A MASS SPECTROMETER USING A DYNAMIC P RESSURE ION

SOURCE

This invention relates to a mass spectrometer; particularly a mass spectrometer

having a pulsed ion source, such as a Matrix Assisted Laser Desorption Ionisation

(MALDI) ion source.

The MALDI ion source has been widely used for biochemical analysis. Typically,

a MALDI ion source includes sample mixed with a radiation absorbing material to

form a matrix which is deposited on a surface of a sample plate; this assists

ionisation of sample following irradiation of the matrix by a laser pulse.

A known instrument comprises a MALDI ion source in combination with a Time-

of-Flight (TOF) mass spectrometer; however, this instrument only allows simple

MS analysis to be performed. In order to couple the MALDI ion source to other,

more versatile types of mass analyser, or to develop hybrid systems suitable for

carrying out tandem mass analysis, different kinds of MALDI - MS interface have

been developed over the past decade. In general, ions generated by a pulsed ion

source, such as a MALDI ion source, have energies proportional to their masses,

and ions having the highest masses have the widest energy distributions. For example, ions having a mass of 10,000Da, say, and having a maximum velocity of

1200msec ^! may have kinetic energies as high as 75eV. Such high energy ions

present a problem when designing an interface between a pulsed ion source, such

as a MALDI ion source, and a mass analyser.

US Patent No. 6,576,893 describes a method for introducing ion pulses generated

by a MALDI ion source into an ion trap, via a high vacuum electrostatic lens, by

application of a pulsed retardation voltage. This method enables ions of high mass

to undergo mass analysis in the ion trap itself, or to be ejected from the ion trap for

subsequent analysis in a TOF analyser. Although, a pulsed retardation voltage is

effective to reduce the kinetic energy of the ions it cannot reduce internal energy

acquired by the ions as a result of the ionisation process, and this can give rise to

unwanted fragmentation of the trapped ions.

US Patent No 6,331,702 describes a different technique whereby ions generated by

a MALDI ion source are transmitted to an orthogonal TOF analyser via an ion

path including a multipole ion guide. The ion guide functions as an interface

between the MALDI ion source and the mass analyser and is effective to convert

pulsed ions to a quasi-continuous ion beam. A quasi-continuous beam of ions is

needed for a quadrupole analyser or a fast pulsing orthogonal TOF. By contrast,

continuous introduction of ions into a quadrupole ion trap is difficult.

High mass protein ions (e.g. ions having masses in excess of 10,000Da) have high

kinetic energies which must be reduced significantly before the ions can be

accepted into the multipole ion guide. This necessitates providing a cooling gas in

the ion path in order to cool the ions and thereby reduce their energy. However, in

order to achieve this, the cooling gas needs to be maintained at a relatively high

pressure, typically greater that 10 ^"2 mbar, and this may give rise to problems such

as electrical discharge in the ion guide. In order to overcome this problem

differential pumping is adopted so that a lower gas pressure may be used in the ion

guide than in the source region, but this adds to the complexity and cost of the

system. Furthermore, even at a pressure as low as 10 ^"2 mbar, axial motion of ions

within the ion guide is effectively brought to a halt, significantly reducing the

efficiency with which ions may be transferred to the analyser for analysis. US

Patent Publication No. 2005/0092912 describes provision of an axial electric field

which is used to accelerate ions along the ion guide to improve the efficiency of

transfer, but this adds yet more complexity and cost to the system.

EP 0964427 A2, US Patent No. 5,965,884 and US Patent No. 6,946,653 also

describe use of ambient gas to reduce both the kinetic and internal energies of ions

generated by MALDI ion sources. Because no effective electrostatic lens system

can be incorporated in the source region where high pressure exists, high

efficiency of transmission is difficult to achieve. Also, the pulsed nature of the

source is not preserved and so this technique cannot be used for ion trap mass analysers.

A paper entitled "Matrix Assisted Laser Desorption/Ionisation Using a New

Tandem Quadrupole Ion Storage Trap, Time of Flight Mass Spectrometer" P.

