycle are typically summed to form a summed TOF spectrum that is saved in a data file.  
         [0080]     The total TOF pulse cycle time shown in the example timing diagram  148  in  FIG. 7  is the sum of time periods  151 ,  152  and  154 . Rapid TOF pulse rates minimize space charge build by trapped ions at RF surface  131 . The ion accumulation at RF surface  131  provides very high duty cycle TOF m/z analysis for a wide range of ion m/z values. When operating the RF surface in TOF pulsing region  133 , higher sensitivity can be achieved over a broader mass range compared with trappulse operation described in U.S. Pat. No. 5,689,111 incorporated herein by reference. Reduction of the trapped ion population spatial and energy spread prior to pulsing into the TOF flight tube increases TOF resolving power compared to conventional orthogonal pulsing TOF mass to charge analysis. The RF surface effectively decouples the energy spread of the initial ion population from the ion population pulsed into the TOF flight tube providing improved consistency in TOF performance with reduced upstream tuning constraints. TOF pulsing region  133  comprising RF surface assembly  104  can be operated in conventional orthogonal pulse and trappulse modes when ion trapping at RF surface  131  is turned off. Ion reflector  106  can be configured at an angle relative to the centerline of TOF flight tube  105  to reflect ions accelerated from trapping surface  131  onto detector  110  without the need to steer the accelerated ion beam.  
         [0081]     The voltage switching sequences described above for a TOF pulse cycle are applied and controlled through the electronics circuit assembly shown as an example in  FIG. 8 . Elements common to those shown in  FIGS. 5 and 6  have retained the same number in  FIG. 8 . RF electrodes configured in RF surface assembly  104  are connected to RF and DC offset power supply  180 . Back electrodes configured in RF surface assembly  104  are connected to DC power supplies  186  and  187  through switch  185 . Side planar electrodes  145  are connected to DC power supplies  189  and  190  through switch  188 . First forward electrode  127  is connected to DC power supplies  192  and  193  through switch  191 . Second forward electrode  128  is connected to DC power supplies  195  and  196  through switch  194 . Ion guide exit lens  125  is connected to DC power supplies  183  and  184  through switch  182 . Electrodes  126  and  200  are connected to dual output DC power supply  197  and steering electrode set  134  is connected to dual output DC supply  198 . Switches  182 ,  185 ,  188 ,  191  and  194  and all power supplies are controlled by logic unit  181  during TOF pulsing sequences with ion trapping at RF surface  131 . Rapid voltage switching and timing sequences shown in timing diagram  148  in  FIG. 7  are software and hardware controlled through logic unit  181 . Logic unit  181  may comprise a commercially available computer or a custom electric circuit. Switches  182 ,  185 ,  188 ,  191  and  194  allow rapid and precise switching between respective power supplies to rapidly apply appropriate voltages to DC electrodes during a TOF pulsing sequence. The applied voltages and switching timing sequence can be changed through the software control program running in logic unit  181 .  
         [0082]     An alternative embodiment of an RF surface assembly configured in a pulsing region of a TOF mass to charge analyzer is diagrammed in  FIG. 9 . RF surface assembly  210  comprises linear RF electrodes including RF electrodes  222 ,  223 ,  224  and  225  extending the length of RF surface  231  and oriented perpendicular to incoming ion beam  227 . RF surface assembly  210  comprises linear DC back electrodes including  213 ,  214 ,  215 ,  216 ,  217  and  218  configured underneath and perpendicular to linear RF electrodes  222  through  225 . Back electrodes including electrodes  213  through  218  are separated by electrically insulating gaps including  220  and  221 . Planar side DC electrodes  205 ,  206 ,  207  and  208  surround all RF electrodes including RF electrodes  222  through  225  and are positioned in the plane formed by the tops of the RF electrodes including RF electrodes  222  through  225 . Side electrodes  211  and  212  are positioned on either side of RF surface assembly  210  to provide additional electric field shaping and to aid in optimizing ion trapping and release functions. Side electrodes  211  and  212 , planar side electrodes  5  through  8  and back electrodes  213  through  218  serve a similar function as the side, planar side and concentric ring back electrodes configured in RF surface assembly  1  shown in  FIG. 1  and described above. DC voltages applied to planar side electrodes  205  through  208  are set during trapping to form a DC energy well with RF surface  231  that aids in trapping ions at RF surface  231 . Separate or common DC voltages may be applied to back electrodes including electrodes  213  through  218  to direct ions to spread out along RF surface  231  or to move ions toward specific locations on RF surface  231 . The amplitude of DC voltage applied to back electrodes  213  through  218  can be adjusted to move trapped ions into or above the plane of RF surface formed by the tops of RF electrodes  222  through  225 .  
         [0083]     RF electrodes including RF electrodes  222  through  225  may be configured as rods, wires traces on circuit boards or other fabrication techniques known in the art. Linear RF electrodes  222  through  225  may be segment along the electrode length allowing further manipulation of trapped ion populations by adjusting the relative offset potentials applied to different segments of the segmented linear RF electrodes. Planar side electrodes and back electrodes may be configured as conductive traces on circuit boards similar to the circuit board configuration described for RF surface assembly  1  shown in  FIGS. 1 and 2 .  FIGS. 10A and 10B  show calculated ion trajectory  226  for an ion trapped above a portion of RF surface  231  with minimum collisional damping of ion translational energy. Ions are trapped by the RF voltage and DC offset voltage applied to RF electrodes  222  through  225  and the DC voltages applied to front electrode  227 , back electrode  230  and side electrodes  228  and  229  as shown in  FIGS. 10A and 10B .  FIG. 10A  is an isometric view of a portion of RF surface  231  and  FIG. 10B  is a side view of a portion of RF surface assembly  210 . Increasing the background pressure at RF surface  231  would reduce trapped ion translational energies through ion collisions to neutral background molecules.  
         [0084]     An alternative embodiment of an RF surface assembly electrode configured in a TOF pulsing region is diagrammed in  FIG. 11 . RF surface  240  comprises linear RF electrodes including  241 ,  242 ,  243  and  244  oriented parallel to the initial direction of ion beam  258 . RF surface assembly  240  is configured similar to RF surface assembly  210  but is rotated 90 degrees relative to the incoming ion beam in a TOF pulsing region. Back electrodes including electrodes  250 ,  251 ,  252  and  253  separated by electrically insulating gaps including  254  and  255  are configured perpendicular to linear RF electrodes  241  through  244 . Voltages applied to side electrodes  256  and  260  and planar side electrodes  245 ,  246 ,  247  and  248  are set to form a DC potential energy well containing RF trapped ions moving along RF trapping surface  257 . Similar to RF trapping surface assembly  210 , voltages applied to back electrodes  250  through  253  can be set adjust trapped ion position relative to the plane of RF surface  257  defined by the top of linear electrodes  241  through  244 . Initial ion trajectories entering parallel to linear RF electrodes  242  and  243  can be constrained to move along the gaps between RF electrodes  241  through  244  by applying the appropriate RF offset and DC fields to surrounding electrodes. Spatial compression of ion trajectories may be improved prior to pulsing into a TOF flight tube using the parallel RF surface  257  linear electrode orientation compared with the embodiment shown in  FIG. 9 . In alternative embodiments of the invention, ions may be directed toward RF trapping surfaces from any direction prior to trapping. Depending on specific applications and TOF pulsing region embodiments, ions may directed toward the RF surface from the front through the front electrode grid, from behind through a ion guide gap in the RF surface or from the sides. Ion populations from different sources and directions can be mixed on trapping RF surfaces. Ions trapped on RF surfaces can be reacted with neutral reagent gas or fragmented with laser or photon induced dissociation.  
