Patent Application: US-6115805-A

Abstract:
the present invention relates to an improved ion mobility spectrometer and method for the analysis of chemical samples . the improvements are realized in the optimization of resolution and sensitivity . increases in sensitivity are realized by preserving a narrow spatial distribution of migrating ions through the use of periodic / hyperbolic field focusing . use of a plurality of drift cells and a new rf field focusing interface are discussed .

Description:
as used herein , “ drift tube diameter ” is defined as the distance from the spectrometer axis to the electrode surface nearest to the spectrometer axis . in the case of multiple coaxial series of electrodes , this distance refers to that from the spectrometer axis to the electrode surface nearest to the spectrometer axis of the innermost coaxial series of electrodes . it is synonymous with the expression “ inner diameter ”. as used herein , a “ combination ” of periodic field focussing and hyperbolic field focusing in an ion drift cell is any coexistence of the two types of fields in the drift cell ; they may be sequential to one another ( i . e ., serial ; and in any order ) or be superimposed ( i . e ., a superposition ) on one another . it may also include multiple field regions in the drift cell . it may also include one or more regions of a superposition and one or more other regions of a sequential combination . as used herein , “ electrode width ” is defined as the ratio of the length , l , of the drift region to the total number , n , of periods in the drift region minus the inter - electrode gap width , g ; alternatively , it is mathematically defined as ( l / n )− g . as used herein , “ focusing ”, when used in reference to a beam of ions , is defined as any imaging event that reduces the spread of the ion beam to any degree ; it does not necessarily require that the reduction result in a focus point . as used herein , “ gaps of a metal helix ” are the distances between the wire or wire - like structures which make up the metal helix . as used herein , a “ heterogeneous electric field ”, or alternatively , an “ electric field exhibiting substantial heterogeneity ” is an electric field in which the deviation from a linear electric field along the spectrometer axis at each electrode or electrode gap is greater than 0 . 10 %. as used herein , a “ homogeneous electric field ”, or alternatively , an “ electric field exhibiting substantial homogeneity ” is an electric field in which the maximum deviation from a linear electric field along the spectrometer axis at each electrode or electrode gap is no more than 0 . 10 %. as used herein , “ hyperbolic focusing field ” for an ion drift cell is defined as a field characterized by nonlinear equipotential lines and further characterized by an asymmetry of the nonlinear equipotential lines along the axis of the spectrometer . as used herein , the abbreviation “ ims ” is defined as ion mobility spectrometry . as used herein , “ inter - electrode gap ” is defined as any distance between electrodes that does not consist of an electrode ; this may , for example , be an insulating material or air . as used herein , “ inter - electrode gap width ” is defined as the distance between adjacent coaxial electrodes within a series . as used herein , maldi is defined as matrix assisted laser desorption ionization . as used herein , the abbreviation “ ms ” is defined as mass spectrometry . as used herein , “ period ” is defined as an electrode at a unique potential . n is the “ number of periods for a given drift tube length ” and is the number of electrodes having unique potentials . as used herein , the expression “ periodic focusing field ” for an ion drift cell is defined as an electric field characterized by alternating periods of substantial homogeneity and substantial heterogeneity in which the regions of substantial heterogeneity as measured by % ( δv / v ) is greater than about 0 . 1 . as used herein , “ potential ” means an electrical potential or synonymously , a voltage . as used herein , “ resistively coated metal helixes ” are continuous metal wires or wire - like structures coated with any resistive material , generally taking the shape of a coil . as used herein , a “ sequential ” hyperbolic field and periodic field refers to a specific combination of the two fields characterized by distinct regions of either field without substantial overlap with the other field ; the order ( i . e ., periodic followed by hyperbolic or vice versa ) is unspecified without more . it is synonymous with a “ sequential combination ”. as used herein , the term “ spectrometer axis ” is defined as the major ( lengthwise ) axis of the spectrometer . this applies herein to both ion mobility instruments and mass spectrometric instruments . as used herein , a “ superposition ” of a hyperbolic field and a periodic field refers to a specific combination of the two fields characterized by overlap of the two fields ( i . e ., the two fields are superimposed on one another ) resulting in an overall resultant field . a “ superposition ” of a hyperbolic field and a periodic field is a specific species of a “ combination ” of a hyperbolic field and a periodic field , the latter encompassing all combinations of the two fields , not only superpositions thereof . as used herein , the abbreviation “ tofms ” is defined as time - of - flight mass spectrometry . as used herein , a “ unit helix thickness ” is the width of the wire or wire - like structure of a resistively coated metal helix . % ( δv / v ) is defined as the percentage deviation from a linear electric field along the spectrometer axis at each electrode or electrode gap . hyperbolic focusing takes advantage of the fact that ions in gases follow very closely a path that is always perpendicular to the equipotential surfaces . here , we address the focussing of ion beams in gases using concave electric fields as hyperbolic field focussing . this type of focussing was used in mobility cells as taught by thekkadath in u . s . pat . no . 