Abstract:
A tandem mass spectrometer is disclosed. A first mass analyzer within a low-pressure region is provided for passing ions therethrough. A collision cell is at an ion outlet of the mass analyzer to provide a location for ions to collide therein with a collision gas to form resultant ions. The resultant ions are then provided to a FAIMS analyzer for separation thereof and the separate resultant ions are provided to a mass analyzer for analysis.

Description:
FIELD OF THE INVENTION  
         [0001]    The present invention relates to an apparatus and method for separating ions, more particularly the present invention relates to an apparatus and method for separating ions based on the ion focusing principles of high field asymmetric waveform ion mobility spectrometry (FAIMS).  
         BACKGROUND OF THE INVENTION  
         [0002]    High sensitivity and amenability to miniaturization for field-portable applications have helped to make ion mobility spectrometry (IMS) an important technique for the detection of many compounds, including narcotics, explosives, and chemical warfare agents as described, for example, by G. Eiceman and Z. Karpas in their book entitled “Ion Mobility Spectrometry” (CRC, Boca Raton, 1994). In IMS, gas-phase ion mobilities are determined using a drift tube with a constant electric field. Ions are gated into the drift tube and are subsequently separated in dependence upon differences in their drift velocity. The ion drift velocity is proportional to the electric field strength at low electric field strength, for example 200 V/cm, and the mobility, K, which is determined from experimentation, is independent of the applied electric field. Additionally, in IMS the ions travel through a bath gas that is at sufficiently high pressure such that the ions rapidly reach constant velocity when driven by the force of an electric field that is constant both in time and location. This is to be clearly distinguished from those techniques, most of which are related to mass spectrometry, in which the gas pressure is sufficiently low that, if under the influence of a constant electric field, the ions continue to accelerate.  
           [0003]    E. A. Mason and E. W. McDaniel in their book entitled “Transport Properties of Ions in Gases” (Wiley, N.Y., 1988) teach that at high electric field strength, for instance fields stronger than approximately 5,000 V/cm, the ion drift velocity is no longer directly proportional to the applied field, and K becomes dependent upon the applied electric field. At high electric field strength, K is better represented by K h , a non-constant high field mobility term. The dependence of K h  on the applied electric field has been the basis for the development of high field asymmetric waveform ion mobility spectrometry (FAIMS), a term used by the inventors throughout this disclosure, and also referred to as transverse field compensation ion mobility spectrometry, or field ion spectrometry. Ions are separated in FAIMS on the basis of a difference in the mobility of an ion at high field strength, K h , relative to the mobility of the ion at low field strength, K. In other words, the ions are separated because of the compound dependent behavior of K h  as a function of the applied electric field strength. FAIMS offers a new tool for atmospheric pressure gas-phase ion studies since it is the change in ion mobility, and not the absolute ion mobility, that is being monitored.  
           [0004]    The principles of operation of FAIMS using flat plate electrodes have been described by I. A. Buryakov, E. V. Krylov, E. G. Nazarov and U. Kh. Rasulev in a paper published in the International Journal of Mass Spectrometry and Ion Processes; volume 128 (1993), pp. 143-148, the contents of which are herein incorporated by reference. The mobility of a given ion under the influence of an electric field is expressed by: K h =K(1+f(E)), where K h  is the mobility of an ion at high electrical field strength, K is the coefficient of ion mobility at low electric field strength and f(E) describes the functional dependence of the ion mobility on the electric field strength. Ions are classified into one of three broad categories on the basis of a change in ion mobility as a function of the strength of an applied electric field, specifically: the mobility of type A ions increases with increasing electric field strength; the mobility of type C ions decreases; and, the mobility of type B ions increases initially before decreasing at yet higher field strength. The separation of ions in FAIMS is based upon these changes in mobility at high electric field strength. Consider an ion, for example a type A ion, which is being carried by a gas stream between two spaced-apart parallel plate electrodes of a FAIMS device. The space between the plates defines an analyzer region in which the separation of ions occurs. The net motion of the ion between the plates is the sum of a horizontal x-axis component due to the flowing stream of gas and a transverse y-axis component due to the electric field between the parallel plate electrodes. The term “net motion” refers to the overall translation that the ion, for instance said type A ion, experiences, even when this translational motion has a more rapid oscillation superimposed upon it. Often, a first plate is maintained at ground potential while the second plate has an asymmetric waveform, V(t), applied to it. The asymmetric waveform V(t) is composed of a repeating pattern including a high voltage component, V 1 , lasting for a short period of time t 2  and a lower voltage component, V 2 , of opposite polarity, lasting a longer period of time t 1 . The waveform is synthesized such that the integrated voltage-time product, and thus the field-time product, applied to the plate during each complete cycle of the waveform is zero, for instance V 1 t 2 +V 2 t 1 =0; for example +2000 V for 10 μs followed by −1000 V for 20 μs. The peak voltage during the shorter, high voltage portion of the waveform is called the “dispersion voltage” or DV in this disclosure.  