Kofer, Rapid Communications in Mass Spectrometry Vol.10, 658-662, 1996

describes use of pulsed gas to cool ions generated by a MALDI ion source in a

hyperboloid 3-D ion trap. In this case, the MALDI sample is deposited on the tip

of a sample probe mounted in the entrance end cap electrode of the hyperboloid

3-D ion trap. However, this arrangement is unsatisfactory because it limits both

the volume and spatial distribution of sample presented for analysis and, in

particular, prevents analysis of multiple samples, during the same session.

Furthermore, surface contamination of the ring electrode and the end cap

electrodes of the ion trap is likely to occur and this degrades the analytical

performance of the ion trap.

It is an object of the invention to provide a mass spectrometer having a pulsed ion

source, such as a MALDI ion source, which at least alleviates the foregoing

problems. More specifically, it is an object of the invention to reduce the kinetic

and internal energies of ions generated by the pulsed ions source in order that they

may be efficiently delivered to and trapped within an ion trap of the mass spectrometer for mass analysis.

According to one aspect of the invention there is provided a mass spectrometer including:

a pulsed ion source,

a first ion trap for trapping ions generated by the pulsed ion source and for

locating trapped ions for subsequent ejection from the first ion trap,

gas inlet means for introducing a pulse of cooling gas into said first ion trap

at a peak pressure suitable for enabling the first ion trap to trap said ions,

pump means for reducing pressure of said cooling gas before the trapped

ions are ejected from the first ion trap, and

a second ion trap for receiving and analysing ions ejected from the first ion

trap,

said pulsed ion source including a flat sample plate on which sample is deposited

and which forms an end wall of the first ion trap, whereby said pulsed ions are

generated inside the first ion trap.

A reduced gas pressure is beneficial because it allows migration of trapped ions to

a low energy region of the first ion trap from which the ions may be ejected over a

relatively short time span. Therefore, this measure may improve the efficiency

with which trapped ions are transferred from the first to the second ion trap. The

reduced gas pressure also allows mass analysis to be performed in the second ion

trap which may share the same vacuum chamber without using differential pumping.

Said pump means may be a vacuum pump, such as a turbomolecular pump.

Said gas inlet means may include an electromagnetically-driven valve, such as a

solenoid valve, or a piezoelectrically-driven valve. Typically, said gas inlet means

introduces said pulse of cooling gas into the first ion trap at a peak pressure in the

range from 5xlO ^'2 mbar to 1 mbar, and said pump means reduces that pressure to a

pressure less than 5xlO ^"3 mbar.

Said valve is preferably held open for a period less than the pump down time

constant achieved by said pump means, preferably less than 5ms.

Preferably, there is a preset delay between activation of said gas inlet means and

subsequent activation of said pulsed ion source.

In preferred embodiments, the pulsed ion source is a MALDI ion source.

The first ion trap may be a multipole (preferably a quadrupole) linear ion trap

having a plurality of poles arranged symmetrically around a longitudinal axis of

the ion trap. In preferred embodiments of the invention, said multipole linear ion trap may

include a gate electrode located at a rear end of said first ion trap, said gate

electrode being selectively biased, in use, to reflect or eject ions.

Said gate electrode may be biased to create an axial DC potential well in the first

ion trap whereby to locate a cloud of said trapped ions in the first ion trap prior to their ejection from the first ion trap. The multipole linear ion trap may be a

segmented multipole (e.g. a quadrupole) linear ion trap wherein each pole includes

a relatively short segment adjacent to said rear end of the first ion trap, each said

relatively short segment being biased to augment said DC axial potential well. Alternatively, a ring electrode may be provided between the gate electrode and the

poles of the multipole linear ion trap, the ring electrode being biased to augment said DC axial potential well.