         [0085]     RF surfaces can be constructed using different fabrication techniques. In an alternative embodiment of the invention diagrammed in  FIG. 12 , small RF electrode dimensions can be achieved using a layered circuit board or layered micro fabrication approach. Smaller and denser RF surface electrode assemblies provide very near field RF trapping above which trapped ions more closely approximate an ideal thin flat continuous sheet of ions prior to pulsing into a TOF flight tube. As described above, reducing the spatial spread of trapped ions prior to pulsing into a TOF mass to charge analyzer improves TOF MS resolving power and mass measurement accuracy. RF surface assembly  280  comprises three dielectric layers  294 ,  285  and  288 . RF electrodes  281  and  282  shaped as half spheres are configured along the top side of dielectric layer  294 . Similar to the spherical RF electrode embodiment diagrammed  FIGS. 1 and 2 , opposite RF voltage phase is applied to adjacent RF electrodes  281  and  282 . RF electrodes  281  with common RF phase applied are connected to conductive trace  284  configured on the bottom side of second dielectric layer  285  through vias or through conductive channels  298 . RF electrodes  282  with opposite applied RF phase, are connected to conductive trace  283  configured on the bottom side of first dielectric layer  294  through vias or through conductive channels  297 . Back DC electrodes  286  positioned in the gaps between RF electrodes  281  and  282  and planar side DC electrodes  289  connect to conductive trace  287  configured on the bottom side of dielectric layer  288  through vias or conductive through channels  299 . Separate DC voltages are applied to side electrodes  292  and  293  and front electrode  290  with grid  291 . Electrical connections to RF and DC power supplies are made to conductive traces configured on the bottom sides of each dielectric layer or circuit board. Operation of RF surface assembly  280  and surrounding DC electrodes with or without collisional cooling of trapped ions in the pulsing region of a TOF mass to charge analyzer is similar to RF surface assembly embodiments described above. Layered or micro fabricated devices as diagrammed in  FIG. 12  reduce the cost and assembly time of multiple RF electrode RF surfaces devices while improving performance for specific applications.  
         [0086]     In alternative embodiments of the invention, RF surfaces can be configured with alternative RF surface contours or shapes. The control of trapped ion location along RF trapping surfaces can be used to steer accelerated ions along different flight paths in TOF flight tubes. An alternative embodiment of RF surface  804  is configured in pulsing region  801  of hybrid TOF mass to charge analyzer  800  as diagrammed in  FIG. 13 . The length of RF surface  804  is increased to allow the storage of an ion population in two RF surface regions  802  and  803  of RF surface assembly  804 . Hybrid TOF MS  800  comprises two multichannel plate detectors operated at separate gain. Ions trapped along RF surface region  802  are accelerated into TOF flight tube  811  and impinge on first TOF detector  805 . Ions trapped along RF surface region  803  are accelerated into TOF flight tube  811  and impinge on second TOF detector  806 . Ion signals acquired from TOF detectors  805  and  806  can be combined to increase the dynamic range and amplitude signal resolution in TOF mass to charge analysis. Alternatively, ions accelerated from RF surface region  802  can be directed to impinge on third TOF detector  810  while ions simultaneously accelerated from RF surface region  804  can be directed to impinge on TOF detector  805  or  806  by applying appropriate voltages to two section steering electrode assembly  812 .  
         [0087]     In an alternative embodiment of the RF surface, a magnetic field can be applied in addition to the electric fields described to provide further control of trapped ion trajectories at the RF surface. When a magnetic field is added, trapped ion trajectories exhibit complex motions due to combined effects of the magnetic field, RF fields and electrostatic fields. Trapping efficiency can be enhanced, ion motion across the surface can be controlled, and, for appropriate phase space conditions, ion to mass selection can be achieved operating with a combination of RF and magnetic fields. A magnetic field can be advantageously applied along the x, y or z axis of the RF surface.  FIGS. 14A through 14E  show examples of calculated ion trajectories with and without the presence of an auxiliary magnetic field applied perpendicular to the plane of the RF surface. RF surface  820  comprising an array of spherical RF electrodes  821  is configured similar to RF surface assembly  1  diagrammed in  FIGS. 1 and 2 . In  FIGS. 14A through 14E  the initial ion kinetic energy parallel to RF surface  820  is 1 eV.  FIG. 14A  shows ion trajectory  822  calculated with RF and DC electric fields applied during ion trapping at RF surface  820 , as described above, in the absence of a magnetic field. Ion trajectory  822  moves over multiple RF pseudo potential wells experiencing multiple turning points prior to being trapped in pseudo potential well  828 . In  FIGS. 14B, 14C ,  14 D,  14 E and  14 F the magnetic field is applied perpendicular to the RF surface plane with magnetic field strength set to 0.1, 0.25, 0.5, 1 and 3 Tesla (T) respectively. As shown in  FIG. 14B  with a 0.1 T magnetic field added to the RF and DC electrical trapping fields, ion trajectory  823  acquires a complex motion with a large radial trajectory motion due to the force of the magnetic field. This lower magnetic field strength can be useful to spread out the ions along the surface to reduce space charge effects. As the magnetic field strength is increased, as illustrated in  FIGS. 14C, 14D ,  14 E and  14 F, the radial component due to the magnetic field force decreases and the frequency of motion about this radius increases as shown in ion trajectories  824 ,  825 ,  826  and  827  respectively. At higher magnetic field strength, ion motion tracks the electrical equipotential surface generated by the RF and DC voltages applied to electrodes comprising surface RF surface assembly  820  as is evident in calculated ion trajectories  826  and  827  of  FIGS. 14E and 14  F respectively. The magnetic field produces a spiral ion motion as the ion moves along the RF surface. This spiral ion motion increases the ion flight path allowing more rapid collisional cooling of ion translational energy for a given background pressure or provides sufficient collisional cooling of ion kinetic energy at lower background pressures. The addition of a magnetic field to the operation of an RF surface permits the trapping of ions above the RF surface, almost entirely independent of the initial ion phase space conditions and reduces collision gas pressure requirements.  
         [0088]     Alternative embodiments of RF surfaces can be configured and operated in different mass to charge analyzer types to provide unique or improved performance. An alternative embodiment of the RF surface is diagrammed in  FIG. 15  wherein RF surface assembly  834  is configured as an ion trapping surface in mass to charge analyzer  830 . Mass to charge analyzer  830  employs crossed magnetic  845  and RF electric fields to effect a mass to charge dependent extraction of trapped ions to external detector  831 . A cross section side view of mass to charge analyzer  830  is diagrammed in  FIG. 15  and a front cross section view of RF surface mass to charge analyzer  830  is shown in  FIG. 16 . Ions  832  are directed into mass to charge analyzer volume  847  through orifice  833  in electrode  835 . Ions travel toward RF surface assembly  834  where they are trapped above RF surface  834  as described previously by the combined forces imposed by the RF and DC voltages applied to RF electrodes  238 , DC electric fields applied to back electrodes  840 , side electrodes  841 ,  842 ,  843  and  844 , front electrode  835  and magnetic field  845 . Magnetic field  845  is applied perpendicular to the plane of RF surface  834 , permeating RF surface assembly electrodes and surrounding electrodes with minimum distortion due to the non-magnetic materials employed. Neutral gas molecules may be introduced into volume  847  or RF surface mass to charge analyzer  830  to provide collisional cooling of trapped ion kinetic energy. Alternatively, laser beam  848  may be directed through orifice  849  in RF surface assembly or along the plane of trapped ion population  850  to effect laser cooling of trapped ion kinetic energy. Individual back electrodes  840  are configured as concentric conductive rings to provide control of trapped ion motion above RF surface  837 . Trapped ions move toward the center region  851  of RF surface  837  directed by magnetic field  845  and electrostatic forces from DC voltages applied to electrostatic DC back electrodes  840 , side electrodes  841  through  844  and front electrode  835  combined with laser or collisional cooling of ion kinetic energy. The trapped ions population is then ‘chirped’ or accelerated out from center region  851  by a transient electric field applied to DC back electrodes  840  and side electrodes  841  through  843 . Accelerated ions have the same kinetic energy, so ions of different mass-to-charge will have a different rotational frequency above RF surface  837  rotating around center region  851  of RF surface  837 . The rotational motion of the ions can be capacitively detected, as is well-known with a Fourier Transform ICR device. Alternatively, the ions may be displaced radially, responding to a common frequency applied to back and/or side electrodes and orbit at different radii due to different kinetic energies dependent on ion mass to charge. A radial electric field may be used in scanning mode to move the orbits of ions to larger radii, eventually exiting the RF field and detected with electron multiplier detector  852  or multichannel plate detector  831 .  