           [0005]    During the high voltage portion of the waveform, the electric field causes the ion to move with a transverse y-axis velocity component v 1 =K h E high , where E high  is the applied field, and K h  is the high field ion mobility under ambient electric field, pressure and temperature conditions. The distance traveled is d 1 =v 1 t 2 =K h E high t 2 , where t 2  is the time period of the applied high voltage. During the longer duration, opposite polarity, low voltage portion of the asymmetric waveform, the y-axis velocity component of the ion is v 2 =KE low , where K is the low field ion mobility under ambient pressure and temperature conditions. The distance traveled is d 2 =v 2 t 1 =KE low t 1 . Since the asymmetric waveform ensures that (V 1 t 2 )+(V 2 t 1 )=0, the field-time products E high t 2  and E low t 1  are equal in magnitude. Thus, if K h  and K are identical, d 1  and d 2  are equal, and the ion is returned to its original position along the y-axis during the negative cycle of the waveform, as would be expected if both portions of the waveform were low voltage. If at E high  the mobility K h &gt;K, the ion experiences a net displacement from its original position relative to the y-axis. For example, positive ions of type A travel farther during the positive portion of the waveform, for instance d 1 &gt;d 2 , and the type A ion migrates away from the second plate. Similarly, positive ions of type C migrate towards the second plate.  
           [0006]    If a positive ion of type A is migrating away from the second plate, a constant negative dc voltage can be applied to the second plate to reverse, or to “compensate” for, this transverse drift. This dc voltage, called the “compensation voltage” or CV in this disclosure, prevents the ion from migrating towards either the second or the first plate. If ions derived from two compounds respond differently to the applied high strength electric fields, the ratio of K h  to K is similarly different for each compound. Consequently, the magnitude of the CV necessary to prevent the drift of the ion toward either plate is also different for each compound. Thus, when a mixture including several species of ions is being analyzed by FAIMS, only one species of ion is selectively transmitted for a given combination of CV and DV. The remaining species of ions, for instance those ions that are other than selectively transmitted through FAIMS, drift towards one of the parallel plate electrodes of FAIMS and are neutralized. Of course, the speed at which the remaining species of ions move towards the electrodes of FAIMS depends upon the degree to which their high field mobility properties differ from those of the ions that are selectively transmitted under the prevailing conditions of CV and DV.  
           [0007]    An instrument operating according to the FAIMS principle as described previously is an ion filter, capable of selective transmission of only those ions with the appropriate ratio of K h  to K. In one type of experiment using FAIMS devices, the applied CV is scanned with time, for instance the CV is slowly ramped or optionally the CV is stepped from one voltage to a next voltage, and a resulting intensity of transmitted ions is measured. In this way a CV spectrum showing the total ion current as a function of CV, is obtained. It is a significant limitation of early FAIMS devices, which used electrometer detectors, that the identity of peaks appearing in the CV spectrum are other than unambiguously confirmed solely on the basis of the CV of transmission of a species of ion. This limitation is due to the unpredictable, compound-specific dependence of K h  on the electric field strength. In other words, a peak in the CV spectrum is easily assigned to a compound erroneously, since there is no way to predict or even to estimate in advance, for example from the structure of an ion, where that ion should appear in a CV spectrum. In other words, additional information is necessary in order to improve the likelihood of assigning correctly each of the peaks in the CV spectrum. For example, subsequent mass spectrometric analysis of the selectively transmitted ions greatly improves the accuracy of peak assignments of the CV spectrum.  
           [0008]    In U.S. Pat. No. 5,420,424 which issued on May 30, 1995, B. L. Carnahan and A. S. Tarassove disclose an improved FAIMS electrode geometry in which the flat plates that are used to separate the ions are replaced with concentric cylinders, the contents of which are herein incorporated by reference. The concentric cylinder design has several advantages, including higher sensitivity compared to the flat plate configuration, as was discussed by R. W. Purves, R. Guevremont, S. Day, C. W. Pipich, and M. S. Matyjaszczyk in a paper published in Reviews of Scientific Instruments; volume 69 (1998), pp 4094-4105. The higher sensitivity of the cylindrical FAIMS is due to a two-dimensional atmospheric pressure ion focusing effect that occurs in the analyzer region between the concentric cylindrical electrodes. When no electrical voltages are applied to the cylinders, the radial distribution of ions should be approximately uniform across the FAIMS analyzer. During application of DV and CV, however, the radial distribution of ions is not uniform across the annular space of the FAIMS analyzer region. Advantageously, with the application of an appropriate DV and CV for an ion of interest, those ions become focused into a band between the electrodes and the rate of loss of ions, as a result of collisions with the FAIMS electrodes, is reduced. The efficiency of transmission of the ions of interest through the analyzer region of FAIMS is thereby improved as a result of this two-dimensional ion focusing effect.  
