Note: Descriptions are shown in the official language in which they were submitted.
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MASS SPECTROMETER
The present invention relates to mass
spectrometers.
With the decoding of the 20-30,000 genes that
compose the human genome, emphasis has switched to the
identification of the translated gene products that
comprise the proteome. Mass spectrometry has firmly
established itself as the primary technique for
idenaifying proteins due to its unparalleled speed,
sensitivity and specificity. Strategies can involve
either analysis of the intact protein, or more commonly
digestion of the protein using a specific protease that
cleaves at predictable residues along the peptide
backbone. This provides smaller stretches of peptide
sequence that are more amenable to analysis via mass
spectrometry.
The mass spectrometry technique providing the
highest degree of specificity and sensitivity is
Electrospray ionisation ("ESI") interfaced to a tandem
mass spectrometer. These experiments involve separation
of the complex digest mixture by microcapillary liquid
chromatography with on-line mass spectral detection
using automated acquisition modes whereby conventional
MS and MS/MS spectra are collected in a data dependant
manner. This information can be used directly to search
databases for matching sequences leading to
identification of the parent protein. This approach can
be used to identify proteins that are present at low
endogenous concentrations. However, often the limiting
factor for identification of the protein is not the
quality of the MS/MS spectrum produced but is the
initial discovery of the multiply charged peptide
precursor ion in the MS mode. This is due to the level
of background chemical noise, largely singly charged in
nature, which may be produced in the ion source of the
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mass spectrometer. Fig. 1 shows a typical conventional
mass spectrum and illustrates how doubly charged species
may be obscured amongst a singly charged background. A
method whereby the chemical noise is reduced so that the
mass spectrometer can more easily target peptide related
ions would be highly advantageous for the study of
protein digests.
A known method used to favour the detection of
multiply charged species over singly charged species is
to use an Electrospray ionisation orthogonal
acceleration time of flight mass analyser ("ESI-oaTOF").
The orthogonal acceleration time of flight mass analyser
counts the arrival of ions using a Time to Digital
Converter ("TDC") which has a discriminator threshold.
The voltage pulse of a single ion must be high enough to
trigger the discriminator and so register the arrival of
an ion. The detector producing the voltage may be an
electron multiplier or a Microchannel Plate detector
("MCP"). These detectors are charge sensitive so the
size of signal they produce increases with increasing
charge state. Discrimination in favour of higher charge
states can be accomplished by increasing the
discriminator voltage level, lowering the detector gain,
or a combination of both. Fig. 2(a) shows a mass
spectrum obtained: with normal detector gain and Fig.
2(b) shows a comparable: mass spectrum obtained with a
reduced detector gain. An important disadvantage of
lowering the detector gain (or of increasing the
discriminator level) is that the sensitivity is lowered.
As can be seen from the ordinate axes of Figs. 2(a) and
(b), the sensitivity is reduced by a factor of
approximately x4 when ~ lower detector gain is employed.
Using this method it is also impossible to pick out an
individual charge state. Instead, the best that can be
achieved is a reduction of the efficiency of detection
of lower charge states with respect to higher charge
states.
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Another ionisation technique that has been recently
coupled to tandem mass spectrometers for biological mass
spectrometry is Matrix Assisted Laser Desorption
Ionisation ("MALDI"). G~hen a MALDI ion source is used
high levels of singly charged matrix related ions and
chemical noise are generated which make it difficult to
identify candidate peptide ions.
It is therefore desired to provide an improved mass
spectrometer and method of mass spectrometry which does
not suffer from some or all of the disadvantages of the
prior art.
According to a first aspect of the present
invention, there is provided a method of mass
spectrometry, comprising the steps of:
providing a packet or pulse of ions;
temporally separating at least some of the ions in
the packet or pulse according to their ion mobility in a
first device;
mass filtering at least some of the ions according
to their mass to charge ratio in a second device;
progressively varying a mass filtering
characteristic of the second device so that ions having
a first charge state are onwardly transmitted in
preference to ions having a second different charge
state;
trapping some ions having the first charge state in
a first ion trap;
releasing a first group of ions from the first ion
trap and orthogonally accelerating the first group of
ions a first predetermined time later;
mass analysing the first group of ions;
trapping further ions having the first charge state
in the first ion trap;
releasing a second group of ions from the first ion
trap and orthogonally accelerating the second group of
ions a second different predetermined time later; and
mass analysing the second group of ions.
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Advantageously, ions with a chosen charge state can
be selected from a mixture of ions having differing
charge states. Another advantage is that sensitivity
for this technique is greater than the known
discriminator level technique as the detector can be run
at full gain and all ions present may be counted.
According to the preferred embodiment the charge
state selection is achieved by coupling an ion mobility
spectrometer to a quadrupole mass filter.
As will be explained in more detail later, at any
instance in time the mass to charge ratio of ions
exiting the combination of the ion mobility spectrometer
and the quadrupole mass filter can be predicted.
Therefore, the mass to charge ratio of ions present in
the first ion trap at any instance can be predicted. A
group of ions having a relatively narrow spread of mass
to charge ratios can be pulsed or otherwise ejected from
the first ion trap and a predetermined time later the
pusher/puller electrode of a TOF mass analyser can be
energised so ws to orthogonally accelerate the ions into
the drift region of the TOF mass analyser. The
predetermined time (or delay time) can be optimised to
that of the mass to charge ratios of the ions present
and hence ejected from the first ion trap at any point
in time. Accordingly, the ions released from the first
ion trap are orthogonally accelerated with a very high
(approximately 100%) duty cycle_(as will be appreciated
by those skilled in the art, if ions having a wide range
of mass to charge ratios were to be simultaneously
ejected from the first ion trap then only a small
percentage (typically < 25~) of those ions would then be
orthogonally accelerated).
In due course ions having higher average mass to
charge ratios will exit the combination of the ion
mobility spectrometer and the quadrupole mass filter and
will therefore be present in the first ion trap. These
ions are released from the first ion trap in another
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pulse but the delay time of the pusher electrode is
increased thereby maintaining a high duty cycle.
By repeating this process a number of times a duty
cycle approaching 100 for ions having the chosen charge
states) across the whole mass range can be achieved.
This represents a significant improvement in sensitivity
over conventional methods.
According to a second aspect of the present
invention, there is provided a method of mass
spectrometry, comprising the steps of:
providing a packet or pulse of ions;
temporally separating at least some of the ions in
the packet or pulse according to their ion mobility in a
first device;
mass filtering at least some of the ions according
to their mass to charge ratio in a second device;
progressively varying a mass filtering
characteristic of the second device so that ions having
a first charge state are onwardly transmitted in
preference to ions having a second different charge
state;
fragmenting or reacting at least some of the ions
having the first charge state into fragment ions or
forming product ions;
trapping at least some of the fragment or product
ions in a first ion trap; and
sending at lest some of the fragment or product
ions upstream of the first ion trap.