5 , 189 , 301 by using a cup shaped electrode . blanchard , u . s . pat . no . 4 , 855 , 595 used also a hyperbolic field focussing method with time varying fields . fig2 ( a ) illustrates a configuration for using hyperbolic field focusing similar to the one claimed by thekkadath . a fixed , single cup shaped electrode 20 generates a hyperbolic - like field close to the center axis . ions are sourced at 5 and sampled at aperture 24 . the field lines of such a configuration and the simulated path of an ion in this field are illustrated in fig3 . the salient feature of the field of fig3 is that is everywhere both nonlinear and asymmetrical . the distortions from linearity extend in one direction only . importantly , in the prior art disclosing hyperbolic fields , there are no discrete regions of one or more distinct sub - fields of any kind ( i . e ., linear fields , non - linear / symmetric fields , or different non - linear / asymmetric fields ) within the drift cell . the fields are uniform within the drift cell ; they are everywhere hyperbolic within the drift cell ; there are no discrete regions of having different resultant fields . referring back to the electrode configuration of fig2 ( a ) that is responsible for the field lines of fig3 , it should be noted that although the cup - shaped geometry is symmetrical , it is arranged ( i . e ., juxtaposed ) around the drift cell in a asymmetrical fashion in that the electrode structure does not extend to the axis defining the aperture plate . in general , a source of asymmetry in the field - generating component ( electrode ) is required . this can come from the configuration of one or more electrodes with respect to the drift cell and / or to one another ( e . g ., asymmetrically arranged electrode ( s ); in which the component electrode ( s ) may have either individual symmetry or asymmetry ). it may also be introduced from the conformation of the individual electrodes in a series ( e . g ., a symmetrical arrangement of electrodes having individual asymmetry , or an asymmetrical arrangement of individually symmetric electrodes , or some combination thereof ). other variations are possible while still achieving a hyperbolic field . the general requirement is a fixed configuration and conformation of electrode ( s ) about the drift tube such that only one resultant field in the drift tube results , and the fixed configuration and conformation must somewhere contain an inherent asymmetry . the focusing of ion beams in gases with periodic fields is described in more detail in u . s . pat . no . 6 , 639 , 213 and incorporated by reference herein . the combination / superposition of hyperbolic and periodic filed focusing is also discussed in pending u . s . application ser . no . 09 / 798 , 030 , filed on feb . 28 , 2001 and incorporated by reference herein . fig2 ( b ) illustrates a mobility drift cell with periodic field focussing taught in said reference . ions are sourced at 5 and migrate in the drift tube under the influence of a field created by ring electrodes 10 and are sampled at aperture 24 . in the embodiment of fig2 ( b ) and external excitation source 6 is used for ionization . the electric field of such a configuration and the path of an ion in this field is illustrated in fig4 . the basic functioning principle is as follows . off - axis ions feel a periodically changing electric field with focusing and defocusing properties . after drifting in a focusing portion of the field , the ion will enter a defocusing portion of the field . however , since the ions will enter the defocusing field at a distance closer to the axis as it entered the focusing field , the defocusing effect will be smaller than the focusing effect previously experienced . hence , during the path of the ion in the device of fig2 ( b ), the focusing properties will dominate and compensate the defocusing effects of the diffusion . we found that combining and superimposing both methods yields the best results , according to our simulations . our embodiments allow building mobility drift cells having the optimum trade - off between mobility resolving power and ion beam focusing . for example , in a mobility - ms with limited pumping speed , the cross section of the ion transmission channel from the mobility section to the ms has to be reduced in order to maintain the pressure differentials . in order to maintain acceptable sensitivity , it may be necessary to increase ion focusing in the mobility cell , trading off some of the mobility resolving power . our simulations show that superimposing hyperbolic field focussing and periodic field focussing helps to minimize the trade off . fig5 illustrates the field lines in the drift cell for a periodic hyperbolic field instrument . cone shaped electrodes as in fig6 ( a ) allow for a maximum portion of hyperbolic focussing in the superposition of the to focussing methods . a series of cone shaped electrodes 11 form a drift tube 10 which terminates at ion aperture 24 . this yields good properties but the electrodes are rather expensive to produce . fig6 ( b ) shows an embodiment with the same ion optical properties but having electrodes 10 that are isolated from each other with a foil or with a thin insulating