With this biasing arrangement trapped ions can migrate axially within the

multipole linear ion trap as the pressure of cooling gas is reduced by said pump

means, coming to rest at the bottom of said DC potential well where they may

congregate to form a short, ovoid ion cloud which may readily be ejected from the i first ion trap. Said gate electrode may be biased to subject ions to an electrostatic

accelerating force towards the gate electrode causing their ejection from the first

ion trap towards the second ion trap.

In another preferred embodent of the invention, said first ion trap is a cylindrical

ion trap including a ring electrode having a longitudinal axis, wherein said flat

sample plate forms an end wall of the ion trap at a front end thereof and a gate

electrode forms an end wall of the ion trap at a rear end thereof.

In the case of a cylindrical ion trap, DC biasing means may be arranged to

establish a dipole electric field between said flat sample plate and said gate

electrode to cause ejection of trapped ions from the first ion trap, and said second

ion trap is arranged to establish a further dipole electric field for retarding the

ejected ions.

The second ion trap may be of any suitable form capable of receiving ejected ions

and performing mass analysis on ions so received, including a quadrupole linear

ion trap which may be a segmented quadrupole linear ion trap or a hyperboloid 3-

D ion trap.

The first and second ion traps may both be linear ion traps, which may be

segmented linear ion traps. In some embodiments, the first and second ion traps

are arranged in series on a common longitudinal axis whereas, in other

embodiments, the first and second ion traps are arranged side-by-side on mutually

parallel axes and means for ejecting trapped ions is arranged to eject ions from the

first ion trap to the second ion trap in a direction orthogonal to said parallel axis.

The first and/or second ion traps may have a tunnel structure formed from printed

circuit board bearing electrically conductive tracks to which high frequency drive

and DC bias voltages are applied in use.

Embodiments of the invention are now described, by way of example with

reference to the accompanying drawings of which:

Figure 1 is a diagrammatic, longitudinal cross-sectional representation of a

mass spectrometer according to the invention.

Figure 2 illustrates a variation of axial DC potential in the first and second ion traps of the mass spectrometer of Figure 1 during both the trapping and

ejection of ions.

Figures 3(a) and (b) are diagrammatic, longitudinal cross-sectional representations of other mass spectrometers according to the invention,

Figure 4 is a diagrammatic, longitudinal cross-sectional representation of yet another mass spectrometer according to the invention,

Figure 5 illustrates the optimum timing a pulse of laser radiation with

respect to a rectangular waveform drive voltage and a sinusoidal waveform drive

voltage applied to the ring electrode of the cylindrical ion trap described with reference to Figure 4, and

Figures 6 and 7 are diagrammatic, longitudinal cross-sectional

representations of yet further mass spectrometers according to the invention.

Referring to Figure 1, the mass spectrometer has an ionisation region 1 and a mass

analysis region 2 housed within a vacuum enclosure 3. It will be appreciated that

all the embodiments described hereinafter include a vacuum enclosure, but for

simplicity this is only illustrated in Figure 1. The ionisation region 1 includes a

first ion trap 10 which is used to trap ions generated by a pulsed ion source, and

the mass analysis region 2 includes a second ion trap 20 effective to receive and

analyse ions ejected from the first ion trap 10. The mass analysis region 2 also

includes an ion detector D for the detection of ions ejected from the second ion

trap 20.

In this embodiment of the invention the first ion trap 10 is a quadrupole linear ion trap whereas the second ion trap 20 is a hyperboloid 3-D ion trap comprising a

ring electrode 21 and two end cap electrodes 22, 23.

The two ion traps 10, 20 are arranged in series on a common longitudinal axis

X-X. The quadrupole linear ion trap comprises four mutually parallel poles 11

arranged symmetrically around the longitudinal axis. The poles 11 are supplied, in

use, with a high frequency rectangular waveform digital drive voltage generated

by a drive unit 12 in the form of a high voltage digital switching circuit. It will be

appreciated that any other suitable form of high frequency drive voltage; for

example, a sinusoidal waveform drive voltage could alternatively be used. A

sinusoidal waveform drive voltage may have a frequency in the range from radio

frequency to audio frequency (suitable for ions having very high mass-to-charge

ratio). As will be described in greater detail hereinafter the drive voltage creates a

high frequency quadrupole field which is effective to constrain radial ion motion

inside the ion trap.