According to the first aspect of the invention it
is possible to achieve a 100% duty cycle because the
parent ions present in the first ion trap at any
particular point in time have a narrow spread of mass to
charge ratios. However, according to the second aspect-
~of the invention ions are fragmented or reacted within
the first ion trap. Therefore, once the ions have been
fragmented or reacted in the first ion trap the ions
present in the first ion trap (gas cell) will have a
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wide range of mass to charge ratios. According to the
preferred embodiment the first ion trap (gas cell)
comprises an ion tunnel ion trap/collision cell which is
not mass selective. Therefore, it is not possible to
simply optimise the ejection of fragment or product ions
from the first ion trap with the TOF mass analyser and
hence a high duty cycle across the mass range can not be
achieved.
It is therefore a feature of the second aspect of
the present invention that instead of releasing fragment
or product ions from the first ion trap and sending the
ions directly downstream to the TOF mass analyser (which
would result in a low duty cycle), the fragment or
product ions are instead sent back upstream of the first
ion trap.
As will be described in more detail in relation to
further embodiments of the present invention, once the
fragment or product ions have been sent upstream they
can then be passed through the ion mobility spectrometer
which separates the fragment or product ions according
to their ion mobility: The fragment or product ions can
then be trapped in the first ion trap and the pusher
electrode of the TOF mass analyser can be arranged to be
energised a predetermined period of time after fragment
or product ions have been released from the.first ion
trap so as to optimise the duty cycle. As fragment or
product ions having higher mass to charge ratios
subsequently arrive at the first ion trap, the delay
time of the pusher electrode can be progressively
increased. As a resultthe fragment or product ions can
be mass analysed with a very high (approximately 1000
duty cycle. This represents a further significant
advance in the art.
The fragment or product ions which are sent
upstream preferably pass through the second device
and/or the first device: In such circumstances, the
second device is arranged to transmit the fragment or
s~ r)
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product ions without substantially mass filtering them.
The fragment or product ions are then preferably trapped
in a second ion trap upstream of the first device.
According to the preferred embodiment, multiply
charged ions (which may include doubly, triply and
quadruply charged ions and ions having five or more
charges) may be preferentially selected and transmitted
whilst the intensity of singly charged ions may be
reduced. In other embodiments any desired charged state
or states may be selected. For example, two or more
multiply charged states may be transmitted.
The second device preferably comprises a quadrupole
rod set mass filter. The quadrupole mass filter may be
operated as a high pass mass to charge ratio filter so
as to transmit substantially only ions having a mass to
charge ratio greater than a minimum value. In this
embodiment multiply charged ions can be preferentially
transmitted compared to singly charged ions i.e. doubly,
triply, quadruply and ions having five or more charges
may be transmitted whilst singly charged ions are
attenuated.
According to another embodiment; the quadrupole
mass filter may be operated as a band pass mass to
charge ratio filter so as to substantially transmit only
ions having a mass to charge ratio greater than a
minimum value and smaller than a maximum value. This
embodiment is particularly advantageous in that multiply
charged ions of a single charge state e.g. triply
charged, may be preferentially transmitted whilst ions
having any other charge state are relatively attenuated.
However, according to another embodiment ions having two
or more neighbouring charge states (e.g. doubly and
triply charged ions) may be transmitted and all other
charge states may be attenuated. Embodiments are also
contemplated wherein non-neighbouring charge states are
selected (e.g. doubly and quadruply charged ions) to the
preference of other charge states.
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The quadrupole mass.filter is preferably.scanned so
that the minimum mass to charge ratio cut-off is
progressively increased during a cycle (which is defined
as the period between consecutive pulses of ions being
admitted into the ion mobility spectrometer). The
quadrupole mass filter may be scanned in a substantially
continuous (i.e. smooth) manner or alternatively the
quadruple mass filter may be scanned in a substantially
stepped manner.
Other embodiments are contemplated wherein the
second device comprises either a 2D ion trap (e.g. a rod
set with front arid/or rear trapping electrodes) or a 3D
ion trap (e.g. a central ring electrode with front and
rear endcap electrodes).
At the upstream end of the mass spectrometer, the
ion source may be a pulsed ion source such as a Matrix
Assisted Laser Desorption Ionisation ("MALDI") ion
source. The pulsed ion source may alternatively
comprise a Laser Desorption Ionisation ion source which
is not matrix assisted.
Alternatively, and more preferably, a continuous
ion source may be used in which case an ion trap for
storing ions and periodically releasing ions is also
preferably provided. Continuous ion sources which may
be used include Electrospray, Atmospheric Pressure
Chemical Ionisation ("APCI"); Electron Impact ("EI"),
Atmospheric Pressure Photon Ionisation ("APPI") and
Chemical Ionisation ("CI") ion sources. Other
continuous or pseudo-continuous ion sources may also be
used. In an embodiment the mass spectrometer may be a
Fourier Transform mass spectrometer or a Fourier
Transform Ion Cyclotron Resonance mass spectrometer.
According to a third aspect of the present
invention there is provided a method of mass
spectrometry, comprising the steps of:
providing a packet or pulse of fragment or product
ions;
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temporally separating at least some of the fragment
or product ions in the packet or pulse according to
their ion mobility in a first device;
trapping some fragment or product ions having a
first ion mobility in a first ion trap;
releasing a first group of fragment or product ions
from the first ion trap and orthogonally accelerating
the first group of ions a first predetermined time
later;
mass analysing the first group of ions;
trapping further fragment or product ions having a
second different ion mobility in the first ion trap;
releasing a second group of fragment or product
ions from the first ion trap and orthogonally
accelerating the second group of ions a second different
predetermined time later; and
mass analysing the second group of ions.
According to this embodiment fragment or product
ions can be mass analysed with a very high
(approximately 100%) duty cycle.
The first device preferably comprises anion
mobility spectrometer or other ion mobility device.
Ions in an ion mobility spectrometer may be subjected to
an electric field in the presence of a buffer gas so
that different species of ion acquire different
velocities and are temporally separated according to
their ion mobility. The mobility of an ion in an ion
mobility spectrometer typically depends inter alia upon
its mass and its charge. Heavy ions with one charge
tend to have lower mobilities than light ions with one
charge. Also an ion of a particular mass to charge
ratio with one charge tends to have a lower mobility
than an ion with the same mass to charge ratio but
carrying two (or more) charges-.
The ion mobility spectrometer may comprise a drift
tube together with one or more electrodes for
maintaining an axial DC voltage gradient along at least
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CA 02407957 2002-10-11
a portion of the drift tube.
Alternatively, the ion mobility spectrometer may
comprise a Field Asymmetric Ion Mobility Spectrometer
("FAIMS"). In one embodiment the FAIMS may comprise two
5 parallel plates. In another embodiment the FAIMS may
comprise two axially aligned inner cylinders surrounded
by a long outer cylinder. The outer cylinder and a
shorter inner cylinder are preferably held at the same
electrical potential. A longer inner cylinder may have
10 a high frequency high voltage asymmetric waveform
applied to it, thereby establishing an electric field
between the inner and outer cylinders. A compensation
DC voltage is also applied to the longer inner cylinder.
A FAIMS acts like a mobility filter and may operate at
atmospheric pressure.