           [0009]    The focussing of ions by the use of asymmetric waveforms has been discussed above. For completeness, the behavior of those ions that are not focussed within the analyzer region of a cylindrical geometry FAIMS is described here, briefly. As discussed previously, those ions having high field ion mobility properties that are other than suitable for focussing under a given set of DV, CV and geometric conditions will drift toward one or another wall of the FAIMS device. The rapidity with which these ions move towards the wall depends on the degree to which their K h /K ratio differs from that of the ion that is transmitted selectively under the prevailing conditions. At the very extreme, ions of completely the wrong property, for instance a type A ion versus a type C ion, are lost to the walls of the FAIMS device very rapidly.  
           [0010]    The loss of ions in FAIMS devices should be considered one more way. If an ion of type A is focussed, for example at DV 2500 volts, CV −11 volts in a given geometry, it would seem reasonable to expect that the ion is also focussed if the polarity of DV and CV are reversed, for instance DV of −2500 volts and CV of +11 volts. This, however, is not observed and in fact the reversal of polarity in this manner creates a mirror image effect of the ion-focussing behavior of FAIMS. The result of such polarity reversal is that the ions are not focussed, but rather are extremely rapidly rejected from the device. The mirror image of a focussing valley, is a hill-shaped potential surface. The ions slide to the center of the bottom of a focussing potential valley (2 or 3-dimensions), but slide off of the top of a hill-shaped surface, and hit the wall of an electrode. This is the reason for the existence, in the cylindrical geometry FAIMS, of the independent “modes” called 1 and 2. Such a FAIMS instrument is operated in one of four possible modes: P1, P2, N1, and N2. The “P” and “N” describe the ion polarity, positive (P) and negative (N). The waveform with positive DV, where DV describes the peak voltage of the high voltage portion of the asymmetric waveform, yields spectra of type P1 and N2, whereas the reversed polarity negative DV, waveform yields P2 and N1. The discussion thus far has considered positive ions but, in general, the same principles apply to negative ions equally.  
           [0011]    A further improvement to the cylindrical FAIMS design is realized by providing a curved surface terminus of the inner electrode. The curved surface terminus is continuous with the cylindrical shape of the inner electrode and is aligned co-axially with an ion-outlet orifice of the FAIMS analyzer region. The application of an asymmetric waveform to the inner electrode results in the normal ion-focussing behavior described above, except that the ion-focussing action extends around the generally spherically shaped terminus of the inner electrode. This means that the selectively transmitted ions cannot escape from the region around the terminus of the inner electrode. This only occurs if the voltages applied to the inner electrode are the appropriate combination of CV and DV as described in the discussion above relating to 2-dimensional focussing. If the CV and DV are suitable for the focussing of an ion in the FAIMS analyzer region, and the physical geometry of the inner surface of the outer electrode does not disturb this balance, the ions will collect within a three-dimensional region of space near the terminus. Several contradictory forces are acting on the ions in this region near the terminus of the inner electrode. The force of the carrier gas flow tends to influence the ion cloud to travel towards the ion-outlet orifice, which advantageously also prevents the trapped ions from migrating in a reverse direction, back towards the ionization source. Additionally, the ions that get too close to the inner electrode are pushed back away from the inner electrode, and those near the outer electrode migrate back towards the inner electrode, due to the focusing action of the applied electric fields. When all forces acting upon the ions are balanced, the ions are effectively captured in every direction, either by forces of the flowing gas, or by the focussing effect of the electric fields of the FAIMS mechanism. This is an example of a three-dimensional atmospheric pressure ion trap, as disclosed in a copending PCT application in the name of R. Guevremont and R. Purves, the contents of which are herein incorporated by reference.  
           [0012]    Ion focusing and ion trapping requires electric fields that are other than constant in space, normally occurring in a geometrical configuration of FAIMS in which the electrodes are curved, and/or are not parallel to each other. For example, a non-constant in space electric field is created using electrodes that are cylinders or a part thereof; electrodes that are spheres or a part thereof; electrodes that are elliptical spheres or a part thereof; and, electrodes that are conical or a part thereof. Optionally, various combinations of these electrode shapes are used.  