material 11 that can at the same time also serve as the sealing the interior of the mobility drift cell from the exterior region . the thin insulating materials may be , for example , kapton film or teflon sheets . such sealing is often required in order to maintain pressure difference or in order to maintain the gas purity in the interior of the cell . ions are sampled at aperture 25 . a simpler and less expensive embodiment is using beveled thick plate electrodes resulting in cone shaped holes along the spectrometer axis is shown in fig7 . the cone angles angle in fig7 are approximately 90 degrees , but changing this angle allows for adjusting the portion of periodic field focusing and hyperbolic field focusing . in the extreme case of a cone angle of 0 degrees , one would obtain the embodiment for pure periodic field focussing described by gillig . fig8 ( a ) teaches an embodiment which uses an even more simple geometry with thin electrode plates 10 . pairs of the plates are electrically connected 17 by resistors 16 which determine the potential of each pair , allowing for the use of unequal potential differences between electrodes . the two electrodes forming one pair preferably have an unequal hole diameter . the difference in this diameter determines the portion of periodic field focusing and hyperbolic field focusing . in one extreme , when the hole diameters are equal , one obtains pure periodic field focussing . alternatively , electrode assemblies having unequal spacing between individual electrodes may be used for the same effect . fig8 ( b ) teaches an embodiment in which the holes of each pair are equal , but instead of shortening the pairs 17 the electrodes forming a pair are connected by resistors 18 of smaller resistance than those connecting the pairs 16 . this allows to superimpose hyperbolic field focussing . in other words , the pair resistor 18 has a very low value , the embodiment will become purely periodic field focussing . in another extreme , when the pair resistors 18 are of equal resistance as the resistors connecting the pairs 16 , a purely homogeneous field without any focussing but with high resolving power will result . fig9 ( a ) teaches an adjustable embodiment of the concept above . also in this embodiment , always two adjacent electrodes form a pair . however , there are two independent voltage dividers chains , which independently supply the potential of the first electrode of each pair and the second electrode of each pair respectively . the voltage dividing resistors 16 have the same resistance in both chains . each chain , however , also incorporates an adjustable resistor 19 which preferably are adjusted to the same value . if the resistance of the adjustable resistors 19 is adjusted to zero , then both plates of each pair will have the same potential , which results in a purely periodic field focusing . the field configuration is then equal to the situation illustrated in fig9 ( b ). if the resistance of the adjustable resistors 19 is adjusted to half the value of chain resistor 16 , then an essentially homogeneous field without any focusing properties will result . if the resistance of the adjustable resistors 19 is adjusted to some value in between the extreme cases just mentioned , a superposition of periodic field focussing and hyperbolic field focussing will result . this embodiment may of course be combined with the embodiment of fig8 ( a ) which uses electrode plates of different hole diameters in each pair . fig1 ( a ) teaches an embodiment with sealed mobility drift cell and a series of cup - shaped electrodes . this embodiment uses also a superposition of periodic field focusing and hyperbolic field focusing . fig1 ( b ) teaches a sealed embodiment of a purely periodic field focussing mobility drift cell using electrodes 10 with t - shape cross section and thin insulators 11 . fig1 and fig1 illustrate in more detail the insulation and sealing between ring electrodes 10 which can be used in all ( periodic , periodic hyperbolic , etc .) embodiments discussed so far . insulating foils or thin plates 10 are used for electrical insulation . seal rings 12 are used for vacuum sealing . additional seal rings 9 may be used for positioning of the electrodes 10 . instead of such rings , a tube may be used . fig1 ( a ) teaches an embodiment with hyperbolic field focussing similar to the prior art embodiment in fig2 ( a ), but including a novel adjustable sliding tube electrode 21 in order to adjust the hyperbolic field inside the cup . this allows adjusting the focusing of the ion beam in respect to its transmission to the ms through the orifice 24 . it also allows determining the trade - off between focussing and mobility resolving power . another possible embodiment involves replacing the sliding tube electrode with an electrode with hyperbolic shaped geometry . fig1 ( b ) teaches a combination of hyperbolic field focusing and periodic field focusing , but instead of superimposing the two focusing fields , the focusing methods are applied serially . hyperbolic field focusing , accomplished through the use of fixed electrode 20 , is used at the location of the pulsed ionization by laser 6 ( or ion shutter for non - pulsed ionization methods ), and periodic field focusing , accomplished through the use of ring electrodes 10 , is applied further downstream the mobility drift cell . this embodiment can of course be combined with any other embodiment discussed so far . in one embodiment , instead of a single mobility cell , a plurality of mobility cells can be used in series , with the each successive mobility cell operating at a lower pressure than the