However, according to a particularly preferred
embodiment, the ion mobility spectrometer may comprise a
plurality of electrodes having apertures wherein a DC
voltage gradient is maintained across at least a portion
of the ion mobility spectrometer and at least some of
the electrodes are connected to an AC or RF voltage
supply. The ion mobility spectrometer is particularly
advantageous in that the addition of an AC or RF voltage
to the electrodes (which may be ring like or otherwise
annular) results in radial confinement of the ions
passing through the ion mobility.spectrometer. Radial
confinement of the ions results in higher ion
transmission compared with ion mobility spectrometers of
the drift tube type.
The ion mobility spectrometer preferably extends
between two vacuum chambers so that an upstream section
comprising a first plurality of electrodes having
apertures is arranged in a vacuum chamber and a
downstream section comprising a second plurality of
electrodes having apertures is arranged in a further
vacuum chamber, the vacuum chambers being separated by a'
differential pumping aperture.
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At least some of the electrodes in the upstream
section are preferably supplied with an AC or RF voltage
having a frequency within the range 0.1-3.0 MHz. A
frequency of 0.5-1.1 MHz is preferred and a frequency of
780 kHz is particularly preferred. The upstream section
is preferably arranged to be maintained at a pressure
within the range 0.1-10 mbar, preferably approximately 1
mbar.
At least some of the electrodes in the downstream
section are preferably supplied with an AC or RF voltage
having a frequency within the range 0.1-3.0 MHz. A
frequency of 1.8-2.4 MHz is preferred and a frequency of
2.1 MHz is particularly preferred. The downstream
section is preferably arranged to be maintained at a
pressure within the range 10-3-10-2 mbar.
The voltages applied to the electrodes in the
upstream section may be such that a first DC voltage
gradient is maintained in use across at least a porti.on~
of the upstream sectiori and a second different DC
voltage gradient may be maintained in use across at
least a portion of the downstream section. The first DC
voltage gradient is preferably greater than the second
DC voltage gradient. Both voltage gradients do not
necessarily need to be linear and indeed a stepped
voltage gradient is particularly preferred.
Preferably, the ion mobility spectrometer comprises
at least 10, 20, 30, 40, 50, 60, 70, 80. 90 or 100
electrodes. Preferably, at least 60%, 65~, 70~, 75~,
80~, 85~, 90~, 95~ of the electrodes forming the ion
mobility spectrometer have apertures which are of
substantially the same size or area. In a particularly
preferred embodiment the ion mobility spectrometer
comprises an ion tunnel comprising a plurality of
electrodes all having substantially similar sized
apertures through which ioris are -transmitted.
An orthogonal acceleration time of flight mass
analyser is particularly preferred although other types
g1
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of mass analysers such as a quadrupole mass analysers or
2D or 3D ion traps may be used according to less
preferred embodiments.
According to a fourth aspect of the present
invention, there is provided a mass spectrometer
comprising:
a first device for temporally separating a pulse or
packet of ions according to their ion mobility;
a second device for mass filtering at least some of
the ions in the packet or pulse according to their mass
to charge ratio, wherein a mass filtering characteristic
of the second device is progressively varied so that
ions having a first charge state are onwardly
transmitted in preference to ions having a second charge
state;
a first ion trap for trapping ions having the first
charge state; and
a mass analyser comprising an electrode for
orthogonally accelerating ions;
wherein the first ion trap is arranged to trap some
ions having the first charge state and then release a
first group of ions which are then orthogonally
accelerated by the electrode a first predetermined time
later and then subsequently mass analysed by the mass
analyser, and wherein the first.ion trap is further
arranged to trap further ions having the first charge
state and then release a second group of ions which are
then orthogonally accelerated by the electrode a second
different predetermined time later and then subsequently
mass analysed by the mass awalyser.
According to a fifth. aspect of the present
invention, there is provided a mass spectrometer
comprising:
a first device for temporally separating a pulse or
packet of ions according to their ion mobility;
a second device for mass filtering at least some of
the ions in the packet or pulse according to their mass
,i
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to charge ratio, wherein a mass filtering characteristic
of the second device is progressively varied so that
ions having a first charge state are onwardly
transmitted i:n preference to ions having a second charge
state;
a first ion trap comprising a gas.for fragmenting
ions into fragment ions or reacting with ions to form
product ions;
wherein the first ion trap is arranged to trap at
least some fragment or product ions and then send the
fragment or product ions upstream of the first ion trap.
According to a sixth aspect of the present
invention there is provided a mass spectrometer
comprising:
a first device for temporally separating at least
some fragment or product ions according to their ion
mobility;
a first ion trap downstream of the first device;
a second ion trap upstream of the.first device; and
a mass analyser comprising an electrode for
orthogonally accelerating ions;
wherein the second ion trap is arranged to release
a packet or pulse of fragment or product ions so that
the fragment or product ions are temporally separated
according to their ion mobility in the first device; and
wherein the first ion trap is arranged to trap some
fragment or product ions having a first ion mobility and
then release a first group of ions so that the first
group of ions is orthogonally accelerated by the
electrode a first predetermined time later and then
subsequently mass analysed by the mass analyser and
wherein the first ion trap is further arranged to trap
further fragment or product ions having a second
different ion mobility and then release a second group
of ions so that the second group of ions is orthogonally
accelerated by the electrode a second different
predetermined time later and then subsequently mass
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analysed by the mass analyser.
According to a seventh aspect of the present
invention, there is provided a method of mass
spectrometry, comprising the steps of:
selecting ions having a desired charge states)
whilst filtering out ions having an undesired charge
state(s);
trapping ions having the desired charge states) in
an ion trap; and
synchronising the release of ions from the ion trap
with the operation of aWelectrode for orthogonally
accelerating ions so that at'least 70%, 80%, or 90~ of
the ions released from the ion trap are orthogonally
accelerated by the electrode.
Preferably, the step of selecting ions having a
desired charge states) comprises passing ions through
an ion mobility spectrometer whilst scanning a
quadrupole mass filter.
According to an eighth aspect of the present
invention there is provided a mass spectrometer,
comprising:
a device for selecting ions having a desired charge
states) whilst filtering out ions having an undesired
charge state(s);
an ion trap for trapping ions having a desired
charge state(s); and
wherein the ion trap is arrangedto release ions in
synchronisation with the operation of an electrode for
orthogonally accelerating ions so that at least 70%,
80~; or 90% of the ions released from the ion trap are
orthogonally accelerated by the electrode.
Preferably, the device for selecting ions'comprises
an ion mobility spectrometer and a quadrupole mass
filter which is scanned in use.
According to a ninth aspect of the present
invention there is provided a method of mass
spectrometry, comprising the steps of:
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selecting ions having a desired charge states)
whilst filtering out ions having an undesired charge
state(s);
fragmenting or reacting at least some of the ions
having a desired charged states) into fragment or
product ions;
trapping at least some of the fragment or product
ions in an ion trap; and
sending at least some of the fragment or product
ions upstream of the ion trap.
Preferably, the step of selecting ions having a
desired charge states) comprises passing ions through
an ion mobility spectrometer whilst scanning a
quadrupole mass filter.
According to a tenth aspect of the present
invention there is provided a mass spectrometer
comprising:
a device for selecting ions having a desired charge
states) whilst filtering out ions having an undesired
charge state(s); and
a device for fragmenting or reacting at least some
of the ions having a desired charge states) so as to
form fragment or product ions;
a device for trapping the fragment or product ions;
and
wherein the device for trapping ions is arranged to
send at least some of the fragment or product ions
upstream of the device for trapping ions.