The second ion trap 20 is driven in similar fashion, but more controlled scanning

functions for mass analysis may be provided.

The ionisation region 1 includes a pulsed ion source comprising, a pulsed laser 13

arranged to direct pulses of laser radiation onto a sample S via a suitable optical

system whereby to generate ion pulses. The sample S is deposited on an

electrically conductive sample plate 14 which forms an end wall of the first ion

trap 10. Therefore, ions generated by pulsed irradiation of sample S are actually

produced inside the ion trap, and this gives improved trapping efficiency. The

sample plate 14 is suitably positioned with respect to the laser beam using a

motor-driven X-Y manipulator stage (not shown). This arrangement allows

multiple samples deposited on the sample plate to be individually analysed without reloading the sample.

In this particular embodiment of the invention, the pulsed ion source is the

preferred MALDI ion source, the sample material being mixed with radiation

absorbing material to form a matrix which is deposited on the sample plate 14 for

exposure to pulses of laser radiation. This arrangement assists the ionisation

process. Alternatively, other known forms of pulsed ion source could be used,

such as, pulsed secondary ion emission, fast atom bombardment and electron

induced ionisation sources.

The ionisation region 1 also includes an electromagnetically-driven solenoid valve

15 (or alternatively a piezoelectrically-driven valve) for locally injecting a high

pressure pulse of cooling gas (e.g. Ar or He gas) into the interior of the first ion

trap 10 via an inlet tube 16 located close to the front end of the ion trap, and a

high-speed pump 17 such as a turbomolecular pump for subsequently reducing the

pressure of the cooling gas within the ion trap to a pressure less the 5xlO ^"3 mbar.

The distance over which gas travels between valve 15 and the first ion trap 10

should be as short as possible. The length of tube 16 should be less than twenty

times the tube diameter, allowing injected gas to be rapidly pumped out, resulting

in a shorter pressure decay tail.

The first ion trap 10 has a conical gate electrode 18 located at the rear end of the

ion trap. As will be described, the gate electrode 18 is used to eject ions from the

ion trap but is also used to assist the trapping process.

A DC voltage source (not shown) biases the sample plate 14 at a first DC potential

with respect to the average axial DC potential on the poles 11 and biases the gate

electrode 18 at a second DC potential with respect to the average axial DC

potential on the poles. While ions are being trapped in the first ion trap, the first

and second DC potentials are both either more positive or more negative than the

average DC potential on the poles according to whether the trapped ions are

positively charged ions or negatively charged ions respectively. Therefore, in the

case of positively charged ions, the flat sample plate 14 and the gate electrode 18

are both biased at DC potentials that are more positive than the average DC

potential on the poles 11. The DC bias voltage may be in the range from several

tens of volts to several hundreds of volts depending on the mass range of the ions

that are to be trapped and the length of the linear ion trap 10, and the DC potential

on the gate electrode 18 is preferably, though not necessarily less than the DC

potential on the sample plate 14. The DC potentials on the flat sample plate 14,

the gate electrode 18 and the poles 11 are as such as to create a potential well on

the longitudinal axis of the first ion trap 10, the bottom of the potential well being

located adjacent the gate electrode 18, as illustrated by curve 21 of Figure 2.

As already explained, high-mass ions generated by the pulsed ion source (e.g. ions

having masses greater than 10,000Da) will generally have high kinetic energies,

typically up to 10OeV, and this energy must be reduced before ions can be efficiently trapped within the first ion trap 10. To that end, a high pressure pulse

of cooling gas is injected into the ion trap via tube 16. This causes rapid cooling

of the pulsed ions with a consequent reduction of their kinetic and internal energies, enabling ions to be trapped within the first ion trap 10 under the

influence of the quadrupole electric field generated by the rectangular waveform

digital drive voltage applied to the poles 11.

In order to trap ions, particularly the more energetic, high mass ions, the pulse of

cooling gas should have a high peak pressure which is then rapidly reduced by

pumping so that ions can easily migrate to a suitable location within the first ion

trap for subsequent ejection.

In order to build up gas pressure quickly high pressure gas is supplied to the inlet

of valve 15. Typically, Helium or Argon gas at a pressure of one atmosphere or

more is used. An electrical activation pulse used to hold valve 15 open may be as

short as lOOμs, and may have a voltage more than ten times that needed to hold the

valve open continuously. The actual valve opening time will depend on the valve

head restoration time, but should be less than the pump down time constant of the

vacuum system, and is typically less than 5ms. While the inlet valve 15 is open,

the gas pressure created within the vacuum system rapidly increases. In theory,

the vacuum system will reach an equilibrium pressure after the pump down time

constant. This is defined as the volume of the ion trap chamber divided by the

effective pumping speed. For example, assuming that the vacuum chamber has a volume of 1 litre and the effective pumping speed for the chamber is 50 litres per

second the pump down time constant is 20ms. This time interval is the time

needed to approach an equilibrium pressure starting from the time when the inlet

valve 15 is opened. The high pressure head at the valve inlet might result in a

pressure well above 10 ^" 'mbar, and this would prevent the turbomolecular pump

from operating if the inlet valve 15 were to be held open continuously. However,

the inlet valve 15 is closed (typically after <5ms) well before the equilibrium

pressure is reached and so the only region of the first ion trap chamber exposed to

the high initial pressure is that in the immediate vicinity of the gas inlet tube 16,

and this pressure will start to fall as soon as the inlet valve 15 is closed.

With a pump down time constant of 20ms, the pressure within the ion trap

chamber may fall from 5x10 ^~2 mbar to below 1 xlO ^"3 mbar in about 60ms. It will

be appreciated that this time estimate does not take account of the detailed

structure within the ion trap chamber, nor the influence of absorption/desorption

and so, in reality, a longer time interval may be needed. Nevertheless, the

described operating procedure does enable a short, high pressure gas pulse to be

generated causing rapid cooling of high kinetic energy ions generated within the

ion trap by the pulsed ion source without the need for any differential pumping.

After a pulse of cooling gas has been injected into the vacuum system there will be

a delay (typically 10ms) before the pulsed ion source is activated, in order to allow

the gas pressure to build up. It normally takes 60ms or more to pump the gas

pressure down and so it is possible to direct a succession of laser pulses onto

sample S during that period so as to generate additional ions for analysis during the same analysis cycle.

As the pressure of cooling gas is reduced by pumping, trapped ions are able to

migrate towards the bottom of the afore-mentioned potential well where they may

congregate to form a short, ovoid ion cloud and the trapped ions may subsequently be ejected from this low energy region.

Before any ions are ejected from the first ion trap 10, a the rectangular waveform

digital drive voltage supplied to the second ion trap 20 is either switched off

altogether or is set at a reduced level lower than that determined by the mass range

of ions that are to be analysed so as to enable ejected ions to enter the trapping

volume of the second ion trap 20. In this regard, use of a high frequency

rectangular waveform digital drive voltage generated by a switching circuit is

advantageous because it can be readily switched off.

In order to eject trapped ions from the first ion trap 10, the gate electrode 18 is

biased at a DC potential that is less positive (for positively charged ions) or less

negative (for negatively charged) than the average DC potential on poles 11.

Curve 22 of Figure 2 illustrates the variation of DC potential along the axis of the

first ion trap during the ejection process and, as will be clear from curve 22, the

DC potential on the gate electrode 18 is well below (typically several tens to

several hundreds of volts below) the DC potential on poles 11, thereby subjecting

the trapped ions to an accelerating force towards the gate electrode 18 causing

their rapid ejection from the first ion trap.

For analyte ions having a mass of 10,000Da the time needed for ejected ions to

reach the centre of the second ion trap may be 40 to 50μs, and ions having higher

or lower masses than this will require longer or shorted times respectively. As

shown by curve 22 of Figure 2, the DC potential on the entrance end cap electrode

22 of the second ion trap 20 is set so as to subject the ejected ions to a retarding

force in the second ion trap. The variation of DC potential on the longitudinal axis

of the second ion trap 20 can be tailored to have a substantially inverted quadratic

form, as shown in Figure 2, and so the lighter, faster ions, which enter the second

ion trap first, are slowed down allowing the heavier, slower ions to catch up

thereby widening the mass range of ions that can be trapped in the second ion trap

and improving the efficiency of transfer. When substantially all the ejected ions

have reached the centre of the second ion trap 20 the high frequency rectangular

waveform digital drive voltage is switched back on, or restored to its normal level,

creating a psuedopotential well for trapping the ions that were transferred. This is

represented by curve 23 of Figure 2.

While cooling gas is being supplied to, and pumped from the first ion trap 10,

some of the cooling gas may diffuse into the second ion trap 20. When ions are

transferred from the first ion trap 10 to the second ion trap 20 the pressure of the

cooling gas in the second ion trap 20 could reach a pressure of about lxlθ ^'3 mbar,

which is entirely suitable for cooling ions and carrying out mass analysis

procedures. Such mass analysis procedures include precursor isolation, collision

induced dissociation and mass dependent ejection, and are well known to persons

of ordinary skill in the art.

The first ion trap 10, described with reference to Figure 1, has a single set of poles

1 1 and it proves difficult satisfactorily to adjust the variation of DC potential along

the axis of ion trap unless the poles 11 are relatively short.

Figure 3(a) shows an alternative embodiment of the invention which alleviates this

problem; in all other respects its operation is substantially the same as the

embodiment described with reference to Figure 1. Many of the component parts

shown in Figure 3(a) are in common with those shown in Figure 1 and are ascribed

like reference numerals.

Referring to Figure 3 (a), each pole 11 is segmented, comprising a relatively long

segment 11 * and a shorter segment I I ¹¹ adjacent to the gate electrode 18.

In this embodiment, the high frequency rectangular waveform digital drive voltage

is supplied to both segments I I ¹ , I I ¹¹ of the poles via a capacitive coupling 30,

and a DC voltage source 31 supplies a DC bias voltage to the shorter segment I I ¹¹

reducing the axial DC potential on the segment with respect to both the axial DC

potential on the longer segment 11 * and on the gate electrode 18 thereby creating a

relatively narrow potential well within which a relatively short packet of ions may

be trapped. When the packet of ions is to be ejected from the first ion trap 10, the

DC potential on the gate electrode 18 is reduced below the DC potential on the

shorter segment I I ¹¹ causing rapid acceleration of the ion packet out of the first

ion trap 10 towards the second ion trap 20.

A further advantage of using a segmented linear ion trap is that the effect of

fringing fields is much reduced, making removal of unwanted ions easier. After

the pressure of cooling gas has been reduced to a pressure below 10 ^~3 mbar,

unwanted ions may be ejected from the ion trap by application of a suitable mass

selective ejection process. This may involve application of a quadrupole DC

voltage to the poles while the amplitude and or frequency of the high frequency

drive voltage is adjusted so as to retain, for subsequent analysis in the second ion

trap 20, only those ions in a selected mass-to-charge ratio and thereby achieve an

acceptable mass resolution for precursor ion selection (up to a few hundreds).

Alternatively, the mass selective ejection process may involve use of a broadband

supplementary drive voltage using the known "SWIFT" or "FNT" technologies,

for example.