previous mobility cell ( s ). although any number of mobility cells can be used , preferably two mobility cells can be placed in series with one another . the two cells would be operated at different pressures which could be accomplished by using different aperture sizes . the following illustrative , non - limiting example is one possibility . the first mobility cell have a small exit aperture and operate at , for example , 100 torr . the second mobility cell may have a larger aperture and operate at lower pressures ; for example , 10 torr . in this embodiment , one or more of the mobility cells can have a combination and / or or a superposition of periodic and hyperbolic fields , or can have combinations of periodic and hyperbolic fields . one or more of the mobility cells can have purely periodic or hyperbolic fields . all combinations of the foregoing are clear to one of skill in the art upon a reading of this description , and all are within the scope of the present invention . the mobility cell can be used as a transport device to move ions from one region to another irrespective of its use as a mobility device . it may therefore be used to connect one mobility cell to another or one mobility cell to a mass spectrometer for example . it would be possible to form ions at high pressure between for example 10 torr and several atmospheres of pressure within one mobility cell which is then separated from a second ( or more ) mobility cell by a small exit aperture . the second mobility cell would be operated at a lower pressure of between 100 - 1 torr and could then act as a transport device to a trap , or a mass spectrometer , or another measuring device or alternatively some other device for manipulating or focusing the ions . fig1 illustrates an embodiment of the ionization region with ionizing beam 6 entering through a windows 32 from behind the sample surface 5 and being redirected with a mirror 30 onto the sample . in the same way , the camera 31 serves to observe the ionization process via a mirror . a rotatable sample holder 40 allows turning several samples into the focus position of the ionizing beam 6 without removing the sample holder 40 . in this way , a number of samples may be sequentially analyzed . many mechanical design variations are possible for this embodiment , particularly those using multiple mirrors , allowing the source of the ionizing beam to be positioned in a variety of positions ; e . g ., it may , for example , be positioned behind the sample holding surface . in fig1 , an embodiment with a moving belt sample holder 41 which allows for manual or automatic sample deposition 42 , sample analysis or separation by mobility cells discussed in previous figures , and sample holder cleaning 43 . ionizing beam 6 , electrodes 10 , insulating spacers 11 and sampling aperture 25 are also illustrated . this embodiment allows the ionizing beam to enter the drift cell essentially orthogonal to the drift cell axis . the sample holder of this embodiment allows one to sequentially expose several samples to the ionizing beam by positioning the samples at various locations on the moving belt . rotation of the belt allows one to proceed from sample to sample for analyses . many mechanical design variations are possible for this embodiment . for example , multiple mirrors can be used to allow for flexibility in the positioning of the source of the ionizing beam . a number of variations on the instrumentation taught above are possible without deviating from the scope of the invention . for instance , the examples above all involve single orifice ( i . e ., single hole ) electrodes . it is possible to utilize electrodes having multiple holes to make up the drift cell . the individual ion paths defined by these holes are different ion channels within which ion mobility can be performed . various combinations of the electrode geometries taught above are possible . in this way , a multiple channel ion mobility instrument can be constructed . additionally , a purely ion transport device can be constructed with the disclosed electrode geometries and configurations . such a device can be used outside of the context of the basic ion mobility spectrometry method . for instance , such an ion transport device would find utility in any application where guiding ions from one instrument or area to another is desirable . for example , applications are possible to transfer ions from an ion source to a mass spectrometer . another notable advantage of using heterogeneous fields in the mobility drift cell as herein described is the increase in discharge voltage when operating the mobility cell close to the paschen minimum . we have observed that one can apply higher voltages across the cell without causing a gas discharge . in addition to the aforementioned to the advantages realized through the use of hyperbolic field focusing , a number of other aspects of the present invention are described below . these additional aspects of the present invention involve a number of instrumental and method refinements resulting in improved apparatuses and methods for separating and analyzing ions in a high - pressure gas . the resulting methods and apparatuses enable analyses having high sensitivity for charged species while maintaining resolution comparable to that achieved in moderate resolution drift tubes known to the art while providing an easily constructed and implemented solution . the apparatus comprises one or two electrodes to which voltages are applied , spaced apart from an aperture plate which samples charged particles . once sampled using the aperture plate , the ions may be detected by a conventional