Preferably, the device for selecting ions comprises
an ion mobility spectrometer and a quadrupole mass
filter which is scanned in use.
According to an eleventh aspect of the present
invention there is provided a method of mass
spectrometry, comprising the steps of:
separating fragment or product ions according to
their ion mobility;
trapping some fragment or product ions in an ion
r'
CA 02407957 2002-10-11
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trap; and
synchronising the release of fragment or product
ions from the ion trap wi h the operation of an
electrode for orthogonally accelerating ions so that at
least 70%, 800, or 90~ of the fragment or product ions
released from the ion trap are orthogonally accelerated
by the electrode.
Preferably, the step of separating fragment or
product ions comprises passing the fragment or product
ions through an ion mobility spectrometer.
According to a twelfth aspect of the present
invention, there is provided a mass spectrometer,
comprising:
a device for separating fragment or product ions
according to their ion mobility; and
an ion trap for trapping some fragment or product
ions;
wherein the ion trap is arranged to release
fragment or product ions in synchronisation with the
operation of an electrode for orthogonally accelerating
ions so that at least 70%, 80%, or 90~ of the fragment
or product ions released from the ion trap are
orthogonally accelerated by the electrode..
Preferably, the device for separating fragment or
product ions comprises an ion mobility spectrometer.
Various embodiments of the present invention will
now be described, by way of example only, and with
reference to the accompanying drawings in which:
Fig. 1 shows a conventional mass spectrum;
Fig. 2(a) shows a conventional mass spectrum
obtained with normal detector gain, and Fig. 2(b) shows
a comparable mass spectrum obtained by lowering the
detector gain;
Fig. 3 shows the known relationship between flight
time in a time of flight mass analyser drift region
versus drift time in an ion mobility spectrometer for
various singly and doubly charged ions;
to
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Fig. 4 shows an experimentally determined
relationship between the mass to charge ratio of a
sample of singly and doubly charged ions and their drift
time through an ion_mobility spectrometer;
Fig. 5 illustrates the general principle of
filtering out singly charged ions according to a
preferred embodiment;
Fig. 6 illustrates the general principle of
selecting ions having a specific charge. state according
to a preferred embodiment;
Fig. 7 shows a preferred embodiment of the present
invention;
Fig. 8(a) illustrates a preferred embodiment of an
ion trap, ion gate and ion mobility spectrometer, Fig.
8(b) illustrates the various DC voltages which may be
applied to the ion trap, ion gate and ion mobility
spectrometer, Fig. 8(c) illustrates how the DC voltage
applied to the ion gate may vary as a function of time,
and Fig. 8(d) illustrates how a quadrupole mass filter
may be scanned according to a preferred embodiment;
Fig. 9 illustrates how the duty cycle of an ion
trap-time of flight mass analyser increases to
approximately 100% for a relatively narrow mass to
charge ratio range compared with a typical maximum duty
cycle of approximately 25% obtained by operating the
time of flight mass analyser in a conventional manner;
Fig. 10 illustrates a first mode of operation
according to a preferred embodiment wherein precursor
ions having a particular desired charge states) are
selected and subsequently mass analysed with a 100% duty
cycle;
Fig. 1l illustrates a second mode of operation
according to the preferred embodiment wherein precursor
ions having a desired charge states) are fragmented or
reacted and stored in a first ion trap;
Fig. 12 illustrates a third mode of operation
according to the preferred embodiment wherein fragment
W
CA 02407957 2002-10-11
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or product ions which have been accumulated in the first
ion trap are sent back to an upstream ion trap whilst
ions continue to be accumulated from the ion source;
Fig. 13 illustrates a fourth mode of operation
according to the preferred embodiment wherein fragment
or product ions are separated according to their ion
mobility and are subsequently mass analysed with a 100
duty cycle; and
Fig. 14 shows a typical experimental cycling of
modes of operation.
Various embodiments of the present invention will
now be described: Fig. 3 shows the known relationship
of flight time in a drift region of a time of flight
mass analyser versus drift time in an ion mobility
spectrometer for various singly and doubly charged ions.
An experimentally determined relationship between the
mass to charge ratio of ions and their drift time
through an ion mobility spectrometer is shown in Fig. 4.
This relationship can be represented by an empirically
derived polynomial expression. As can be seen from
these figures, a doubly charged ion having the same mass
to charge ratio. as a singly charged ion will take less
time to drift through an ion mobility spectrometer
compared with a singly charged ion. Although the
ordinate axis of Fig. 3 is given as the flight time
through the drift region of a time of flight mass
analyser, it will be appreciated that this correlates
directly with the mass to charge ratio of. the ion.
If a mass filter is provided in combination with an
ion mobility spectrometer, and if the mass filter is
scanned (i.e. the transmitted range of mass to charge
ratios is varied) in synchronisation with the drift of
ions through the ion mobility spectrometer, then it is
possible to arrange that only ions having a particular
charge state (e.g. multiply charged ions) will be
transmitted onwardly e.g. to a mass analyser. The
ability to be able to substantially filter out singly
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charged background ions and/or to select ions of one or
more specific charge states for analysis represents a
significant advance in the art.
Fig. 5 illustrates the principle of charge state
selection. The known data of Fig. 3 and the
experimentally derived data of Fig. 4 can be interpreted
such that all ions having the same charge state can be
considered to fall within a distinct region or band of a
2D plot of mass to charge ratio versus drift time
through an ion mobility spectrometer. In Fig. 5 singly
and doubly charged ions are shown as falling within
distinct bands with an intermediate region therebetween
where very few ions of interest are to be found. Triply
and quadruply charged ions etc. are not shown for ease
of illustration only. The,large area below the "scan
line" can be considered to represent singly charged ions
and the other area can be considered to represent doubly
charged ions.
According to a preferred embodiment, a mass filter
is provided which is synchronised with the operation of
an ion mobility spectrometer. Considering Fig. 5, it
can be seen that at a time around 4 ms after ions have
first entered or been admitted to the drift region of
the ion mobility spectrometer, ions may be emerging from
the ion mobility spectrometer with various different
mass to charge ratios. Those ions which emerge with a
mass to charge ratio of approximately 1-790 are most
likely to be singly charged ions whereas those ions
emerging with a mass to charge ratio of approximately
1070-1800 are most likely to be doubly charged ions.
Very few, if any, ions will emerge at that point of time
with a mass to charge ratio between,790-1070 (which
corresponds with the intermediate region of the graph).
Therefore, if the mass filter is set at this particular
point in time so as to transmit only ions having a mass
to charge ratio > 790 then it can be assumed that .the
majority of the singly charged ions will not be onwardly
CA 02407957 2002-10-11
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transmitted whereas doubly charged ions (and ions having
a higher charge state) wild. be substantially onwardly
transmitted. If the mass filter is operated as a high
pass mass filter and if the minimum cut-off mass to
charge ratio of the mass filter follows in real time the
"scan line" shown in Fig. 5 (i:e, if i.t tracks the upper
predetermined mass to charge ratio for singly charged
ions as a function of time) then it will be appreciated
that only multiply charged ions will substantially be
onwardly transmitted.