In a different embodiment, shown in Figure 3(b), the first ion trap 10 includes a

ring electrode 32 positioned between the poles 11 and the gate electrode 18. The

DC voltage source 31 biases the ring electrode 32 with a DC potential which is a

few volts lower than the average axial DC potential on the poles 11 creating an

axial potential well at the centre of the ring electrode 32. Ions that have been

cooled by the cooling gas will steadily migrate to this point and become trapped in

the axial direction by the DC potential well being constrained in the radial

direction by the fringing quadrupole field generated by the high frequency drive

voltage supplied to the poles 11, and they remain in the potential well until they

are ejected from the first ion trap 10 by reducing the DC potential on the gate

electrode 18 in the manner already described.

Figure 4 shows yet another embodiment of the invention. Again, many of the

component parts shown in Figure 4 are in common with those shown in Figures 1

and 3 and are ascribed like reference numerals. In this embodiment, a cylindrical

ion trap 40 replaces the linear ion trap 10 of the embodiments described with reference to Figures 1 and 3.

The cylindrical ion trap 40 comprises a cylindrical ring electrode 41 which is

supplied with a suitable high frequency drive voltage which may be a high

frequency rectangular waveform digital drive voltage or alternatively a sinusoidal

waveform drive voltage.

As before, the sample plate 14 forms an end wall at the front end of the ion trap 40

and, in this embodiment, the gate electrode 18 also forms an end wall at the rear

end of the ion trap 40. Again, the pulsed ion source is a MALDI ion source and in

this embodiment laser pulses are directed onto the sample S along the longitudinal

axis X-X of the first and second ion traps. Alternatively, the laser pulses could be

directed onto the sample via a suitable window formed in the cylindrical ring

electrode 41. A sample mask 42 is also provided. A part of sample S which is to

be exposed to the laser pulses is aligned with an opening 43 in the sample mask 42

whereas other parts of the sample S are protected from such exposure, and from

exposure to ions generated as a result of the ionisation process. The timing of the

laser pulses preferably has a predetermined phase relationship with respect to the waveform of the drive voltage applied to the cylindrical ring electrode 41. As

illustrated in Figure 5, the optimum timing for the generation of positively-charged

ions is when the phase of the drive voltage is between 270° and 350°, as

represented by arrow 51, whereas the optimum timing for the generation of

negatively-charged ions is when the phase of the drive voltage is between 90° and

170°, as represented by arrow 52, these phases being referenced with respect to 0°

phase which occurs at the zero crossing time on the rising part of each waveform.

As described before, a pulse of cooling gas is injected into the interior of the first

ion trap 40 via tube 16 and the pressure of cooling gas is subsequently reduced by

pumping. Again, the timings of the pulsed irradiation of sample S and of the

injection of cooling gas are synchronised, with a short delay after the cooling gas

is injected. As a result of this, an ion cloud is trapped at the centre of the first ion

trap 40.

In order to eject the trapped ions a dipole electric field is rapidly established

between the sample plate 14 and the gate electrode 18 subjecting the trapped ions

to an accelerating force in the direction of the second ion trap 20. At the same

time, a dipole electric field, of opposite polarity, is established between the two

end cap electrodes 22, 23 of the second ion trap 20 whereby ions entering the

trapping volume of the second ion trap 20 are retarded and brought to a halt near

the centre of the ion trap. While ions are being transferred in this way, the high

frequency drive voltages supplied to both ion traps are turned off or set at a

reduced level. An additional electrostatic lens 44 is provided between the first and

second ion traps 40, 20 to focus ions as they are being transferred.

A variation of axial DC potential on axis X-X can be modified by appropriately

biasing the sample plate 14, gate electrode 18 and ring electrode 41 of the first ion trap 40 and the two end cap electrodes 22,23 and the ring electrode 21 of the

second ion trap 20, and this can be used to influence the characteristics of ion

transfer whether to improve the efficiency with which ions are transferred between

the ion traps and/or to increase the mass range of ions that are transferred.

PCT/CA2005/00086 describes an ion trap arrangement having a tunnel structure

formed from printed circuit board (PCB) bearing electrically conductive tracks

that can be used to generate electric fields required for ion trapping, transmission

of ions between trapping and analysis sections of the arrangement, and ion

analysis.