ims detector ( consisting of an electron multiplier and associated electronics ) or a mass spectrometer . ions can be produced by any number of means including in part electrospray ionization , laser ionization , photoionization , electron ionization , chemical ionization , electric field ionization , surface ionization , radioactive ionization , discharge ionization , multiphoton ionization , etc ., with the chosen method of ionization being matrix assisted laser desorption ionization ( maldi ). the laser is the preferred example of an ionizing beam excitation . in one embodiment of the invention ions are produced by maldi in a well - defined ion packet thereby eliminating the need for an additional means of gating , i . e . with a bradury - nelson gate . once formed , ions are made to flow by a suitable arrangement of electric fields produced by one or two easily manufactured electrodes . the ions are then separated by mobility , sampled through an aperture plate and either focused into the source region of a time - of - flight mass spectrometer to enable mass analysis of the mobility separated ions , or focused onto a conventional ims detector to enable mobility analysis of the exiting ions . the resolution attainable with an ion mobility spectrometer is determined by a combination of the effect of a finite pulse width of originating ions and the total potential drop experienced by the ions . in one embodiment of the present invention , maldi is the preferred ionization method and the ion packet formed is of extremely short duration ( 4 nanosecond laser pulse width ) and composed of a limited number of ions ( space charge effects on resolution are negligible ). therefore , the resolution of a maldi / ims spectrometer is diffusion limited and predominantly a function of the applied potential ( experimentally verified by observing a constant increase in resolution with applied voltage ), determined by the discharge properties of the buffer gas employed . it is an object of the present invention to maximize the sensitivity of the ims drift cell while maintaining the resolution within the diffusion limited regime and simultaneously constructing the apparatus in a simple manner , i . e . with a minimum number of electrodes ( 1 or 2 ). an additional advantage realized with the use of maldi ionization is its amenability to the analysis of large molecules , particularly biologically important molecules . maldi is a rather gentle ionization technique , thereby minimizing fragmentation of large biomolecules , particularly proteins and nucleic acids . this facilitates elucidation of sequence and structure . analysis of such samples is simplified by minimizing fragmentation , resulting in less cluttered spectra . other soft ionization techniques such as electrospray ionization enjoy similar advantages . when mass spectrometry is used as a detection scheme , a two dimensional pre - selection of ion is realized ; one based upon simplification of ion population at the outset , and another based upon the use of mass spectrometry in addition to ion mobility . also described herein are instrumental improvements in the detection architecture of an ion mobility spectrometer . as used herein , the ion detector refers to any instrumental apparatus in fluid and electronic communication with the sample ionization and drift cell instrumentation and which ultimately outputs data which characterizes the sample under analysis . the ion detector may be a conventional aperture grid / collector / amplifier assembly typically used in mobility analysis . alternatively , it may also comprise more complex instrumentation and electronics such as that which may enable mass spectrometric analysis of the chemical species separated by mobilities . in the latter case , a consistent problem with prior art instruments in throughput losses that occur in going from a high pressure stage ( ion mobility drift cell ) to a low pressure stage ( the mass spectrometer ). instrumental modifications are described herein that represent improvements in ion throughput in comparison to conventional instruments . fig1 is a schematic view of a spectrometer 60 . spectrometer 60 comprises an ion mobility cell 64 , fed from an ion source 68 . a lens system 72 , focuses ions into a housing having a detector 76 , and an orthogonal time - of - flight mass spectrometer 80 . a laser 84 may be used as apart of the ion source 68 in selected applications . the laser generates gaseous molecular ions from a solid matrix / analyte sample introduced into ion mobility cell 64 through vacuum interlock 88 and deposited on probe tip or multiple well plate 92 . the small packet of maldi formed ions drift in a buffer gas under the influence of a suitable electric field applied between back electrode 96 and aperture plate 100 . following ion mobility separation in ion mobility cell 64 , ions are sampled through a 200 - 500 micron diameter aperture 104 , and pass sid surface ( or other dissociation element ) 128 . with a mobility cell buffer gas pressure of 1 - 10 torr helium the analyzer chamber 112 is kept below 1 × 10 31 5 torr by a small high vacuum pump 116 . ions exiting aperture 104 are focused by lens system 72 onto either detector 76 to record the ion mobility arrival time distribution or into the time - of - flight source 108 where arriving ion packets are pulse focused orthogonally into a 20 cm long flight tube 120 . mass spectra are then recorded with detector 124 using normal ion counting techniques . the acquired mass spectra can either be used for m / z identification or plotted as a function of ion mobility . fig1 shows the equipotential lines of a