According to other embodiments the mass filter may
track the lower predetermined mass to charge ratio for
doubly charged ions. The cut-off mass to charge ratio
may also lie for at least a portion of a cycle within
the intermediate region which separates the regions
comprising singly and doubly charged ions. The minimum
cut-off mass to charge ratio of the mass filter may also
vary in a predetermined or random manner between the
upper threshold of the singly charged ion region, the
intermediate region and the lower threshold of the
doubly charged ion region. It will also be appreciated
that according to less preferred embodiments, the
minimum cut-off mass to charge ratio may fall for at
least a portion of time within the region considered to
comprise either singly or doubly charged ions. In such
circumstances, ions of a potentially unwanted charge
state may still be transmuted; but the intensity of
such ions will nonetheless be reduced.
Accordi~.g to a preferred embodiment the minimum
cut-off mass to charge ratio is varied monthly, and is
preferably increased with time. Alternatively, the
minimum cut-off mass to charge ratio may be increased in
a stepped manner.
Fig. 6 illustrates how the basic arrangement
described in relation to .Fig. 5 may be extended so that
ions of a specific charge states) may be selected. In
the arrangement illustrated in Fig. 6 the mass filter is
CA 0240795 7 2002-10-11
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operated as a band pass mass to charge ratio filter so
as to select ions of a specific charge state (iri this
case triply charged ions) in. preference to ions having
any other charge state. At a time T after ions have
first been admitted or introduced into the ion mobility
spectrometer, the mass filter, being operated in a band
pass mode, is set so as to transmit ions having a mass
to charge ratio > P and < Q, wherein P preferably lies
on the upper threshold of the region containing doubly
charged ions and Q preferably liw on the lower
threshold of the region containing quadruply charged
ions. The upper and lower mass cut-offs P,Q are
preferably smoothly increased with time so that at a
later time T', the lower mass to charge ratio cut-off of
the band pass mass to charge ratio filter has been
increased from P to P' and the upper mass to charge
ratio cut-off of the band pass mass to charge ratio
filter has been increased from Q to Q'. As with the
arrangement described in relation to Fig. 5, the upper
and lower mass to charge ratio cut-offs do not need to
follow the lower and upper thresholds of any particular
charge state region, and according to the other
embodiments the upper and lower cut-offs may fall within
one or more intermediate regions and/or one or more of
the bands in which ions having a particular charge state
are to.be found. For example; in one embodiment, the
lower and upper mass to charge ratio cut-offs may simply
follow the thresholds of the region comprising doubly,
triply, quadruply etc. charged ions. According to other
embodiments two, three, four or more charge states may
be selected in preference to any other charge. state
(e.g. doubly and tripl~r charged ions may be
transmitted). Embodiments are also contemplated wherein
non-neighbouring charge states (e.g. doubly and
quadruply charged ioxis) are transmitted but not any
other charge states.
Fig. 7 shows a preferred embodiment of the present
CA 02407957 2002-10-11
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invention. An ion mobility spectrometer 4 is provided.
A pulse of ions is admitted to the ion mobility
spectrometer 4. A continuous ion source, e.g. an
electrospray ion source, preferably generates a beam of
ions 1 which are trapped in an upstream-ion trap 2
upstream of the ion mobility spectrometer 4. In one
embodiment ions are then pulsed out of the upstream ion
trap 2 by the application of an extraction voltage to an
ion gate 3 at the exit of the upstream ion trap 2.
The upstream ion trap 2 may comprise a quadrupole
rod set having a length of approximately 75 mm.
However, according to a more preferred embodiment the
upstream ion trap 2 comprises an ion tunnel ion trap
comprising a plurality of electrodes having apertures
therein through which ions are transmitted. According
to this embodiment a separate ion gate 3 does not need
to be provided. The apertures are preferably all the
same size or area. In other embodiments at least 60%,
65%, 70~, 75%, 80%, 850, 90% or 95% of the electrodes
have apertures which are substantially the same size or
area. The ion tunnel ion trap 2 may preferably comprise
at least 20, 30, 40 or 50 electrodes. Adjacent
electrodes are preferably connected to opposite phases
of an AC or RF voltage supply so that ions are radially
confined in use within the ion tunnel ion trap 2.
According to the preferred embodiment the voltages
applied to at least some of the electrodes forming the
upstream ion trap 2 can be independently controlled. In
one mode of operation a "V" shaped axial DC potential
profile may be created so that a single trapping region
is formed within the ion trap 2. According to another
mode of operation it is possible to create a "W" shaped
potential profile i.e. two trapping regions are provided
within the ion trap 2.
The voltage applied to the ion gate 3 and/or to a
region of the ion trap 2 may be dropped for a short
period of time thereby causing ions to be ejected from
CA 02407957 2002-10-11
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the ion trap 2 in a substantially pulsed manner into the
ian mobili y spectrometer 4.
In less preferred embodiments, a pulsed ion source
such as a Matrix Assisted Laser Desorption Ionisation
("MALDI") ion source or a Laser Desorption Ionisation
ion source may be used instead of a continuous ion
source. Tf a pulsed ion source is used, then ion trap 2
and ion gate 3 may be omitted in some modes of
operation.
The ion mobility spectrometer 4 is a device which
causes ions to become temporally separated based upon
their ion mobility. A number of different forms of ion
mobility spectrometer may be used.
In one embodiir~ent, the ion mobility spectrometer 4
may comprise an ion mobility spectrome er consisting of
a drift tube having a number of guard rings distributed
within the drift tube. The guard rings may be
interconnected by equivalent valued resistors and
connected to a DC voltage source. A linear DC voltage
gradient is generated along the length of the drift
tube. The guard rings are not connected to an AC or RF
voltage source.
In another embodiment, the ion mobility
spectrometer 4 may comprise a Field Asymmetric Ion
Mobility Spectrometer ("FAIMS").
According to a particularly preferred embodiment
the ion mobility spectrometer 4 comprises an ion tunnel
arrangement comprising a number of ring, annular or
plate electrodes, or more generally electrodes having an
aperture therein through which ions are transmitted.
The apertures are preferably all the same size or area
and are preferably circular: In other less preferred
embodiments at least 60°s, 65%, 700, 750, 80%, 85%, 90%
or 95% of the electrodes have apertures which are
substantially the same size or area. A schematic
example of a preferred ion mobility spectrometer 4 is
shown in Fig..8(a). The ion mobility spectrometer 4 may
CA 02407957 2002-10-11
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comprise a plurality of electrodes 4a,4b which are
either arranged in a single vacuum chamber or, as shown
in Fig. 8(a), are arranged in two adjacent vacuum
chambers separated by a differential pumping aperture
Apl. In one embodiment, the portion of the ion mobility
spectrometer 4a in an upstream vacuum chamber may have a
length of approximately 100 mm, and the portion of the
ion mobility spectrometer 4b in a downstream vacuum
chamber may have a length of approximately 85 mm. The
ion trap 2, ion gate 3 and upstream portion 4a of the
ion mobility spectrometer 4 are all preferably provided
in the same vacuum chamber which is preferably
maintained, in use, at a pressure within the range 0.1-
l0 mbar. According to less preferred embodiments, the
.vacuum chamber housing the upstream portion 4a may be
maintained at a pressure greater than l0 mbar up to a
pressure at or near atmospheric pressure: Also,
according to less preferred embodiments; the vacuum
chamber may alternatively be maintained at a pressure
below 0.l mbar.