           [0013]    As discussed above, one previous limitation of the cylindrical FAIMS technology is that the identity of the peaks appearing in the CV spectra are not unambiguously confirmed due to the unpredictable changes in K h  at high electric field strengths. Thus, one way to extend the capability of instruments based on the FAIMS concept is to provide a way to determine the make-up of the CV spectra more accurately, such as by introducing ions from the FAIMS device into a mass spectrometer for mass-to-charge (m/z) analysis. Advantageously, the ion focusing property of cylindrical FAIMS devices acts to enhance the efficiency for transporting ions from the analyzer region of a FAIMS device into an external sampling orifice, for instance an inlet of a mass spectrometer. This improved efficiency of transporting ions into the inlet of the mass spectrometer is optionally maximized by using a 3-dimensional trapping version of FAIMS operated in nearly trapping conditions. Under near-trapping conditions, the ions that have accumulated in the three-dimensional region of space near the spherical terminus of the inner electrode are caused to leak from this region, being pulled by a flow of gas towards the ion-outlet orifice. The ions that leak out from this region do so as a narrow, approximately collimated beam, which is pulled by the gas flow through the ion-outlet orifice and into a small orifice leading into the vacuum system of a mass spectrometer.  
           [0014]    Additionally, the resolution of a FAIMS device is defined in terms of the extent to which ions having similar mobility properties as a function of electric field strength are separated under a set of predetermined operating conditions. Thus, a high-resolution FAIMS device transmits selectively a relatively small range of different ion species having similar mobility properties, whereas a low-resolution FAIMS device transmits selectively a relatively large range of different ion species having similar mobility properties. The resolution of FAIMS in a cylindrical geometry FAIMS is compromised relative to the resolution in a parallel plate geometry FAIMS because the cylindrical geometry FAIMS has the capability of focusing ions. This focusing action means that ions of a wider range of mobility characteristics are simultaneously focused in the analyzer region of the cylindrical geometry FAIMS. A cylindrical geometry FAIMS with narrow electrodes has the strongest focusing action, but the lowest resolution for separation of ions. As the radii of curvature are increased, the focusing action becomes weaker, and the ability of FAIMS to simultaneously focus ions of similar high-field mobility characteristics is similarly decreased. This means that the resolution of FAIMS increases as the radii of the electrodes are increased, with parallel plate geometry FAIMS having the maximum attainable resolution.  
           [0015]    Note that, while the above discussion refers to the ions as being “captured” or “trapped”, in fact, the ions are subject to continuous ‘diffusion’. Diffusion always acts contrary to focussing and trapping. The ions always require an electrical, or gas flow force to reverse the process of diffusion. Thus, although the ions are focused into an imaginary cylindrical zone in space with almost zero thickness, or within a 3-dimensional ion trap, in reality it is well known that the ions are actually dispersed in the vicinity of this idealized zone in space because of diffusion. This is important, and should be recognized as a global feature superimposed upon all of the ion motions discussed in this disclosure. This means that, for example, a 3-dimensional ion trap actually has real spatial width, and ions continuously leak from the 3-dimensional ion trap, for several physical, and chemical reasons. Of course, the ions occupy a smaller physical region of space if the trapping potential well is deeper.  
           [0016]    Of course, other apparatus for separating ions are known in the prior art, for instance an apparatus based on mass spectrometric techniques such as a radio-frequency quadrupole mass spectrometer. Further, tandem arrangements of such apparatus are known for producing collisionally induced dissociation of ionic species prior to a final mass analysis step, a field of study often referred to as tandem mass spectrometry. Of course, in many cases there are several possible fragment ions that have a same mass-to-charge ratio, and in the prior art tandem mass spectrometry system these ions are indistinguishable. It would be advantageous to provide a method and an apparatus to separate fragment ions which have a same mass-to-charge ratio in dependence upon a property of the ions other than a mass-to-charge ratio before providing the ions for the final mass analysis step.  
         OBJECT OF THE INVENTION  
         [0017]    In order to overcome these and other limitations of the prior art, it is an object of the present invention to provide an apparatus for separating collisionally induced fragment ions having a substantially same mass-to-charge ratio prior to providing the fragment ions to a mass analyzer.  
         SUMMARY OF THE INVENTION  
         [0018]    In accordance with the invention there is provided a tandem mass spectrometer comprising a first mass spectrometer within a low pressure region, a collision cell and a second mass analyzer within the low pressure region, characterized in that between the collision cell and the second mass spectrometer is disposed a FAIMS analyzer.  