         [0089]     In an alternative embodiment of the invention, two RF surface assemblies  861  and  862  are configured in analysis cell  860  of a Fourier Transform Inductively Coupled Resonance mass spectrometer (FTICR MS or FTMS) as diagrammed in  FIG. 17 . Ions  863  are directed into FTICR MS analyzer cell  860  through orifice  865  in electrode  867  and RF surface assembly  261 . Ions travel toward RF surface  868  where they are trapped as described previously by the combined RF, electrostatic and magnetic field forces generated by RF voltages applied to RF electrodes and DC voltages applied to surrounding DC electrodes. Neutral gas molecules may be introduced in FTMS cell  860  for collisional cooling of trapped ions  872 . Alternatively, laser beam  873  may be directed through orifice  874  in RF surface assembly  862  to effect laser cooling of trapped ion kinetic energy. By adjusting the relative potentials applied to electrodes comprising RF surface assemblies  861  and  862  and the DC potential applied to surrounding electrodes  870  and  871 , ions are directed toward the center of RFMS cell  860 . The ions are then ‘chirped’ out from the center of FTMS cell  860  to larger orbits for detection through capacitive coupling with FTMS cell  860  side pickup electrodes  870  and  871 . RF surface assemblies  861  and  862  configured in FTMS cell  860  increase trapping efficiency for ions with a broader energy spread than can be trapped with a DC electrode FTMS cell. In addition, the voltages applied to electrodes comprising RF surface assemblies  861  and  862  can be set equal after ion chirping and during ion detection to minimize variations in DC field along the axis of FTMS cell  860 . The near field axial direction trapping provided by the operation of RF surfaces  861  and  862  with back and surrounding electrodes provides essentially an electrostatic field free region in volume  864  during mass to charge analysis improving the FTMS analysis resolving power.  
         [0090]     During operation of the embodiments of the invention described above and shown in  FIGS. 1 through 17 , ions are trapped at or above RF surfaces and released or accelerated from the RF surfaces. Alternative embodiments of the RF surface comprise ion guides integrated into the RF surface. Ions trapped along the RF surface of such RF surface embodiments are directed to move into and through the ion guide integrated into the RF surface. Front DC electrodes configured with RF surfaces comprising ion guides, aid in focusing and trapping ions and transferring ions through orifices into vacuum from atmospheric pressure ion sources or through partitions in multiple vacuum stages. DC focusing electrodes configured with RF surface and ion guide embodiments of the invention improve ion transport efficiency from atmospheric pressure into vacuum and through multiple vacuum stages in mass spectrometer instruments. Alternative embodiments of the integrated RF surface and ion guide assemblies are configured and operated to provide multiple functions in addition to ion transport. Ion guide assemblies comprising ion tunnel or conduit sections along the ion guide length reduce neutral gas transmission between vacuum stages while providing efficient ion transmission. Ion guides configured in RF surfaces may extend through multiple vacuum stages and comprise multiple segments along the ion guide length. Ion transport, ion trapping, mass to charge selection, collision induced dissociation (CID) fragmentation, ion mobility separation and ion-neutral and ion-ion reaction functions can be performed in ion guides comprising entrance regions configured in RF surfaces.  
         [0091]     Spherical electrode RF surface assembly  300  comprising multipole ion guide assembly  308  configured and operated at or near atmospheric pressure is diagrammed in  FIGS. 18, 19  and  20 . A side cross section view of RF surface assembly  300  comprising multipole ion guide assembly  308  configured with forward DC electrodes  330 ,  331  and  332  and capillary  322  with orifice or bore  338  into vacuum is diagrammed in  FIG. 18 . FIG.  19  shows a side cross section view of RF surface assembly  300  configured in an atmospheric pressure ion source comprising Matrix Assisted Laser Desorption Ionization (MALDI) and forward DC electrodes  352  and  353 . A magnified top view of RF surface assembly  300  is diagrammed in  FIG. 20 . A top view diagram of the center portion of back electrode circuit board  303  of RF surface assembly  300  is diagrammed in  FIG. 21 . Referring to  FIGS. 18, 19 ,  20  and  21 , RF surface assembly  300  comprises spherical electrodes  301  and  302  and the hemisphere shaped entrance ends  312  and  313  of ion guide poles  310 A,  310 B,  311 A and  311 B comprising multipole ion guide assembly  308 . RF voltage of opposite phase is applied to adjacent electrodes  301  and  302  comprising RF surface  344 . Similar to operation of RF surface assembly  1  diagrammed in  FIGS. 1 and 2  described above, four RF surface spherical electrodes surrounding a common center region form a four electrode set. Four electrodes  310 A,  310 B,  311 A and  311 B form a four hemisphere shaped RF electrode set at RF surface  344  and extend through RF surface assembly  300  forming multipole ion guide  308 . All RF electrodes comprising RF surface  344  are evenly spaced in the embodiment of RF surface  300  shown in  FIGS. 18 through 20 . Common RF amplitude and frequency and a common DC offset is applied to all RF spherical electrodes including  301  and  302  with opposite RF phase applied to adjacent electrodes. The same RF frequency and phase is applied to ion guide electrodes  310 A,  310 B,  311 A and  311 B, however, a different RF amplitude and DC offset may be applied to optimize ion focusing and transmission into ion guide center channel  320 . Ion guide poles or electrodes  310 A,  310 B,  311 A and  311 B slide through an opening in RF surface insulator  302  and through opening  371  in back electrode circuit board  303 . Ion guide poles or electrodes  310 A,  310 B,  311 A and  311 B are electrically insulated from surrounding spherical RF electrodes and back DC electrodes. In one embodiment of the invention, hemisphere shaped entrance ends  312  and  313  of ion guide electrodes  310 A,  310 B,  311 A and  311 B are configured parallel to the tops of surrounding spherical electrodes  301  and  302  along RF surface  344 . Alternatively, RF surface assembly  300  can be configured with hemisphere shaped entrance ends  312  and  313  of multipole ion guide assembly  308  positioned above or below the plane of RF surface  344 . Ion guide assembly  308  is configured as a subassembly within RF surface assembly  300  and can be repositioned relative to RF surface  344  to optimize performance for a given application.  