In an embodiment the electrodes comprising the ion
trap 2 are maintained at a DC voltage Vrfl~ Ion gate 3
may be held normally at a higher DC voltage Vtrap than
Vrfl~ but the voltage applied to the ion gate 3 may be
periodically dropped to a voltage Vexrract which is
preferably lower than Vxf1 thereby causing ions to be
accelerated out of the ion trap 2 and to be admitted
into the ion mobility spectrometer 4.
According to a more preferred embodiment, ion trap
2 may comprise an ion tunnel ion trap 2 preferably
having a V-shaped axial DC potential profile in a mode
of operation. In order to ,release ions from the ion
trap 2 the DC voltage gradient on the second
(downstream) half of the ion trap 2 may be lowered or
otherwise reduced or varied so as to accelerate ions out
of the ion trap 2.
Adjacent electrodes which form part of the ion trap
x
CA 02407957 2002-10-11
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2 are preferably connected to opposite phases of a first
AC or RF voltage supply. The first AC or RF voltage
supply preferably has a frequency within the range 0.1-
3.O MHz, preferably 0.5-1.1 MHz, further preferably 780
kHz.
Alternate electrodes forming the upstream section
4a of the ion mobility spectrometer 4 are preferably
capacitively coupled to opposite phases of the first AC
or RF voltage supply.
The electrodes comprising the ion trap 2, the
electrodes comprising the upstream portion 4a of the ion
mobility spectrometer 4 and the differential pumping
aperture Ap1 separating the upstream portion 4a from the
downstream portion 4b of the ion mobility spectrometer 4
are preferably interconnected via resistors to a DC
voltage supply which in one embodiment comprises a 400 V
supply. The resistors interconnecting electrodes
forming the upstream portion 4a of the ion mobility
spectrometer 4 may be substantially equal in value in
which case an axial DC voltage gradient is obtained
similar to that shown in Fig. 8(b). The DC voltage
gradient is shown for ease of illustration as being
linear, but may more preferably be stepped. The. applied
AC or RF voltage is superimposed upon the DC voltage and
serves to radially confine ions within the ion mobility
spectrometer 4. The DC voltage Vtrap or Vextract applied to
the ion gate 3 preferably floats on the DC voltage
supply. The first AC or RF voltage supply is preferably
isolated from the DC voltage: supply by a capacitor.
In a similar manner; alternate electrodes forming
the downstream portion 4b of the ion mobility
spectrometer 4 are preferably capacitively coupled to
opposite phases of a second AC or RF voltage~supply.
The second AC or RF voltage supply preferably has a
frequency in the range 0.1-3.0 MHz, preferably 1.8-2.4 ,
MHz, further preferably 2.1 MHz. In a similar manner to
the upstream portion 4a, a substantially linear or
t
CA 02407957 2002-10-11
- 26 -
stepped axial DC voltage gradient is maintained along
the length of the downstream portion 4b of the ion
mobility spectrometer 4. A~ with the upstream portion
4a, the applied AC or RF voltage is superimposed upon
the DC voltage and serves to radially confine ions
within the ion mobilityspectrometer 4. The DC voltage
gradient maintained across the upstream portion 4a is
preferably not the same as the DC voltage gradient
maintained across the downstream portion 4b. According
to a preferred embodiment, the DC voltage gradient
maintained'across the upstream portion 4a is greater
than the DC voltage gradient maintained across the
downstream portion 4b.
The pressure in the vacuum chamber housing the
downstream portion 4b is preferably in the range 10-3 to
10-2 mbar. Accordirig to less preferred embodiments, the
pressure may be above 10-Z mbar, and could be similar in
pressure to the pressure of the vacuum chamber housing
the upstream portion 4a. It is believed that the
greatest temporal separation of ions occurs in the
upstream portion 4a due to the higher background gas
pressure. If. the pressure is too low then the ions will
not make enough.collisions with gas molecules for a
noticeable temporal separation of the ions to occur.
The size of the orifice in the ion gate 3 is
preferably of a similar size or is substantially the
same internal diameter or size as the differential
pumping aperture Apl. Downstream of the ion mobility
spectrometer 4 another differential pumping aperture Ap2
may be provided leading to a vacuum chamber housing a
quadrupole mass filter 5. Pre- and post-filters 14a,14b
may be provided.
In another embodiment the ion mobility spectrometer
4 may comprise an ion tunnel comprised of a plurality of
segments. In one embodiment 15 segments may be
provided. Each segment may comprise two electrodes
having apertures interleaved with another two electrodes
CA 02407957 2002-10-11
- 27 _
having apertures. All four electrodes in a segment are
preferably maintained at the same DC voltage but
adjacent electrodes are connected to opposite phases of
the AC or RF supply. The DC and AC/RF voltage supplies
are isolated from one another. Preferably, at least 90~
of all the electrodes forming the ion tunnel comprised
of multiple segments have apertures which are
substantially similar or the same in size or area.
Typical drift times through the ion mobility
spectrometer 4 are of the order of a few ms.
An important feature of the preferred embodiment is
the provision of a mass filter 5 which is varied in a
specified manner in conjunction with the operation of
the ion mobility spectrometer 4. According to the
preferred embodiment a quadrupole rod set mass filter 5
is used.
Tf the mass filter 5 i synchronised to the start
of a pulse of ions being admitted into the ion mobility
spectrometer 4, then the mass filter 5 can be set to
transmit (in conjunction with the operation of the ion
mobility spectrometer 5) only those ions having a mass
to charge ratio that corresponds at any particular point
in time with the charge state of the ions of interest.
Preferably, the mass filter 5 should be able to sweep
the chosen mass to charge ratio range on at least the
time scale of ions drifting through the drift region.
In other words, the mass filter 5 should be able to be
scanned across the desired mass to charge ratio range in
a few milliseconds. Quadrupohe mass filters 5 are
Capable of operating at this speed.
According to the preferred embodiment, either the
AC (or RF) voltage and/or the DC voltage applied to the
quadrupole mass filter 5 may be swept in synchronisation
with the pulsing of ions into the ion mobility
spectrometer 4. As discussed above in relation to Figs.
5 and 6, the quadrupole mass filter 5 may be operated in
either a high pass or band pass mode depending on
CA 02407957 2002-10-11
28 -
whether e.g. multiply charged ions are preferred iri
general, or whether ions having a specific charge state
are preferred. The varying of a mass filtering
characteristic of the quadrupole mass filter 5 is such
that ions having a favoured charge state (or states) are
preferably'onwardly transmitted, preferably to the at
least near exclusion of other charge states, for at
least part of the cycle time Tm between pulses of ions
being injected into the ion mobility spectrometer 4.
Figs. 8(c) and (d) show the inter-relationship between
ions beingpulsed out of the ion trap 2 into the ion
mobility spectrometer 4, and the scanning of the mass
filter 5. Synchronisation of the operation of the mass
filter 5 with the drift times of desired ions species
through the ion mobility spectrometer 4 enables a duty
cycle of approximately 100 to be obtained for ions
having the charge states) of interest.