prior art device displaying a linear electric field formed by applying a voltage across a series of equally spaced rings through a resistor chain or across a tube coated with a resistive material . the linear electric field assures that all ions experience the same field independent of radial diffusion if sampled before experiencing the fringing nonlinear fields near the side wall . in the case a of stacked ring / insulating spacer assembly several factors can degrade this ideal situation , e . g . alignment becomes critical , machining errors multiply with drift cell length , resistors must be perfectly matched , and the insulating spacers eventually degrade leading to perturbations in the linear field . it is also very difficult to coat a tube evenly with a resistive material . an alternative method to produce a linear electric field is simply to apply a voltage drop across two parallel discs as shown in fig1 . this method is simple but unless the discs are very large the maximum drift distance that can be used is very limited due to the non - linearity produced by fringing fields . to increase the drift distance yet maintain adequate resolution at the expense of field linearity a radius of curvature has been added to the electrode yielding focusing properties to increase the drift cell sensitivity . fig1 shows the equipotential lines formed between an electrode with a 6 ″ radius of curvature and a grounded flat plate . note that the region of linearity may be lengthened by using a vacuum can of insulating material , e . g . glass or plastic in which case the penetrating fields are eliminated . this embodiment of the present invention is easy to manufacture and assemble , and is very robust . the drift cell interior is accessible by removing the top view port for cleaning resulting in short down times between experiments . the device also provides moderate resolution ( 20 - 40 ) and high sensitivity ( 10 femtomoles of loaded sample ). field correcting ring electrode fig2 illustrates the equipotential lines in an embodiment of the present invention having a field correcting ring in addition to flat disc electrode . a device so configured can be adjusted to produce an interior electric field ranging from linear to highly non - linear and all combinations between . fig2 illustrates the equipotential lines in another embodiment having a flat ( planar ) electrode and a second movable electrode . fig2 illustrates the apparatus in cross - section . a cylindrical electrode 140 , is shown in cross - section with a planar electrode 148 . ions travel through the field lines towards collector plate 144 . the cylindrical electrode 140 can be moved towards and away from the collector plate 144 . in this way , such a device can be adjusted to produce and interior electric field ranging from linear to highly non - linear and a continuous range of combinations in between . the embodiment of the present invention as depicted in fig1 is limited to a drift / buffer gas pressure of 1 - 50 torr due to a single stage of pumping on the ion detector and mass spectrometer . a higher operating buffer gas pressure allows for a higher electrode voltage and subsequent higher resolution . to maintain a collision free vacuum in the analyzer chamber at higher drift cell pressures requires either the use of larger vacuum pumps or an additional stage of differential pumping . but a standard interface operating at ca . 1 torr would compromise the sensitivity of the apparatus due to excessive ion losses . several reported attempts have been made to increase the ion transmission in an interface region . smith et al . implemented an ion funnel ( pct wo 97 / 49111 ), consisting of a series of decreasing diameter ring electrodes to which an alternating rf voltage and linear dc voltage is applied . krutchinsky et al . used a segmented rf only quadrupole ( proceedings of the 43rd asms conference , 1995 , 126 ). both could increase the ion transmission significantly . it is a further object of the present invention to provide a simple , yet highly efficient ion interface to transport ions through an intermediate region between a high background pressure device and a high vacuum device . without compromising the small scale dimensions of the apparatus an alternative embodiment comprising a radio frequency focusing interface . in this embodiment , ions exiting aperture 104 ( see fig1 ) encounter a combination of a rf electric field and a dc electric field in the presence of buffer gas collisions . the resulting ion trajectories are shown in fig2 , illustrating the superb focusing characteristics of this device . the field amplitude and the frequency of the rf applied to this device can be varied to match the elution times of the mobility separated ions so that as each mobility separated ion enters this rf device the cooling and focusing of the ions through aperture 12 will be optimal . thus , for example the rf amplitude and frequency can be increased as a function of time so that the peptides in fig2 each experience optimal cooling and focusing as they enter the region between the exit of the ion mobility cell and the entrance to the tofms . with reference to fig2 , a particularly useful and powerful embodiment of this device is for the case when ions have been separated on the basis of their charge to volume ratio by an ims cell prior to their entering the rf interface . in this case the amplitude or frequency of the rf field can be continuously optimized to maximize the transmission of the particular charge to volume ratio which is present at any particular time relative to the start of the ims separation . this is very useful for