         [0092]     Spherical electrodes  301  comprising RF surface assembly  300  with common RF voltage applied, connect to RF power supply  350  through connecting posts  304  extending through insulator  302  with conductor or circuit board  306  linking all common voltage RF spherical electrodes. Similarly, spherical electrodes  302  comprising RF surface assembly  300  with common RF voltage applied, connect to RF power supply  350  through connecting posts  305  extending through insulator  302  with conductor or circuit board  307  linking all common voltage RF spherical electrodes. Multipole ion guide assembly  308  mounting electrodes  314  and  315 , separated by insulator  317 , are electrically and mechanically attached to electrode pairs  310 A with  310 B and  311 A with  311 B through connections  319  and  318  respectively. Multipole ion guide assembly  308  may be constructed as described in U.S. Pat. No. 5,852,294 incorporated herein by reference or comprise other construction types known in the art. Mounting electrodes  315  and  316  and insulator  317  are configured to minimize the neutral gas conductance opening size along multipole ion guide assembly  308  as described in U.S. Pat. No. 5,852,294. Multipole ion guide electrodes  310 A and  310 B connect to RF power supply  350  through mounting electrode  314 . Similarly, multipole ion guide electrodes  311 A and  311 B connect to RF power supply  350  through mounting electrode  315 . Separate concentric back electrodes  340 ,  341 ,  342  and  343  configured on the top surface of circuit board  303  are separated by electrically insulating gaps  370  on back electrode circuit board  303  as shown in  FIG. 21 . Back electrodes  340  through  343  connect to DC power supply  351  through vias  347  in circuit board  303  and conductive traces  364  on the back side of circuit board  303 . The voltages applied to back electrodes  340  through  343  are set to optimize the DC repelling field penetration between spherical RF electrodes during RF surface operation. DC front electrodes  330 ,  331  and  332  connect to DC power supply  346 . All RF and DC power supplies are connected to a logic unit for software program or manual control.  
         [0093]     Referring to  FIG. 18 , ions  345  generated in atmospheric pressure ion source  348  are directed through opening  349  in front DC electrodes  330  and  331  driven by the focusing electric fields formed from the electrostatic potentials applied to front DC electrodes  330 ,  331  and  332  and the offset potentials applied to RF electrodes comprising RF surface assembly  300 . DC electric accelerating and focusing fields, as depicted for illustration by lines  335 ,  336  and  337 , focus ions  345  toward centerline  321  as they move against heated countercurrent drying gas  333  toward RF surface  344 . DC voltages applied to back electrodes  340  through  343  and the RF and DC voltage applied to RF electrodes comprising RF surface  344  provide a near repelling field preventing approaching ions  345  from hitting electrodes comprising RF surface assembly  300 . Ions trapped above RF surface  344  move toward centerline  321  driven by relative voltages applied to concentric back electrodes  340  through  343  and by gas flow  334  sweeping through the center channel  320  in multipole ion guide assembly  308 . Ions entering channel  320  are swept through the length of ion guide  308  driven by gas flow and exit at ion guide exit end  326 . The voltage applied to DC electrodes  368  shown in  FIG. 21  is set to counteract or shield the repelling DC field applied to back electrode  340  from penetrating into channel  320  of multipole ion guide  308 . Shielding or neutralizing the DC repelling electric field in channel  320  allows the ions traversing the length of ion guide  308  to pass by the back electrode plane driven by gas dynamics. The same gas flow that sweeps ions  324  through the length of ion guide channel  320 , continues to sweep ions  324  into and through orifice or bore  338  in capillary  322 . Ions entering vacuum from atmospheric pressure through capillary bore  338  are mass to charge analyzed as will be described below. Electrically insulating and mounting element  325  provides a mounting function for RF surface assembly  300  with capillary  322  while providing a gas seal to insure that all gas flow passing through capillary bore  338  also passes through multipole ion guide channel  320 . The offset potential applied to ion guide electrodes  310 A,  310 B,  311 A and  311 B is maintained close to or equal to the DC voltage applied to capillary entrance electrode  323 . By maintaining a neutral DC electric field in entrance region of capillary  322 , ion movment into capillary bore  338  is driven primarily by gas dynamics and not electric fields that, when present, can direct ions to impinge on capillary entrance electrode  323 .  
         [0094]     The embodiment of the invention shown in  FIG. 18  combines DC and RF fields with gas dynamics forces to improve ion transmission from atmospheric pressure ion sources into vacuum. The RF fringing fields generated at the entrance end of multipole ion guide  308 , configured in RF surface assembly  300 , provides a repelling force to prevent ions from impinging on multipole ion guide  308  electrodes operating at or near atmospheric pressure in atmospheric pressure ion source  348 . Multiple electrostatic front electrodes  330  and  331 , configured with small separating gap  339 , and front electrode  332  are configured to provide maximum focusing of ions from a large gas volume toward center of RF surface  344 . A weak electric field is maintained between DC electrode  332  and the offset potentials applied to RF electrodes comprising RF surface assembly  300  to minimize the electrostatic force driving ions onto the RF electrodes. Collisional damping of ion motion at atmospheric pressure reduces the near field RF repelling force generated by the RF electrodes. The RF and DC offset voltages applied to RF electrodes comprising RF surface  344  and the DC voltages applied to surrounding DC electrodes are set to provide a balance of electric field strength and gas dynamics to maximize ion transmission efficiency into and through ion guide  308 . RF voltage applied to RF electrodes including  310  and  302  and multipole ion guide electrodes  310 A,  310 B,  311 A and  311 B provides sufficient repelling force to compensate for the ion defocusing forces occurring in the weak electrostatic fields as ions approach centerline  321  of RF surface  344 . Focusing ions in DC only fields toward a DC capillary entrance electrode results in a substantial loss of ion current on the capillary entrance electrode. Near the capillary entrance, strong focusing electric DC only fields drive the ions to the face and edge of the capillary entrance electrode overcoming the gas flow forces sweeping into the capillary orifice into vacuum. A weak DC only focusing electric field in an atmospheric pressure ion source fails to focus ions effectively to the centerline reducing ion current entering a capillary orifice into vacuum. Multipole ion guide  308  forms an effective ion transport device at atmospheric pressure bridging a strong DC focusing electric far field with a minimum or zero DC field at the capillary entrance electrode allowing gas dynamics to provide the dominate force sweeping ions into bore  338  of capillary  322 . The near RF field generated by RF electrodes comprising RF surface assembly  300  prevents ions from impinging on electrode surfaces when defocusing occurs in weak DC fields maintained near RF surface  344 .  
         [0095]     Referring to  FIG. 19 , atmospheric pressure MALDI ion source  374  comprises MALDI target  358  with sample  359 , RF surface assembly  300  and front DC electrodes  352  and  353 . Laser beam  362  is directed to impinge on sample  359  positioned on MALDI target  358  using mirror  363 . Ions  360  produced by a laser pulse are focused toward ion source centerline  375  and directed toward RF surface  344  by DC fields depicted for illustration by lines  354  and  355 . Ions following trajectories  361  moving toward RF surface  344  are driven by DC electrostatic fields against countercurrent gas flow  333 . As ions  360  approach RF surface  344  their trajectories are controlled by a balance of back electrode repelling DC fields penetrating through gaps between RF electrodes, repelling near RF electric fields, attracting DC offset potentials, gas dynamics and forward DC fields imposed by DC voltages applied to front electrodes  352 ,  353  and MALDI target  358 . Ions directed toward centerline  375  of RF surface  344  are swept into and through multipole ion guide  308  by gas flow  334 . Ions  377  exiting ion guide  308  are swept into and through capillary bore  338  by the same gas flow  334 . RF surface assembly  300  can be configured with alternative ion guide geometries and different orifices into vacuum. Orifices into vacuum can be configured as but not limited to dielectric capillaries, heated conductive capillaries, sharp edged orifices, nozzles or other orifice shapes known in the art. RF surface assembly  300  may comprise alternative RF electrode shapes including but not limited to grids and points, linear, point or spherical electrodes arranged in patterns that accommodate specific ion guide geometries. Ion guide  308  may be configured as a quadrupole, hexapole, octapole or an guide with a higher number of poles. Ion guide electrode cross section shapes may be round, flat or hyperbolic. Alternatively, Ion guide  308  may be configured with sequential RF disks. The electrodes or poles comprising multipole ion guide  308  may be segmented along the length of ion guide  308  with different DC offset potentials applied to different ion guide segments. The ability to apply multiple DC offset potentials to ion guide  308  electrodes provides additional control to move ions through the length of segmented ion guide  308  or to trap ions in guide  308  during ion source operation. Segmented ion guide  308  can be operated as an ion mobility separation device in atmospheric pressure MALDI ion source  374  to provide separation of ions by ion mobility prior to mass to charge analysis.  
         [0096]     RF surface assemblies comprising multipole or sequential disk ion guides and front and back DC electrodes can be configured and operated in vacuum to improve ion transmission efficiency through vacuum stages and through partitions between vacuum pumping stages. Multipole ion guides, configured according to the invention, extend through vacuum partitions providing an efficient ion tunnel or conduit while minimizing neutral gas conductance. Multipole ion guides configured according to the invention, serve both as RF surfaces and ion guides extending into multiple vacuum stages. Ion guides may be configured with one or more ion tunnel or conduit sections and multiple open vacuum pumping sections where neutral gas is pumped away through gaps between ion guide electrodes. Ion guides operated in vacuum may comprise segments with different offset potentials applied to different segments along the ion guide length. Ion guides configured according to the invention, can be operated to provide mass to charge selection or isolation, CID fragmentation, ion-neutral and ion-ion reaction regions, ion mobility separaton and/or ion trapping and release functions.  
         [0097]     RF surface assembly  400  comprising multipole ion guide assembly  401  is configured to transfer ions from vacuum stage  402  into vacuum stage  403  through vacuum partition  404  as diagrammed in  FIG. 22 . Opposite Phase RF voltage is applied to adjacent electrodes on RF surface  413  as previously described. Spherical RF electrodes  411  and  412  held in position by insulator  423  form RF surface  412  with Multipole ion guide electrode  414  and  415 . Entrance end  442  of multipole ion guide extends into vacuum pumping stage  402  and ion guide exit end extends into vacuum pumping stage  443 . Back electrodes  421  and  422  are configured on the top surface of circuit board  420 . Repelling electrical potentials are applied to back electrodes  421  and  422  to move ions above RF surface and toward centerline  440  where they enter ion guide channel  438 . Repelling potentials applied to back electrodes  421  and  422  prevent ions from remaining trapped in the RF pseudo potential wells formed between RF spherical and multiple ion guide electrode sets. Neutral gas flowing from an atmospheric pressure ion source exis bore  408  of capillary  410  as a free jet expansion into vacuum stage  402  forming barrel shock  431  and normal shock  432  as is known in the art. The size of barrel shock and the position of normal shock  432  along axis  440  are determined by the background vacuum pressure maintained in vacuum stage  402 . Capillary  410  is positioned in vacuum stage  402  so that normal shock  432  occurs in just outside of opening  444  of DC electrode  434 . Ions  407  exiting capillary bore  408  are swept along by the neutral carrier gas and the DC electric fields formed by DC electrical potentials applied to capillary exit electrode  433  and electrode  434  and the offset potential applied to RF electrodes comprising RF surface  413 . Ions passing through normal shock  432  continue to move through subsonic neutral gas flow and are focused toward centerline  440  by and the entrance end  442  of ion guide assembly  401  by DC electric fields depicted approximately by lines  430 . Background neutral gas flow  428  flowing through ion guide channel  438  into vacuum pumping stage  403  provides additional force in moving ions  407  into ion guide channel  438 . As ions approach RF surface  413  the near RF repelling field and the back electrode DC repelling fields penetrating through gaps between RF electrodes prevent ions from hitting RF electrodes. Ions moving toward RF surface  413  are focused toward centerline  407  due to DC fields  430  and gas flow  428  with translational energy damping due to collisions with background gas. Ions entering channel  438  of multipole ion guide  401  are trapped in the radial direction by the RF voltage applied to multipole electrodes  414  and  415 . Gas flow through channel  438  moves radially trapped ions  437  through the length of ion guide  401  exiting in vacuum pumping stage  403  at ion guide exit end  443 .  
         [0098]     Multipole ion guide subassembly  401 , configured in RF surface assembly  400 , forms a conduit or channel through vacuum stage partition  404  that minimizes the conductance of neutral gas from vacuum pumping stage  402  to vacuum pumping stage  403  while maximizing ion transport efficiency. Ion guide mounting electrodes  425  and  426  separated by insulator  334  form electrical and mechanical connections to ion guide electrodes  414  and  415  while minimizing the cross sectional area through multipole ion guide  401 . Insulators  423  and  445  form a vacuum seal with mounting element  427  preventing gas flow around ion guide  401 . Tube element  424  decreases the gas volume surrounding ion guide electrodes  413  and  414  minimizing neutral gas exchange through gaps between ion guide  401  electrodes along length  447  of ion guide  40  between insulator  404  and mounting electrode  425 . Gas flow around ion guide electrodes  414  and  415  is prevented or minimized by insulator  423  and mounting electrodes  425  and  426  with insulator  445 . Gas exchange through gaps between ion guide electrodes  415  and  416  is minimized by tube element  425  along ion guide section  447 . This combination creates a gas flow conduit through channel  438  of ion guide assembly  401  extending the length of ion guide section  447  through which a gas pressure drop occurs in gas flowing between vacuum stages  402  and  403 . Neutral gas conductance decreases with increasing conduit section length  447  in ion guide  104  with no loss in ion transfer efficiency though ion guide  401 . Longer ion guide conduit section lengths  447  provide higher resistance to gas flow between vacuum pumping stages. This results in lower downstream vacuum pressures for the same vacuum pumping speed or allows the reduction of vacuum pumping speed, vacuum pump size and cost. Alternatively, ion tunnel or conduit sections configured in multipole ion guides extending into multiple vacuum stages allows larger ion guide sizes, for a given vacuum pumping speed, increasing the ion transfer efficiency and ion trapping volume. Ion guide assembly  401  also comprises non conduit or open section  448  along which neutral gas  441  can be pumped away through gaps in ion guide electrodes  414  and  415  while ions remain radially trapped until exiting ion guide exit end  443  at  435 .  
         [0099]     Ion guide assembly  401  configured in RF surface assembly  400  serves itself a portion of the RF surface for efficiently transferring ions into channel  438  of ion guide  401 . Multipole ion guide also provides the functions of efficiently transferring ions from vacuum stage  402  to vacuum stage  403  and trapping ions radially during collisional cooling of ions being transported through the length of ion guide  401 . A mono velocity ion beam exiting capillary bore  408  is converted to a mono energetic ion beam in ion guide  401  with exiting ions  435  having an average energy equal to the offset potential of ion guide  401  and a narrow energy spread. Ion guide  401  configured as a quadrupole forms a parabolic energy well in channel  438  that focuses ions to centerline  407  as collisional cooling of ion translation energies occurs. Ion focusing along centerline  407  due to collisional cooling provides a narrow cross section ion beam  435  with low energy spread exiting ion guide  401  at ion guide exit end  443 . Channel  438  formed by ion guide  401  serves as the neutral gas conductance conduit from vacuum stage  402  through  403 . The length to equivalent diameter ratio of conduit or ion tunnel section  447  of ion guide  401  can range from 2 to 10 to over 100 with longer length to diameter rations providing decreased neutral gas flow for the same upstream vacuum pressure. In alternative embodiments of the invention, ion guide  401  can be configured with segments along its length to move ions selectively along the length of ion guide  401  controlled by axial DC fields. In applications where ions need only be focused from a small cross sectional area into a multipole ion guide, a minimum size RF surface can be configured using only the ion guide electrodes.  