Figure 6 shows another embodiment of the invention which is based on this kind

of arrangement.

Referring to Figure 6, the mass spectrometer comprises a first linear ion trap 61

and a second linear ion trap 71 which are arranged in series on a common

longitudinal axis X-X.

As already described, the two ion traps 61,71 have a tunnel structure, being

formed from PCB 62 bearing electrically conductive tracks supplied with

appropriate high frequency drive and DC bias voltages. As before, the first ion

trap 61 is used to trap ions generated by a pulsed ion source and the second ion

trap 71 is used to receive and analyse ions ejected from the first ion trap 61.

Again, the pulsed ion source is the preferred MALDI ion source. Laser pulses are

directed along axis X-X and are focused by a suitable lens system 69 onto sample

S deposited on a sample plate 65 which forms an end wall at the front end of the first ion trap 61.

The two linear ion traps 61,71 are separated by a gate electrode 63 having an

orifice. Tons generated by the pulsed ion source are trapped within the first ion

trap 61 with the assistance of pulsed cooling gas introduced into the interior of the

first ion trap 61 via tube 67 in the manner already described with reference to the

earlier embodiments. As before, the pressure of cooling gas is reduced by

pumping.

The electrically conductive tracks are capable, when supplied with suitable high

frequency drive and DC bias voltages, of generating trapping multipole fields for

confining ions in the radial direction and DC fields for trapping or transferring

ions axially within the tunnel structure. By this means, ions trapped in the first ion

trap 61 are readily transferred to the second ion trap 71 in known manner for

analysis. The second ion trap 71 includes an ion detector 64 which detects ions

ejected from the second ion trap 71 by a mass selective ejection technique in a

direction orthogonal to axis X-X.

Figure 7 shows an alternative embodiment of the invention having a tunnel

structure similar to that described with reference to Figure 6. This embodiment

has component parts in common with the embodiment described with reference to

Figure 6, and these are ascribed like references numerals.

The embodiment differs from that of Figure 6, in that the first and second ion traps

61,71 are arranged side-by-side on mutually parallel axes X-X, Y-Y. As before,

the first ion trap 61 is used to trap ions generated by a pulsed ion source (again a

MALDI ion source) with the assistance of pulsed, high pressure cooling gas

introduced into the interior of the ion trap via tube 67. Again, the sample plate 65

forms an end wall of the first ion trap 61 and laser pulses are focused onto sample

S along axis X-X. Trapped ions are ejected from the first ion trap 61 and are

transferred via a suitable slit or hole into the second ion trap 71, for analysis, in a

direction orthogonal to axes X-X and Y-Y. This may be accomplished using

dipole acceleration in the first ion trap 61 and dipole retardation in the second ion

trap 71 in similar fashion to the ejection process described with reference to Figure

3. In this embodiment, the required transverse electrical fields are generated by

application of suitable pulsed voltage to electrically conductive tracks on the PCB

structure. As in the case of the embodiment described with reference to Figure 6,

the second ion trap 71 includes an ion detector 64 which detects ions ejected from

the second ion trap 71 using mass selective ejection in a direction orthogonal to

axes X-X and Y-Y. Furthermore, provided the pressure of cooling gas in the first

ion trap 61 is reduced by pumping to an appropriate level, ions in a selected mass

range may be transferred to the second ion trap 71 using mass selective resonance

ejection whereby tandem mass analysis can be carried out.

In general, the described embodiments employ a pulsed ion source in combination

with a dynamic gas pressure enabling high efficiency cooling of ions as well as

improved ion mobility during ion transportation thereby reducing or eliminating

the need for differential pumping which would otherwise add to the cost and

complexity of the instrument, and improving the efficiency with which ions maybe

trapped in the first ion trap and subsequently ejected for mass analysis in the

second ion trap. Whereas some embodiments have been described with reference

to positively charged ions, negatively charged ions may be readily accommodated

by simple reversing polarities as necessary as will be apparent to those of ordinary skill in the art.