maldi - ims experiments in which the singly ionized charge state is predominant . ims of familial classes of biomolecules have been found to have a predictable relationship between the charge to volume and the charge to mass of each ion in the familial class . this relationship is different for most familial classes of singly charge biomolecular ions ( e . g ., lipids , peptides , oligonucleotides ) so that each ion of a familial class lies along a distinct familial “ trend line ” in the two dimensional plot of mobility drift time vs . m / z . thus , the time of arrival of an ion with a particular m / z can be predicted by the familial trend line and the mobility drift time ( which is related to the ion &# 39 ; s volume to charge ratio ) so the rf amplitude , or frequency can be continuously computer controlled and optimized for the transmission of the specific m / z of each ion in the familial trend line . thus , the rf field would have optimal characteristics for low m / z values at the start of the im separation and very different field characteristics as the larger m / z ions eluted from the im cell at longer mobility drift times . an approximately linear increase of m / z values along a familial trend line occurs . it is a reasonable approximation to increase the amplitude of the rf - voltage which is applied to the rods to be proportional to the square root of the time measured relative to a zero time when the initiation of the ionization event occurs . the coefficient of proportionality is the slope of the familial trend line . such a time changing rf - field thus synchronized to the elution of ions at the end of the mobility cell would allow to record small ions without defocusing and losing them due to possible instability of their motion for large rf - fields necessary for the focusing and transport of larger ions . also it would allow the effective focusing of ions of large masses for essentially the same width ion beams for ions of all masses . since multi - charged ions would be focused even better than for the singly charged ions such an approach will focus all ions well below 1 mm diameter ion beams as the corresponding simulations show . the length and the number of the sections and the dc voltages applied to them should be found by computer simulation for providing enough time for desired ion focusing without losing of their separation received before in mobility cell and without decomposing of the ions . any broadening of the mobility resolution because of the increased residence time of ions in the rf assembly could be almost completely removed by numerical deconvolution of the mobility resolved spectra after first determining — either experimentally or theoretically — the residence time as a function of mass of the ions within the rf assembly . fig2 shows a schematic of an alternative embodiment of one section of the present invention comprising the aperture plate by which ions are sampled . the mobility chamber housing 176 at high pressure terminates at 168 and is separated from the analyzer chamber 180 at vacuum by a multi - capillary interface , e . g . a microchannel plate 160 . analyzer chamber 180 . high ion transmission ( ions depicted by direction of travel 170 ) can be achieved by reverse biasing a semi - conductive capillary in the presence of gas flow and a temperature gradient as described in u . s . pat . no . 5 , 736 , 740 to franzen . electrode 168 is contained inside but electrically isolated from the mobility vacuum housing 176 and electrode 164 is contained within , but electrically isolated from , the analysis chamber 180 . electrodes 168 and 164 can be biased either to retard or accelerate the passage of ions 170 through the microchannel array 160 . the preferred embodiment of the present invention utilizes a bundle of capillaries acting as a pressure stop and ion interface to reduce the vacuum pump requirements . the optimum diameter to length ratio will depend on the required pressure drop as well as on the absolute pressure . the diameter of the microchannel interface can be much larger than a single aperture thereby transmitting ions that diffuse in the radial direction in the drift chamber that would otherwise be lost . a further alternate embodiment of the present invention comprises pre - selecting parent ions by their mobility for fragmentation . the form of fragmentation includes in part , methods known in the art such as collision - induced dissociation ( cid ), surface - induced dissociation ( sid ), electron impact or photo - induced dissociation with the preferred method of dissociation being sid . in fig1 , the sid surface 128 is located between lens system 72 and time - of - flight source 108 and preferably is comprised of a rotatable fine mesh grid . the advantage of the present invention embodiment is the simultaneous detection of parent and fragment ions : fragment ions will appear at the same mobility time as the parent ions without scanning the entire mass range at a specific mobility drift time . to eliminate any energy differences between the parent and fragment ions that occur during the dissociation process a rf focusing quadrupole onto which a linear electric field in superimposed is located behind the sid grid . all ions are cooled by collisions in the rf quadrupole and therefore arrive at the time - of - flight source simultaneously . because higher energy collisions in cid result in a greater degree of fragmentation , the collision energy may be increased by using an electric field to accelerate the ions within the expanding gas flow during transmission from the ion mobility drift cell to the mass spectrometer . one of the