           [0019]    In accordance with another embodiment of the invention there is provided an apparatus for separating ions comprising:  
           [0020]    a) a first analyzer region defined by a space between first and second spaced apart electrodes;  
           [0021]    b) a collision region in operational communication with the first analyzer region for providing ions to the first analyzer region, the collision region defined by a space between two electrodes, the collision region having a first gas inlet, the first gas inlet for providing a flow of a collision gas within the collision region;  
           [0022]    c) an ion source for providing ions to the collision region; and,  
           [0023]    f) a voltage source for providing at least a voltage to at least one of the first and second electrodes of the first analyzer region, to form an electric field therebetween, the electric field for effecting a separation of the resultant ions having an approximately same mass-to-charge ratio, wherein the ions provided to the first analyzer region include the collisionally induced fragment ions.  
           [0024]    In accordance with another aspect of the invention there is provided a method for separating ions comprising the steps of:  
           [0025]    providing ions to a mass spectrometer for transmission therethrough to a collision region having a collision gas therein;  
           [0026]    colliding the ions with the collision gas to produce a plurality of resultant ions; transporting the resultant ions through an electric field resulting from application of an asymmetric waveform to an electrode to perform a separation thereof; and,  
           [0027]    providing some of the separated ions to a mass spectrometer for analysis.  
           [0028]    In accordance with yet another embodiment of the invention there is provided a method according to claim 20 wherein electric field is formed by the following steps:  
           [0029]    i) providing a first asymmetric waveform and a first direct-current compensation voltage, to at least one electrode, to form an electric field therebetween, the first asymmetric waveform for effecting a difference in net displacement between two different ions in the time of one cycle of the applied first asymmetric waveform; and,  
           [0030]    ii) setting the first compensation voltage for effecting a separation of the fragment ions having an approximately same mass-to-charge ratio, to support selective transmission of the ions within the first analyzer region. 
       
    
    
     BRIEF DESCRIPTION OF THE DRAWINGS  
       [0031]    [0031]FIG. 1 shows three possible examples of changes in ion mobility as a function of the strength of an electric field;  
         [0032]    [0032]FIG. 2 a  illustrates the trajectory of an ion between two parallel plate electrodes under the influence of the electrical potential V(t);  
         [0033]    [0033]FIG. 2 b  shows an asymmetric waveform described by V(t);  
         [0034]    [0034]FIG. 3 shows a simplified block diagram of an MS/MS/FAIMS/MS system according to the present invention;  
         [0035]    [0035]FIG. 4 shows a simplified block diagram of a MS/MS/FAIMS/MS system according to a first embodiment of the invention;  
         [0036]    [0036]FIG. 5 shows a simplified schematic diagram of a FAIMS analyzer useable in the system according to the present invention;  
         [0037]    [0037]FIG. 6 shows a first possible electrical connection to the FAIMS analyzer of FIG. 5;  
         [0038]    [0038]FIG. 7 shows a second possible electrical connection to the FAIMS analyzer of FIG. 5; and,  
         [0039]    [0039]FIG. 8 shows a simplified block diagram of a MS/MS/FAIMS/MS system, including the FAIMS analyzer of FIG. 5, according to a second embodiment of the invention.  
     
    
     DETAILED DESCRIPTION OF THE INVENTION  
       [0040]    Referring to FIG. 1, shown are three possible examples of the change in ion mobility properties with increasing electric field strength, as was discussed previously. The separation of ions in FAIMS is based upon a difference in these mobility properties for a first ion relative to a second ion. For instance, a first type A ion having a low field mobility K 1,low  is other than separated in a FAIMS device from a second type A ion having a second different low field mobility K 2,low , if under the influence of high electric field strength, the ratio K 1,high /K 1,low  is equal to the ratio K 2,high /K 2,low . Interestingly, however, this same separation is achieved using conventional ion mobility spectrometry, which is based on a difference in ion mobilities at low applied electric field strength.  
         [0041]    Referring to FIG. 2 a , shown is a schematic diagram illustrating the mechanism of ion separation according to the FAIMS principle. An ion  1 , for instance a positively charged type A ion, is carried by a gas stream  2  flowing between two spaced apart parallel plate electrodes  3  and  4 . One of the plates  4  is maintained at ground potential, while the other plate  3  has an asymmetric waveform described by V(t), applied to it. The peak voltage applied during the waveform is called the dispersion voltage (DV), as is shown in FIG. 2 b . Referring still to FIG. 2 b , the waveform is synthesized so that the electric fields during the two periods of time thigh and t low  are not equal. If K h  and K are identical at high and low fields, the ion  1  is returned to its original position at the end of one cycle of the waveform. However, under conditions of sufficiently high electric fields, K h  is greater than K and the distances traveled during t high  and t low  are no longer identical. Within an analyzer region defined by a space  8  between the first and second spaced apart electrode plates,  3  and  4 , respectively, the ion  1  experiences a net displacement from its original position relative to the plates  3  and  4  as illustrated by the dashed line  5  in FIG. 2 a.    