         [0100]     An alternative embodiment to the invention is diagrammed in  FIG. 23  wherein multipole ion RF surface and multipole ion guide assembly  450  is configured to replace RF surface assembly  400  shown in  FIG. 22 . Opening  451  through DC electrode  452  is reduced to sharpen ion focusing towards centerline  457  with reduced DC voltage differentials applied between electrode  452  and the offset potential applied to ion guide  458  electrodes  460  and  461 . The length of ion funnel or conduit section  455  of ion guide assembly  458  has been increased and RF electrode insulator  423  has been replaced by mounting electrode  462  and  463  with insulator  464  assembly. Dual mounting electrode sets configured along the length of ion guide assembly  458  strengthens the assembly while further reducing effective cross section area of internal channel  465 . Ion guide assembly  458  provides identical functions as described for ion guide assembly  401  described above at reduced size, cost and complexity of operation. Larger RF surface and ion guide assembly  400  shown in  FIG. 22  can focus ions into ion guide  401  from a larger cross sectional area. When ion populations are constrained to smaller sampling cross sections, ion guide assembly  458  may be preferred to reduce cost and complexity without reducing ion transmission performance. Embodiments of RF surfaces comprising ion guides can be configured to provide maximize performance for specific applications or instrument types while reducing overall instrument cost and complexity.  
         [0101]     Multiple RF surfaces comprising ion guides can be configured in mass spectrometer instruments to provide optimal analytical performance. Electrospray ion source mass analyzer  480  diagrammed in  FIG. 24  comprises Electrospray ion source  485 , RF surface ion guide assembly  481  operating at atmospheric pressure, dielectric capillary  482 , vacuum RF surface and ion guide assembly  483  and mass analyzer  484 . RF surface assembly  481  comprising ion guide assembly  487  provides improved ion transport efficiency from ES source  485  into first vacuum pumping stage  488 . RF surface assembly  483  comprising ion guide assembly  490  with ion tunnel or conduit section  491  provides increased ion transfer efficiency from first vacuum stage  488  into second vacuum stage  492 . Ions traversing the length of ion guide  490  undergo collisional damping of kinetic energy reducing ion energy spread focusing ions toward the centerline of ion guide  490 . Decreasing the cross section and energy spread of the ion beam exiting ion guide  490  improves the performance of down stream ion beam transmission, ion manipulation, ion focusing and mass to charge analysis functions.  
         [0102]     Alternative combinations of ion sources and mass to charge analyzers can be configured using RF surfaces comprising ion guides. Atmospheric pressure ion source comprising  501  comprising RF surface and ion guide assembly  502  delivers ions to first vacuum pumping stage  511  in a direction orthogonal to centerline  510  of hybrid mass to charge analyzer  500 . MALDI sample target  506  is configured in first vacuum stage  511  positioned orthogonal to centerline  510 . RF surface assembly  503  comprising ion guide assembly  512  is configured to transfer ions entering first vacuum stage  511  into second vacuum stage  513 . Ions  508  exiting Electrospray ion source  501  are directed toward RF surface  517  and focused to centerline  510  by electrostatic fields maintained in first vacuum chamber  511 . The same electrostatic fields direct MALDI generated ions  507  toward RF surface  517  while focusing ions  507  toward centerline  510 . Electrospray ion source  501  and MALDI ion generation can occur separately or simultaneously during mass to charge analysis. One source of ions may be used as calibration ions for the second source of ions during mass to charge analysis. Voltages applied to DC electrodes  518 , capillary exit electrode  520 , MALDI sample target  506  and the RF and back electrodes, comprising RF surface  517 , direct ions into channel  521  of ion guide  512 . Gas flowing from first vacuum stage  511  into second vacuum stage  513 , through ion tunnel or conduit section  522  of ion guide  512 , moves ions through ion guide  512 . Ions  53  exiting ion guide  512  are directed into ion guide  504  by a difference in offset potentials applied to each ion guide. Typically the background vacuum pressure in second vacuum stage  513  is maintained above 1×10 −4  torr so that ions accelerated from ion guide  512  into ion guide  504  with with sufficient acceleration energy undergo collision induced dissociation CID in guide  504 . Alternatively, ions can be transferred from on guide  512  into ion guide  504  at lower axial acceleration energy to avoid CID fragmentation of ions. Ion guide  504  extends into second and third vacuum pumping stages  513  and  514  respectively transferring ions through vacuum partition  524 . Ion guide  504  may be operated in single pass or ion trapping and release mode. Parent ions and/or fragment ions traversing or trapped in ion guide  504  undergo collisional cooling of translational energies prior to exiting ion guide  505 . Ion guide  504  can be operated in mass to charge selection or isolation, ion fragmentation, MS/MS or MS n  mode followed by mass to charge analysis in vacuum fourth vacuum stage  515 . Ions exiting ion guide  504  are mass to charge analyzed by mass to charge analyzer  505 . Mass to charge analyzer  505  may comprise but is not limited to TOF, quadrupole, triple quadrupole, magnetic sector, three dimensional ion trap, linear ion trap FT MS or orbitrap mass to charge analyzers.  
         [0103]     Multipole ion guides comprising RF surfaces and multiple ion tunnel sections can be configured to extend through multiple sequential vacuum stages improving ion transmission while reducing gas conductance between vacuum pumping stages. A cross section side view diagram of multipole ion guide assembly  530  configured to extend into four vacuum stages is shown in  FIG. 26 . Multipole ion guide assembly  530  comprises RF surface  548 , electrodes  531  and  532 , first, second and third ion tunnel sections  533 ,  534  and  535  respectively and open pumping sections  547  and  543 . Ions exiting capillary  538  are directed into center channel  540  of ion guide  534  as previously described. Ions are directed through the length of ion guide by gas flow passing into sequential vacuum pumping stages. Ions entering ion guide center channel  540  at entrance end  553 , positioned in first vacuum chamber  541 , pass through ion tunnel section  533  and move into second vacuum pumping stage  542 . Ions remain trapped in the radial direction as they traverse the length of ion guide  530  passing through second and third vacuum stages  542  and  543  respectively. Ions exit in fourth vacuum stage  544  where they are subjected to further manipulation and/or mass to charge analyzed in mass to charge analyzer  537 . Ion tunnel or conduit section  533  comprises three mounting electrode and insulator assemblies  555  configured to minimize the effective neutral gas flow cross section through ion tunnel section  533 . The configuration of ion tunnel section  533  minimizes space charge buildup on insulators external to ion guide center channel  540  and reduces neutral gas flow through vacuum partition  550 . Alternatively, ion tunnel or conduit section  534  comprises two mounting electrode and insulator assemblies and tube element  554  to minimize neutral gas conductance through vacuum partition  551 . Ion tunnel section  535  comprises two mounting electrode and insulator assemblies to reduce neutral gas conductance through vacuum partition  551 . A portion of the neutral gas flow passing through ion tunnel sections  532  and  534  passes through gaps between electrodes  531  and  532  and is pumped away along ion guide sections  547  and  545  respectively.  