Referring back to Fig. 7, a downstream ion trap 6
is provided downstream of the ion mobility spectrometer
4 and the quadrupole mass filter 5. According to a
particularly preferred embodiment, the downstream ion
trap 6 comprises a collision (or gas) cell 6. Ions may
be arranged so that they are sufficiently energetic when
they enter the collision cell 6 that they collide with
gas molecules present in the gas cell 6 and fragment
into daughter ions. Subsequent mass analysis of the
daughter ions yields valuable mass spectral information
about the parent ion(s). Ions may also be arranged so
that they enter the gas or collision cell 6 with much
less energy, in which case they may not substantially
fragment. The energy of ions entering the collision
cell 6 can be controlled by e:g. setting the level of a
voltage gradient experienced by the ions prior to
entering the collision cell 5. Since the voltage
gradient can be switched near instantaneously, the
collision cell 6 can, iri effect, be considered to be
switchable between a relati~rely high fragmentation mode
CA 02407957 2002-10-11
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and a relatively low fragmentation mode.
According to other less preferred embodiments
instead of fragmenting ions in the gas cell 6, ions can
be arranged to react with a gas present in the gas cell
6 to form product ions.
According to a particularly preferred embodiment,
the gas cell 6 may comprise an ion tunnel ion trap
similar to the upstream ion trap 2 and the ion mobility
spectrometer 4 according to the preferred embodiment.
As such, the gas cell 6 may comprise a plurality of
electrodes having apertures therein. The electrodes may
take the form of rings or other annular shapes or
rectangular plates. The apertures are preferably all
the same size or area. In other embodiments at least
60~, 65~, 70~, 75%, $0~, 85~, 90~ or 950 of the
electrodes have apertures which are substantially the
same size or area. The gas cell 6 may comprise
approximately 50 electrodes: Adjacent electrodes are
preferably connected to opposite phases of an AC or RF
voltage supply sa that ions are radially confined in use
within the ion tunnel ian trap 6. According to the
preferred embodiment the voltages applied to at least
some of the electrodes forming the gas cell 6 can be
independently controlled. This enables numerous
different axial DC voltage profiles to be created along
the length of the ion tunnel ion trap. ~Tn one mode of
operation a "V" shaped potential profile is created so
that a single trapping region is provided within the gas
cell 6. A V-shaped DC potential profile comprises an
upstream portion having a negative DC voltage gradient
and a downstream portion having a positive DC voltage
gradient so that (positive) ions become trapped towards
the centre of.the ion trap 6. If the positive DC
voltage gradient maintained across the downstream
portion of the ion trap 6 is then changed to a zero
gradient or more preferably to a negative gradient, then
(positive) ions will be accelerated out the ion trap 6
CA 02407957 2002-10-11
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as a pulse of ions.
According to a particularly preferred embodiment,
the gas cell 6 may act both as an ion trap and as a
collision cell. The ion tunnel ion trap/collision cell
6 may comprise. a plurality of segments (e.g. 15
segments),, each segment comprising four electrodes
interleaved with another four electrodes. All eight
electrodes in a segment are preferably maintained at the
same DC voltage, but adjacent electrodes are preferably
supplied with opposite phases of an AC or RF voltage
supply. A collision gas preferably nitrogen or argon
may be supplied to the collision cell 6 at a pressure
preferably of 10-3-10-2 mbar. Ions may be trapped and/or
fragmented in the ion trap/collision cell by appropriate
setting of the DC voltages applied to the electrodes and
the energy that ions are arranged to have upon entering
the ion trap/collision cell 6.
Ion optical lenses 7 may be provided downstream of
the collision cell 6 .to help guide ions through a
further differential pumping aperture Ap3 and into an
analyser chamber containing a mass analyser. According
to a particularly preferredembodiment, the mass
analyser comprises an orthogonal acceleration time of
flight mass analyser 1l having a pusher and/or pulley
electrode 8 for injecting ions or otherwise orthogonally
accelerating them into an orthogonal drift region. A
reflectron 9 is preferably provided for reflecting ions
travelling through the orthogonal .drift region back
towards a detector l0. As is well known in the art, at
least some of the ions in a packet of ions entering an
orthogonal acceleration time of flight mass analyser
will be orthogonally accelerated into the orthogonal
drift region. Ions will become temporally separated in
the orthogonal drift region in a manner dependent upon
their mass to charge ratio. Ions having a lower mass to
charge ratio will travel faster in the drift region and
will reach the detector 10 prior to ions having a higher
s . y
CA 02407957 2002-10-11
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mass to charge ratio. The time it takes an ion to drift
through the drift region and to reach the detector 10
can be used to accurately determine th:e mass to charge
ratio of the ion in question. The intensity of ions and
their mass to charge ratios can be used to produce a
mass spectrum.
According to other less preferred embodiments, the
downstream ion trap (gas cell) 6 may comprise a 3D-
quadrupole ion trap comprising a central doughnut shaped
electrode together with two endcap electrodes or a 2D
ion trap. According to another less preferred
embodiment; the downstream ion trap 6 may comprise a
hexapole ion guide. However, this embodiment is less
preferred since no axial DC voltage gradient is present
to urge ions out of the hexapole ion guide. It is for
this reason that anion tunnel ion trap is particularly
preferred.
Various modes of operation will now be described.
A first mode of operation will now be described in
relation to Fig. 10. According to this mode of
operation the ion source can remain permanently on. A
single upstream ion trap 2 is used and ions from the ion
source are trapped in a "V" shaped potential in the
upstream ion trap 2. The voltage applied across the
second (downstream) half of the ion trap 2 is
periodically dropped so that the "V" shaped potential is
changed to a preferably linear potential gradient which
causes ions to be accelerated out of the ion trap 2 and
into the ion mobility spectrometer 4 which according to
the preferred embodiment comprises an upstream portion
4a and a downstream portion 4b.
The ions become temporally separated as they pass
through the ion mobility spectrometer 4. The ions then
pass to a quadrupole mass filter 5 which is swept across
the mass scale in a synchronised manner with the ion
mobility spectrometer 4. As has already been described
above, by synchronising the operation of the mass filter
'~. yr
CA 02407957 2002-10-11
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with the ion mobility spectrometer 4 it is possible to
select precursor ions having a desired charge state(s).
The precursor ions are then trapped and
periodically released from a downstream ion trap 6 which
5 according to the preferred embodiment is a fragmentation
or collision cell 6. Due to the dispersion afforded by
the ion mobility spectrometer 4, lighter ions of the
selected charge state arrive in the gas cell 6 first.
It is apparent from Fig. 6 that at any particular
point in time precursor ions having the desired charge
state arriving at the ion tunnel/collision cell 6 will
have a relatively small spread of mass to charge ratios.