         [0042]    If a type A ion is migrating away from the upper plate  3 , a constant negative dc compensation voltage CV is applied to plate  3  to reverse or “compensate” for this offset drift. Thus, the ion  1  does not travel toward either plate. If two species of ions respond differently to the applied high electric field, for instance the ratios of K h  to K are not identical, the compensation voltages necessary to prevent their drift toward either plate are similarly different. To analyze a mixture of ions, the compensation voltage is, for example, scanned to transmit each of the components of a mixture in turn. This produces a compensation voltage spectrum, or CV spectrum.  
         [0043]    Referring to FIG. 3, a simplified block diagram of an MS/MS/FAIMS/MS system is shown. The ion source  11  is selected from a group including: electrospray ionization; corona discharge ionization; ionization by radioactivity; and, ionization by ultraviolet light. The ions are transferred into a low pressure region, for instance a vacuum chamber  9 , through an interface  12 , which optionally includes a differentially pumped region that serves to minimize the volume of gas which travels from the outside of the vacuum chamber into the vacuum chamber. Of course, if the ionization takes place at reduced pressure, for example within the vacuum chamber  9 , then optionally electron impact ionization or chemical ionization are used to produce the ions. The interface  12  includes an orifice (not shown), which permits some of the ions produced by the ion source  11  to enter the vacuum chamber  9 . The ions that pass through the interface  12  enter a first mass analyzer  10 , which is optionally one of a quadrupole analyzer, an ion trap mass analyzer, and a time-of-flight mass spectrometer. Of course, other types of mass analyzers are known and are used optionally.  
         [0044]    The mass analyzer  10  serves to separate an ion species of interest from a complex mixture of ions provided to the mass analyzer  10  through the interface  12 . The ion species that are selected within mass analyzer  10  are transmitted to a high pressure chamber  13  which is supplied by a collision gas inlet  14 . The transmitted ions are collided with a collision gas as they move longitudinally through the space between a set of rf-only quadrupoles of collision cell  15  within high pressure chamber  13  to fragment the ions into a plurality of smaller sub-units thereof. In the case of MS/MS experiments, it is usual to refer to the transmitted ions as the parent ions, and to the collisionally induced fragment ions as the daughter ions. The daughter ions have structure that is related to the structure of the parent ion. In normal practice the daughter ions are analyzed within another mass analyzer, and the identities of the daughter ions are determined to provide structural insights into the structure of the parent ion. Since the daughter ions have lower mass and are less complex than the original parent ions, it is in certain cases possible to deduce the structure of the parent ions from the identities of the daughter ions. This is typically one of the methods used to identify the structures of peptide molecules, which are the result of a tryptic digestion of a protein. By analyzing the peptide molecules, the structure of the protein is deduced. By analyzing the structures of the daughter ions that are produced from a collisional dissociation of the parent peptide ion, the structure of the peptide may be deduced. These complex experiments can be used to determine the primary sequence structure of proteins.  
         [0045]    Still referring to FIG. 3, the fragment ions which are produced inside of the collision cell  15  are separated in FAIMS  16 . FAIMS  16  is not used as the final mass analyzer, but rather is used to optionally separate ions which have equal m/z, and which would be other than separated in the final mass analyzer  19 . A detector, not shown, registers the transmission of an ion through the system.  
         [0046]    Advantageously, FAIMS separates ions independently of their m/z ratio. This has the important consequence that in many cases isobaric ions, for example two different species of ions having a same m/z ratio, are separated by FAIMS although they are other than separated by mass analyzers, including high resolution mass analyzers, which are extremely expensive instruments requiring bulky vacuum equipment and an expert operator. In contrast, the FAIMS device is relatively inexpensive, compact and simple to operate. It is a further advantage of FAIMS that the capability of FAIMS to separate ions having similar high field mobility properties improves as the m/z ratio of the ion is decreased. This is completely consistent with the requirements of the system described herein, where FAIMS is required to separate fragment ions, rather than the parent ions which may have higher m/z. FAIMS is therefore ideally suited to separation of the ions produced by collisions of the parent ion with a bath gas.  