         [0104]     Multipole ion guides may be configured with different pole shapes and mounting electrode and insulating elements. Three alternative electrode shapes with insulating elements comprised in ion tunnel sections are diagrammed in  FIG. 27 . Quadrupole ion guide assembly  567  shown in  FIG. 27A  comprises electrodes  560  with hyberbolic cross section shapes and square insulator  561  to minimize gas neutral gas flow through ion tunnel or conduit sections. Quadrupole ion guide assembly  568  shown in  FIG. 27B  comprises round cross section electrodes with insulator  563  shaped to minimize gas flow through ion conduit sections. Square quadrupole ion guide  570  shown in  FIG. 27C  comprises flat electrodes  564  and square insulator  565  to minimize gas flow through conduit sections. Of the three embodiments diagrammed in  FIG. 27  round rod quadrupole  568  provides higher gas flow between rods for more efficient vacuum pumping of neutral gas in open ion guide sections. Where open sections are not required along multipole ion guide lengths, the hyperbolic or flat electrode shapes may provide maximum ion transmission while minimizing neutral gas conductance between vacuum pumping stages. The diameter of circle drawn inside and just intersecting the quadrupole electrodes diagrammed in  FIG. 27  defines the inner diameter of the center channel of multipole ion guide. The length of ion tunnel sections between vacuum pumping sections extend at least two inner diameters in length and may be configured to extend over tens or hundreds of diameter lengths. As will be described below, long ion guides may comprise sections with different offset potentials applied to aid in controlling ion motion longitudinally along the ion guide length.  
         [0105]     Ion guides extending into multiple vacuum pumping stages comprising ion tunnel sections can be configured as multipole or sequential RF disk ion guides. Multipole ion guides can be configured as quadrupole, hexapole, octopoles or ion guides with more than eight poles. One embodiment of a sequential RF disk ion guide comprising an ion tunnel or conduit section configured to mount through a vacuum pumping stage partition is diagrammed in  FIG. 28 . A side cross section view of sequential disk ion guide  580  is diagrammed in  FIG. 28A  with an end view diagrammed in  FIG. 28 B . Sequential disk ion guide assembly  580  comprises sequential disks  581  and  582  where RF voltage of opposite phase but equal amplitude and phase is applied to adjacent disks. DC electrodes  594  and  595  are positioned at entrance  587  and exit  590  ends respectively of sequential RF disk ion guide  580  to shield the RF voltage fields produced by the first  581  and last RF disk electrodes. DC voltages are applied to DC electrode  594  to aid in focusing ions into channel  591  of sequential disk ion guide  580 . Common DC offset voltage can be applied to sequential disks along the length of sequential disk ion guide  580 . Alternatively, different DC offset voltages can be applied to different RF disks along the length of sequential disk ion guide  580  to control movement of ions in the axial direction of ion guide  580 . Sequential disk ion guide  580  can be configured in vacuum pumping stages where multiple collisions between ions and neutral gas occur as ions traverse the length of ion guide. A moving DC offset waveform or “T” wave can be applied sequentially to RF disk electrodes to move ions progressively through ion guide  580  effecting ion mobility separation of species in the the ion population through ion collisions with neutral background gas as is known in the art. Ions can be trapped in or moved through ion guide  580  by applying different DC offset voltages potentials or DC offset voltage gradients to different RF disk electrodes. Ions can be accelerated through ion guide channel  591  with steeper DC offset voltage gradients applied to cause ion CID fragmentation.  
         [0106]     Insulating disks  585  configured between RF disks electrodes  581  and  582  along the length of ion guide  580  provide a mechanical spacer and electrically insulating function between RF disk electrodes. Insulating disks  585  also prevent neutral gas flowing through center channel  591  from exiting through the gaps between the RF disk electrodes. Sequential disk ion guide  580  extends from vacuum pumping stage  592  to downstream vacuum pumping stage  593  through vacuum stage partition  584 . Ions  588  entering ion guide entrance  587  in vacuum stage  592  transverse the length of ion guide  580  through ion guide center channel  591  and exit at ion guide exit  589  in vacuum pumping stage  593 . The length to diameter ratio of ion guide center channel  591  exceeds a ration of 2 to 1 forming an ion tunnel or conduit to transport ions efficiently through vacuum partition  580  while reducing neutral gas conductance between vacuum pumping stages  592  and  593 . Sequential disk ion guide  580 , configured as an ion tunnel between vacuum pumping stages, provides the multiple functions of transferring ions through vacuum stage partitions with collisional cooling of ion kinetic energies and reducing neutral gas conductance between vacuum pumping stages. In addition sequential disk ion guide  580  can be operated to conduct ion trapping and release, ion mobility and ion CID fragmentation functions for ion populations traversing the length of center channel  591  of sequential disk ion guide  580 . Sequential disk ion guides can be configured to extend into multiple vacuum system comprising one or more ion tunnel sections and one or more open pumping sections. Neutral gas pumping can be achieved in sections of sequential disk ion guide  580  by configuring spacers  585  with radial slots or gaps to allow passage of neutral gas through the gaps between adjacent RF disk electrodes.  
         [0107]     Multipole ion guides comprising RF surfaces and one or more ion tunnel sections can be segmented with different DC offset voltages applied to different segments to control ion motion in the axial direction along the ion guide length. A cross section side view of segmented multipole ion guide assembly  600  is diagrammed in  FIG. 29 . Ion guide  600  comprises RF surface  601 , first ion tunnel section  608 , first multipole segment  623 , second multipole segment  624 , open pumping section  611  and second ion tunnel section  610 . Entrance end  625  of segmented multipole ion guide assembly  600  is positioned in first vacuum pumping stage  614 . Multipole ion guide assembly  600  extends through second vacuum pumping stage  615  with exit end  627  positioned in third vacuum pumping stage  617 . First multipole ion guide segment  623 , comprises electrodes  604  and  605 , first ion tunnel section  608  configured to transfer ions between vacuum pumping stages  614  and  615 , open vacuum pumping section  611  in vacuum pumping stage  615  and a portion of second ion tunnel section  610 . Second multipole ion guide segment  624  comprises electrodes  606  and  607  and a portion of second ion tunnel section configured to transfer ions between vacuum stages  615  and  617 . In one embodiment of the invention, the same RF amplitude frequency and phase are applied to linearly aligned electrodes in first and second multipole ion guide segments  623  and  624  respectively. Different DC offset potentials can be applied to multipole ion guide segments  623  and  624  to control ion motion through multipole ion guide  600 . In an alternative embodiment of the invention the same RF frequency and phase is applied to multipole ion guide segments  623  and  624  with the ability to apply different RF amplitudes.  
         [0108]     Ions exiting capillary  613  are directed into center channel  625  of multipole ion guide  600 . Ions move through the length of multipole ion guide segment  623  driven by gas flow from vacuum pumping stage  614  into vacuum pumping stage  615 . Different DC offset potentials are applied to first and second multipole ion guide segments  623  and  624  respectively. In one operating mode, relative DC offset potentials are applied to ion guide segments  623  and  624  to move ions from first segment  623  into  624 . In a second operating mode relative DC offset potentials are applied to ion guide segments  623  and  624  to trap ions in first segment  623 . In a third operating mode, the DC offset potentials applied to ion guide segment  623  and multipole ion guide  620  are set at greater amplitude than the DC offset potential applied to ion guide segment  624 , trapping ions in multipole ion guide segment  624 . Ions can be accelerated from first segment  623  into second  624  with sufficient energy to cause ion CID fragmentation. Conversely, ions trapped in second segment  624  can be accelerated into first segment  623  to cause ion CID fragmentation. In the embodiment shown, gap  612  separating first segment  623  and second segment  624  is positioned in ion tunnel section  610 . The kinetic energy of ions traversing multipole ion guide  600  is collisionally cooled reducing ion energy spread. Ions exiting multipole ion guide  600 , pass into multipole ion guide  620  where they are transferred to mass to charge analyzer  621 , positioned in vacuum pumping stage  618 , with or without further ion manipulation in multipole ion guide  620 . Segmented multipole ion guide assembly  600  can be configured with more than two and with breaks between segments positioned in different locations along multipole ion guide assembly  600 .  
         [0109]     A cross section side view of hybrid multipole ion guide TOF mass to charge analyzer  640  comprising two segment multipole ion guide  641  is diagrammed in  FIG. 30 . Segmented multipole ion guide assembly  641  comprises RF surface  662 , first segment  660 , first ion tunnel section  645 , first open vacuum pumping section  646 , second segment  661 , second ion tunnel  647 , second open pumping section  648  and third ion tunnel  650 . Hybrid multipole ion guide TOF mass to charge analyzer  640  comprises Electrospray ion source  642 , atmospheric pressure RF surface assembly comprising ion guide assembly  663 , capillary  644 , segmented multipole ion guide assembly  641 , RF surface  658  in TOF orthogonal pulsing region  664  and multipole ion reflector, multiple detector TOF flight tube  657 . Two segment multipole ion guide assembly  641  extends from first vacuum pumping stage  652 , through second vacuum pumping stage  653  and extends into third vacuum pumping stage  654 . Ion tunnels or conduits  645 ,  647  and  650  reduce the neutral gas flow between vacuum stages while retaining high ion transfer efficiency. Gap  651  separating first multipole ion guide segment  660  and second segment  640  is positioned in open vacuum pumping section  646  located in second vacuum stage  653 . Common RF amplitude, frequency and phase is applied electrodes sequentially aligned in to both ion guide segments  660  and  661 . Ions produced in Electrospray ion source  642  are directed through multipole ion guide  663  of RF surface assembly  643  and into the bore of capillary  644 . Ions swept through the bore of capillary  643  exit in first vacuum stage  652  and are focused into center channel  655  of segmented multipole ion guide  641 . Ions traversing through ion tunnel  645 , configured along first ion guide segment  660 , move into second ion guide segment  661  driven by a difference in DC offset potentials maintained between first and second ion guide segments  660  and  661  respectively. Ions can be accelerated from first ion guide segment  660  into second ion guide segment  661  with sufficient energy to cause ion CID fragmentation. Ions may be trapped in second ion guide segment  661  by raising the DC potential applied to ion guide exit electrode  668 . The kinetic energy of ions traversing the length of second ion guide segment  661  in single pass or trap and release mode is collisionally cooled, reducing the energy spread the ion beam entering TOF pulsing region  664 . Ions entering TOF pulsing region  664  may be trapped above RF surface  658  and subsequently accelerated into TOF flight tube  657  and mass to charge analyzed as described above. TOF flight tube is configured in fourth vacuum pumping stage  657 .  
         [0110]     An alternative embodiment of the invention is shown in  FIG. 31  where three segment ion guide  680  comprises curved ion guide segment  683  and single quadrupole mass to charge analyzer  683 . Single quadrupole mass spectrometer assembly  700  comprises Electrospray ion source  693 , RF surface assembly  694  with ion guide assembly  695 , capillary  697 , three segment multipole ion guide assembly  680  with RF surface  704 , quadrupole mass to charge analyzer  683 , electron multiplier detector  703  and four vacuum pumping stages  698 ,  699 ,  701  and  702 . Three segment multipole ion guide assembly  680  comprises three straight segments  681 ,  682 , curved segment  683 , RF surface  704 , first ion tunnel section  684 , first open vacuum pumping section  689 , second ion tunnel section  685 , second open vacuum pumping section  690 , third ion tunnel section  688  and third open vacuum pumping section  683 . First gap  707  separating first ion guide segment  681  from second ion guide segment  682  is configured in first open vacuum pumping section  689  positioned in second vacuum pumping stage  699 . Second gap  708  separating second ion guide segment  682  from curved third ion guide segment  683  is configure in third ion tunnel  688  configured to transfer ions from third vacuum stage  701  into forth vacuum stage  702 . Ions produced in Electrospray ion source  693  are transferred through RF surface and ion guide  695  into the bore of capillary  697 . Ions exiting the bore of capillary  697  into first vacuum stage  698  are focused into center channel  691  of three segment ion guide  680 . In one embodiment of the invention common RF frequency amplitude and phase is applied to all three segments of three segment multipole ion guide  680 . Different DC offset voltages applied to first, second and third multipole ion guide segments  681 ,  682  and  683  respectively are set to move ions through multipole ion guide center channel  691  and into quadrupole mass to charge analyzer  683  through DC electrodes  692 . Ions mass to charge analyzed in quadrupole  683  are detected by electron multiplier detector  703 .  
         [0111]     Three segment multipole ion guide assembly  680  provides high ion transmission efficiency through four vacuum pumping stages while reducing the flow of neutral gas between vacuum pumping stages. Reduced gas flow between vacuum pumping stages without decreasing ion transfer efficiency maintains high sensitivity performance with lower vacuum pumping cost. Contamination cluster and aerosol species exiting capillary  697  pass through the gap in the poles of curved third multipole ion guide segment while radially trapped ions are transferred to quadrupole mass to charge analyzer  683 . This separation of contamination species and analyte ions reduces signal noise due to contamination species in acquired mass spectra. Ions can be accelerated from first ion guide segment  681  into second ion guide segment  682  with sufficient energy to cause ion fragmentation in second segment  682  by applying appropriate relative DC offset potentials to ion guide segments  681  and  682 . The kinetic energy of ions traversing first and second segments  681  and  682  respectively is reduced due to collisions with neutral background gas. This reduction in ion kinetic energy provides an ion beam with low energy spread and reduced cross section entering quadrupole mass to charge analyzer  683 . A low energy spread ion beam focused into quadrupole  683  with low translational energy improves quadrupole mass to charge analysis resolving power and sensitivity.  
         [0112]     RF surfaces and ion guides configured according to the invention can be combined with different ion sources and mass to charge analyzer known in the art. Ions traversing ion guides configured according to the invention can be subjected to ion manipulation functions including but not limited to kinetic energy cooling, trapping, mass to charge filtering, ion mobility separation, fragmentation, ion-molecule reactions, ion-ion reactions, charge reduction of multiply charged ions and combinations of these functions. RF surfaces can be shaped in non planar shapes including but not limited to curved, inverted cones or hemispheres. The inner diameter to length aspect ratios of ion tunnel or conduit sections can range from 2 to 1 to hundreds to 1. Configurations of ion guides may include but not limited to multipole ion guides or sequential RF disk ion guides. Multipole ion guides may be configured as quadrupoles, hexapoles, octopoles or comprise more than eight poles. Multipole ion guides may be configured with parallel poles, poles angled relative to the ion guide centerline, round poles with uniform diameter along the length or round poles with tapered diameters along the length. Multipole ion guides may comprise one or more segments. Ion guide segments or different ion guides connected to different RF power supplies can be aligned to transfer ions between them with or without a DC lens positioned between the sequential ion guides. Junctions between ion guide segments or different ion guides can be made in ion tunnels or in open vacuum pumping ion guide sections. Multiple ion guide assemblies may be configured with different shaped electrode cross sections. Different segments of the same ion guide may comprise different shaped cross sections connecting to a common RF power supply or different RF power supplies that operate with the same frequency and phase.  
         [0113]     Although the present invention has been described in accordance with the embodiments shown, one of ordinary skill in the art will recognize that there can be variations to the embodiments and such variations would fall within the spirit and scope of the present invention.