many applications of the apparatus is in the field of proteomics , specifically protein mixture analysis . current analytical techniques are time consuming and labor intensive but a gas phase separation method such as ion mobility spectrometry is more congruous with mass analysis so by combining the separation step and the mass analysis into a single instrument as in the present invention the throughput of the system is greatly increased . also , the present invention displays increased sensitivity in the analysis of protein mixtures over a typical maldi time - of - flight mass spectrometry experiment . to compare the two methods a two component mixture consisting of a tryptic digest of bovine hemoglobin α and β was analyzed on the apparatus of the present invention and on a state of the art high resolution time - of - flight mass spectrometer . the ion mobility experiment , for which the 3 - dimensional plot of mass spectra is shown in fig2 , observed a greater percentage of the total amino acids present in the sample relative to the optimized maldi - tof protocol ( 94 % amino acid coverage for both hemoglobin α and β versus 75 % and 68 % on the maldi - tof instrument ). the observed increase in % coverage is attributed to the increased sensitivity of the present invention . as a further test a more complex mixture consisting of horse heart cytochrome c , chicken egg white lysozyme , bovine serum albumin , bovine hemoglobin α and bovine hemoglobin β was used . the same sample was analyzed using optimized sample preparation procedures on both the apparatus of the present invention and the maldi - tof instrument . the table shown in fig2 clearly illustrates that the apparatus of the present invention yields higher overall % amino acid coverage and individual % amino acid coverage for a complex protein mixture . in addition , the apparatus of the present invention demonstrates higher sensitivity toward lysine terminated digest fragments . ( krause , e . et al . anal . chem . 1999 , 71 , 4160 - 4165 ). this phenomenon is typified in the case of cytochrome c , for which both experiments result in 60 % of the total predicted arginine terminated fragments being observed , but the experiment using the apparatus of the present invention results in the observation of a much greater percentage of the lysine terminated fragments ( 52 % versus 16 %). the results suggest that performing maldi / ion mobility / mass analysis of protein mixtures where ions are formed in a low pressure environment ( is this case 5 torr helium ) involves a different desorption process than when ions are formed by maldi in a high vacuum environment . this statement is further supported by a comparison of spectra obtained in the two environments . if the same digest sample is analyzed with the high vacuum instrument using the same matrix and sample preparation as with the apparatus of the present invention the % coverage for a protein digest or a digest of a complex protein mixture is extremely low and only a few fragments are identifiable . therefore , further objects of the embodiment include simplification , increased throughput , increased overall sensitivity , and increased sensitivity toward lysine terminated digest fragments present in complex mixtures . although the present invention and its advantages have been described in detail , it should be understood that various changes , substitutions and alterations can be made herein without departing from the spirit and scope of the invention as defined by the appended claims . moreover , the scope of the present application is not intended to be limited to the particular embodiments of the process , machine , manufacture , composition of matter , means , methods and steps described in the specification . as one of ordinary skill in the art will readily appreciate from the disclosure of the present invention , processes , machines , manufacture , compositions of matter , means , methods , or steps , presently existing or later to be developed that perform substantially the same - function or achieve substantially the same result as the corresponding embodiments described herein may be utilized according to the present invention . accordingly , the appended claims are intended to include within their scope such processes , machines , manufacture , compositions of matter , means , methods , or steps . all patents and publications mentioned in the specification are indicative of the level of those skilled in the art to which the invention pertains . all patents and publications are herein incorporated by reference to the same extent as if each individual publication was specifically and individually indicated to be incorporated by reference . u . s . pat . no . 4 , 390 , 784 june 1983 browning , et al . u . s . pat . no . 4 , 855 , 595 august 1989 blanchard u . s . pat . no . 5 , 235 , 182 august 1993 avida et al . u . s . pat . no . 5 , 189 , 301 february 1993 thekkadath u . s . pat . no . 5 , 736 , 740 april 1998 franzen u . s . pat . no . 5 , 905 , 258 may 1999 clemmer et al . u . s . pat . no . 5 , 789 , 745 august 1998 martin et al . u . s . pat . no . 6 , 040 , 573 march 2000 sporleder et al . u . s . pat . no . 6 , 051 , 832 april 2000 bradshaw pct wo 98 / 08087 february 1998 bradshaw pct wo 97 / 49111 december 1997 smith et al . pct wo 00 / 08454 february 2000 guevremont , et al . pct wo 00 / 08455 february 2000 guevremeont , et al . pct wo 00 / 08456 february 2000 guevremont , et al . pct wo 00 / 08457 february 2000 guevremont , et al . barnes , d . w . et al ., phys . rev . lett ., 1961 , 6 , 110 . septier , a . 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