         [0047]    Referring to FIG. 4, a first preferred embodiment of the components mass analyzer  10 , high pressure chamber  13 , collision cell  15 , FAIMS analyzer  16  and mass analyzer  19  are shown. The first mass analyzer is shown as a set of quadrupole rods  10 , into which is flowing a mixture of ions  21 . This analyzer  10  separates the mixture of ions  21 , and transmits only ions of a substantially same m/z. The ions thus selected pass through an ion-inlet orifice  22  into a pressurized chamber  13  containing collision cell  15  and FAIMS  16 . The collision gas enters the chamber  13  through a gas inlet  14  and because of the pumping system (not shown) which keeps the chamber evacuated, the gas exits from high pressure chamber  13  through ion-inlet orifice  22  and an ion-outlet orifice  24 .  
         [0048]    Still referring to FIG. 4, the ions which enter the chamber  13  pass into collision cell  15 , which includes a set of rf-only quadrupole rods for physically confining the parent ions and the resultant daughter ions within the center longitudinal axis of the quadrupole rod structure. A mixture including the original parent ions and the collisionally produced fragments are passed out of the collision cell  15  and pass into a FAIMS apparatus  16  comprising at least first and second spaced apart electrodes, defining an analyzer region  25  therebetween. By application of an asymmetric waveform, and a compensation voltage to at least one of the first and second electrodes of FAIMS, an ion with the appropriate change in high field mobility properties relative to its low field mobility properties is selected from the mixture of fragment ions provided from the collision cell  15 . An electrical controller (not shown) is connected to at least one of the first and second electrodes for, in use, applying the asymmetric waveform, and a compensation voltage to effect ion separation. The ions are carried through the FAIMS analyzer region  25  by the flow of gas which is exiting through the ion-outlet orifice  24 . The ions with the appropriate properties are transmitted-through the analyzer region  25  of FAIMS device  16 , and out of the ion-outlet orifice  24  of the high pressure chamber  13 . Higher or lower flows of gas along the length of the analyzer can be achieved by optionally placing appropriate baffles  28  mounted around the FAIMS  16  to modify the difference in gas pressure before entrance of FAIMS in region  17  relative to the pressure at the outlet region of FAIMS in region  18 . Optionally, high pressure chamber  13  is structurally divided into two compartments one of which houses the collision cell  15 , and the second of which houses the FAIMS  16 .  
         [0049]    Still referring to FIG. 4, the ions which exit from ion-outlet orifice  24  in the high pressure chamber  13  are mass analyzed by quadrupole assembly  19 . A detector  20  is used to register those ions which are transmitted through the system.  
         [0050]    The FAIMS  16  shown in FIG. 4 comprises first and second spaced-apart parallel plate electrodes, defining an analyzer region  25  therebetween. Of course, other FAIMS electrode geometries are known and are optionally used in place of the two-electrode parallel plate FAIMS shown in FIG. 4. For instance, a FAIMS device is selected from the group including: FAIMS comprising n curved-electrode bodies (n 2); FAIMS comprising n parallel, flat plate electrodes (n 2); and, FAIMS comprising at least first and second coaxially aligned and substantially overlapping concentric cylindrical electrodes. Further optionally, a curved surface is provided along at least one of the leading and trailing edges of at least an electrode of the FAIMS according to any of the above electrode geometries for further focussing the ions to achieve improved ion transmission efficiency through the FAIMS  16 .  
         [0051]    The system shown in FIG. 4 suffers one limitation which is overcome by using a novel arrangement of electrodes in FAIMS. If the FAIMS device  16  in FIG. 4 is not needed, for example the separation of isobaric daughter ions produced within the rf-only quadrupole assembly  15  is other than required, then the efficiency of ion transmission through the FAIMS  16  limits the overall sensitivity of the system. Although it is practical to remove a FAIMS which is coupled external to the vacuum chamber  9 , the removal of FAIMS  16  within the vacuum chamber  9  as shown in FIG. 4 is other than practical.  
         [0052]    Referring to FIG. 5 and to FIG. 8, shown is a FAIMS  99  which is built in the same physical configuration as a quadrupole mass analyzer, comprising four parallel rods  50 . The electrode geometry shown schematically in FIG. 5 FAIMS is usable as a FAIMS analyzer by application of an asymmetric waveform to at least a parallel rod electrode  50 . The remaining rods may be maintained at some other fixed dc voltage. If the asymmetric waveform is applied to one of the four rods, the other three act as the fixed, constant voltage counter electrode. The electric fields between the rods  50  permits the separation of ions in exactly the manner described previously for FAIMS of other physical geometries.  
         [0053]    Referring now to FIG. 6, shown is a first possible electrical connection to the quadrupole FAIMS described with reference to FIG. 5. The asymmetric waveform is generated in a supply  111  and provided to one rod  50  of the set of four rods  50 . In this case, the remaining three rods  50  are held at constant voltage by one of grounding to zero volts, and by application of dc voltages through supply  110 .  
         [0054]    Referring to FIG. 7, shown is a second possible electrical connection to quadrupole FAIMS described with reference to FIG. 5. The asymmetric waveform is generated in a supply  112  and provided to an opposing pair of rods  50 . The remaining opposing pair of rods  50  are held at constant voltage by one of grounding to zero volts, and by application of dc voltages through supply  113 .  
         [0055]    In other systems there is no advantage to the quadrupole structure, however, in the system described with reference to FIG. 5 through FIG. 8, the quadrupole rods  50  are advantageous because the FAIMS is in effect removed from the system by application of the regular sinusoidal waveforms to the rods. This means that the electrical controls (not shown) to the rods from outside of the vacuum system permits the set of rod  99  to function as one of a FAIMS and a rf-only quadrupole, but not at a same time. Optionally, the set of rod  99  functions as a quadrupuole mass analyzer.  
         [0056]    Referring again to FIG. 8, the first mass analyzer is shown as a series of quadrupole rods into which is flowing a mixture of ions  21 . This analyzer  10  separates the mixture of ions  21 , and transmits only ions of a substantially same m/z. The ions thus selected pass through an ion-inlet orifice  22  into a high pressure chamber  13 . The collision gas enters the chamber  13  through a gas inlet  14  and because of the pumping system (not shown) which keeps the chamber evacuated, the gas exits from chamber  13  through ion-inlet orifice  22  and an ion-outlet orifice  24 . The ions which enter the chamber  13  pass into collision cell  15 , which includes a set of rf-only quadrupole rods for physically confining the parent ions and the resultant daughter ions within the center longitudinal axis of the quadrupole rod structure. A mixture including the original parent ions and the collisionally produced fragments are passed out of collision cell  15  and pass into a FAIMS apparatus  99  comprising four parallel rods defining an analyzer region  27  therebetween. By application of an asymmetric waveform, and a compensation voltage to at least one of the four parallel rod electrodes of FAIMS, an ion with the appropriate change in high field mobility properties relative to its low field mobility properties is selected from the mixture of fragment ions provided from the collision cell  15 . An electrical controller (not shown) is connected to at least one of the four parallel rod electrodes for, in use, applying the asymmetric waveform, and a compensation voltage to effect ion separation. The ions are carried through the FAIMS analyzer region  27  by the flow of gas which is exiting through the ion-outlet orifice  24 . The ions with the appropriate properties are transmitted through the analyzer region  27  of FAIMS device  99 , and out of the ion-outlet orifice  24  of the high pressure chamber  13 . Higher or lower flows of gas along the length of the analyzer can be achieved by optionally mounting appropriate baffles (not shown) around the FAIMS  99  to modify the difference in gas pressure before entrance of FAIMS in region  17  relative to the pressure at the outlet region of FAIMS in region  18 . Optionally, high pressure chamber  13  is structurally divided into two compartments one of which houses the collision cell  15 , and the second of which houses the FAIMS  99 .  
         [0057]    Still referring to FIG. 8, the ions which exit from ion-outlet orifice  24  in the high pressure chamber  13  are mass analyzed by quadrupole assembly  19 . A detector  20  is used to register those ions which are transmitted through the system.  
         [0058]    Optionally, the two separate sets of quadrupole rods of collision cell  15  and FAIMS  99  are merged into a single set of segmented rods having small electrically insulating regions between closely space, longitudinally aligned rods. Further optionally, the two separate sets of quadrupole rods of collision cell  15  and FAIMS  99  are replaced by a single set of rods. The ions entering this cell would be fragmented during collisions with a gas held in the cell  13 , but instead of a rf-only quadruupole operation, the electrical signals to the rods would be set for operation as FAIMS. This is accomplished by application of an asymmetric waveform to at least one, but not all, of the rods. By application of the appropriate DV and CV for the prevailing bath gas number density conditions in the cell, separation of ions based on the difference of ion mobility properties at high and low electric fields is accomplished, and in normal operation of FAIMS. If FAIMS is not needed, the quadrupole assembly is operated in the normal fashion by application of sinusoidal waveforms to the pairs of opposite rods, as is well known in the field of mass spectrometry. The need to physically remove the FAIMS apparatus from the system when other than in use is therefore eliminated.  
         [0059]    Of course, numerous other embodiments could be envisioned, without departing significantly from the teachings of the present invention.