In order to achieve a maximum_duty cycle, the
precursor ions are released or pulsed out of the
i5 downstream ion trap 6. A predetermined period of time
later the ions are orthogonally accelerated by
energising a pusher electrode 8 of the oa-TOF mass
analyser 11. Substantially all the ions arriving at the
pusher electrode 8 will be orthogonally accelerated into
the drift region of the mass analyser 1l. This process
can, if desired, be repeated a number of times (for
example 4-5 packets of ions can be sent to the mass
analyser 11 without changing the delay time of the
pusher electrode 8 relative to the release of ions from
the ion trap 6). However; as time progresses, the ions
arriving in the ion trap 6 will have a relatively higher
average mass to charge ratio (but the spread of mass to
charge ratios of the ions present in the ion trap 6 at
any instance remain relatively low). When these ions
are then released from the ion trap 6 the delay time
before the pusher electrode 8 is energised is increased
so as to ensure that these ions are also orthogonally
accelerated with a near 100 duty cycle.
By optimising the ion trap-TOF (gas cell-pusher)
6,8 in this way precursor ions having a desired charge
state can be selected and undesired background ions can
be removed, and the precursor ions can be orthogonally
yr
CA 02407957 2002-10-11
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accelerated in the drift region of a TOF mass analyser
1l with a near 100 duty cycle across the whole mass
range of interest. This represent a significant advance
in the art.
In addition to varying, preferably increasing, the
predetermined time delay of the pusher electrode 8 it is
also possible to adjust the length of the extraction,
pulse from the ion trap 6 such that the size of the
packet of ions released from the ion trap 6 exactly
fills the pusher electrode 8.
A second mode of operation will now be described in
relation to Fig. 11.. In the first mode of operation it
was possible to mass analyse multiply charged precursor
ions with a high duty~cycle having removed, for'example,
singly charged background ions. It order to help
identify the precursor ions, the precursor ions can be
fragmented (or reacted) and the fragment (or product)
ions mass analysed.
According to the second mode of operation,
precursor ions are fragmented (or reacted) and trapped
in gas cell 6. Fig. 11 shows how fragment ions are
generated and accumulated from precursor ions of the
chosen charge state. In this case the first stages i.e..
upstream ion trap 2, ion mobility spectrometer 4 and
quadrupole mass filter 5 are operated in a similar
manner to the first mode of operation except that the
ions exiting the quadrupole mass filter 5 are arranged
to be accelerated by a collision voltage into the gas
cell 6 so as to induce fragmentation in the gas cell 6.
The gas cell 6 is also operated as an ion trap to
accumulate ions. Fragment ions are not then pulsed out
of the ion trap 6 directly into the TOF mass analyser
11. Instead, as will be apparent from consideration of
the third and fourth modes of operation described in
more detail below, the fragment ions are sent back
upstream of the ion trap 6. According to less preferred
embodiments, a collision voltage may not be provided and
CA 02407957 2002-10-11
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precursor ions may instead be passed to the gas cell 6_
to react with a gas to form product ions.
A third mode of operation will now be described
with reference to Fig. l2. After sufficient fragment
(or product) ions have been accumulated in the gas cell
6, the potentials on the gas cell 6 are reversed and a
second trapping stage 2b is preferably created in a
downstream region of the upstream ion trap 2. This is
preferably achieved by providing a "W" shaped potential
profile across the ion tunnel ion trap 2. However,
according to less preferred embodiments two discrete ion
traps may be provided. The upstream region 2a of the
upstream ion trap 2 may continue to accumulate ions
generated by the ion source 1.
The fragment (or product) ions present in the
downstream ion trap 6 are accelerated out of the
collision cell 6 and pass back through the quadrupole
mass filter 5 and the ion mobility spectrometer 4a,4b.
The mass filter 5 in this Mode of operation is
preferably operated in a wide band pass mode so that the
fragment (or product) ions are not substantially mass
filtered. As such, the mass filter 5 operates as an RF-
only ion guide with a high transmission for all ions.
The fragment (or product) ions having passed
through both the mass filter 5 and the ion mobility
spectrometer 4a,4b then accumulate in the downstream
region 2b of the upstream ion trap 2.
A fourth mode of operation will now be described in
relation to Fig. l3. As can be seen, the fragment (or
product) ions which have been accumulated in the
downstream region 2b of the upstream ion trap 2 during
the third mode of operation are now analysed in a
similar but not identical manner to the way in which the
precursor ions were analysed in first mode of operation.
As such the fragment (or product) ions can be
orthogonally accelerated into the mass analyser with a
near 1000 duty cycle.
CA 02407957 2002-10-11
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The fragment (or product) ions are released from
the downstream region 2b of the upstream ion trap 2 and
are temporally separated in the ion mobility
spectrometer 4a,4b. However, in contrast to the first
mode of operation, the quadrupole mass filter 5 is
preferably not swept. Rather; the mass filter 5 is
preferably operated in a v,iide bandpass mode so as not to
mass filter the fragment (or product) ions. As such,
the quadrupole mass filter 5 operates in an RF-only ion
guide mode.
In a similar manner to first mode of operation,
temporally separated fragment (or product) ions are
received and trapped in the gas cell/ion trap 6. The
fragment (or product) ions are then periodically
released from the ion trap 6 and are orthogonally
accelerated in the drift region of the TOF mass analyser
11 after a predetermined time delay by energising the
pusher electrode 8. As with the first mode of
operation, as time progresses the fragment (or product)
ions arriving at the downstream ion trap 6 have a higher
average mass to charge ratio and accordingly the delay
time can be adjusted (i.e. increased) so that the
fragment (or product) ions continue to be orthogonally
accelerated into the TOF mass analyser 11 with a near
100 duty cycle.
After completion of the fourth mode of operation,
the instrument preferably returns to the first mode of
operation and the whole cycle may be repeated as shown
in Fig. 14.
The accumulation of the ions in the three trapping
stages means that no ions are lost whilst other
experiments are being performed. It should be noted
that the proportion of time spent in each of the four
modes shown in Fig. 14 can be varied according to the
desired experiment e.g. it may be desirable to spend a
large amount of time accumulating fragment (or product)
ions so as to achieve good signal to noise.
CA 02407957 2002-10-11
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According to the preferred embodiment the mass
filter (e. g. quadrupole 5) has been shown and described
as being downstream of the ion mobility spectrometer 4
in all modes of operation. However, according to other
embodiments the mass filter (e.g. quadrupole 5) may be
arranged upstream of the ion mobility spectrometer 4.
Furthermore, although the preferred embodiment has
been described in relation to being able to filter out
e.g. singly charged ions in preference to multiply
charged ions, other embodiments are contemplated wherein
singly charged ions are preferentially selected and
onwardly transmitted whilst other charge states) are
attenuated.
Other embodiments are also contemplated wherein the
AC or RF voltage supplied to the electrodes) in either
the second ion trap 2, the ion mobility spectrometer 4
or the first ion trap/gas cell 6 may be non-sinusoidal
and may, for example, take the form of a square wave.
Yet further embodiments are contemplated wherein
other types of mass filter 5 are used instead of (-or in
addition to) a quadrupole mass filter 5. For example, a
RF ring set or a RF ion trap (either 2D or 3D) may be
used.
Although the present invention has been described
with reference to preferred embodiments, it will be
understood by those skilled in the art that various
changes in form and detail may be made without departing
from the scope of the: invention. as set forth in the
accompanying claims:
