Note: Descriptions are shown in the official language in which they were submitted.
CA 02318855 2000-07-24
WO 99/38193 PCT/US99/,01335
Mass Spectrometry with Multipole Ion Guides
Field of Invention
This invention relates to the field of mass spectrometric analysis of chemical
species. More
particularly it relates to the configuration and operation use of multiple
multipole ion guide
assemblies in higher pressure vacuum regions.
. r'
Background of the Invention.
Mass Spectrometers (MS), have been used to solve an array of analytical
problems involving
solid, gas and liquid phase samples with both on-line and off line techniques.
On-line Gas
Chromatography (GC), Liquid Chromatography (LC), Capillary Electrophoresis
(CE) gas
and other solution sample separation systems have been interfaced on-line to
mass
spectrometers configured with a variety of ion source types. Some ion source
types operate at
or near atmospheric pressure and other ion source types produce ions in
vacuum. Mass
spectrometers operate in vacuum with different mass analyzer types requiring
different
vacuum background pressure for optimal performance. The present invention
comprises a
configuration of one or more multipole ion guides configured in a mass
spectrometer.
Although the invention can be applied to multipole ion guides comprising any
number of
poles, the description of the invention given below will present quadrupole or
four pole ion
guide assemblies. Higher mass to charge separation resolution can be achieved
with
quadrupole ion guides when compared with the performance of ion guides
configured with
more that four poles. Quadrupole ion guides have been configured as the
primary elements in
single and triple quadrupole mass analyzers or as part of hybrid mass
spectrometers that
include Time-Of Flight, Magnetic Sector, Fourier Transform and even three
dimensional
quadrupole ion trap mass analyzers. Typically, quadrupole ion guides operated
in mass to
charge selection mode, are run in background vacuum pressures that avoid or
minimize ion to
neutral background gas collisions. A wider range of background pressures have
been used
when operating quadrupoles in RF only ion transmission mode. For some
applications,
pressure in a quadrupole ion guide operating in RF only ion transmission mode
is maintained
sufficiently high to promote collisional damping of ion kinetic energy or
Collisional Induced
CA 02318855 2004-04-29
Dissociation (CID) fragmentation of ions traversing the ion guide length.
Commercially available, quadrupole mass analyzers with electron multiplier or
photomultiplier detectors are operated in analytical mass to charge selection
mode at
background pressures typically below 2 x 10'~ torr range. There are examples
of multipole
ion guides operated at elevated background pressures I vacuum with some degree
of ion mass
to charge separation. U.S. Patent Numbers 5,401,962 and 5,613,294 describe a
small
quadrupole array with an electron ionization (EI).~ion source and a faraday
cup detector which
can be operated as a low mass to charge range gas analyzer at background
pressures up to 1 x
~ torr. Performance of this short quadrupole array begins to decrease when the
background
pressure increases to the point where the mean free path of an ion is shorter
than the
quadrupole rod length. U.S. Patent Number 5,179,278 describes a quadrupole ion
guide
configured to transmit ions from an Atmospheric Pressure Ionization (APB
source into a
three dimensional quadrupole ion trap. The quadrupole ion. guide described in
Patent
Number 5,179,278 can be operated as a trap to hold ions before releasing the
trapped ions into
the three dimensional quadrupole ion trap. During ion trapping, the potentials
applied to the
f rods or poles of this qttadrupole ion guide can be set to Iimit the range of
ion mass to charge
values released to the ion trap. The quadrupole ion guide can also be operated
with resonant
frequency excitation collisional induced dissociation fragmentation of trapped
ions prior to
introducing the trapped fragment ions into the three dimensional ion trap.
After the
quadrupole ion guide has released its trapped ions to the three dimensional
ion trap, it is
refilled during the three dimensional ion trap mass analysis time period. A
quadrupole ion
guide that extends coatinuously through multiple vacuum pumping stages is
described in
U.S. Patent No. 6,011,259 dated January 4, 2000. A portion of the quadrupole
ion guide
length is positioned in a vacuum region that pressures greater than one
millitorr insuring ion
and neutral gas background collisions. U.S. Patent No. 6,011,259 dated January
4, 2000
describes a hybrid mass spectrometer wherein the multiple vacuum stage
multipole ion guide
is configured with a Time-Of Flight (TOF) mass analyzer. As described, the
quadrupole ion
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WO 99/38193 PCT/US99/01335
guide is operated in combinations of ion transmission, ion trapping, mass to
charge selection
and CID fragmentation modes coupled with Time-Of Flight mass to charge
analysis. The
hybrid quadrupole Time-Of Flight apparatus and method described provides a
range of
MS/MSn mass analysis functions. In an improvement over the prior art, one
embodiment of
the present invention comprises multiple quadrupole ion guides configured ~ d
operated in a
higher pressure vacuum region of a hybrid TOF mass analyzer improving the mass
analyzer
MS/MSn performance and analytical capability.
Multipole ion guides operated in RF only mode at elevated pressures have been
used as an
effective means to achieve damping of ion kinetic energy during ion
transmission from
Atmospheric Pressure Sources to mass analyzers. A quadrupole ion guide,
operated in RF
only mode in background pressures greater than 10~ torr, configured to
transport ions from
an API source to a quadrupole mass analyzer is described in U.S. patent
4,963,736. Ion
collisions with the neutral background gas serve to damp the ion kinetic
energy during ion
transmission through the ion guide. This potentially can reduce the primary
ion beam
eneergy spread and improve ion transmission efficiency. Multipole ion guides
operated in
elevated background pressures have been used extensively as collision cells
for the CID
fragmentation of ions in triple quadrupoles and hybrid magnetic sector and TOF
mass
analyzers. Ion guides configured and operated as collision cells are run in RF
only mode with
a variable DC offset potential applied to all rods. U.S. Patent Number
5,847,386 describes the
configuration a multipole ion guide assembly configured to create an electric
field along the
ion guide axis to move ions axially through a collision cell or to promote CID
fragmentation
within a collision cell by oscillating ions axially back and forth within the
individual ion guide
assembly length. As described, the ion guide assembly with an axial field is
operated in RF
only mode with a common RF applied to all poles of the quadrupole ion guide
assembly.
Multipole ion guide collision cells that have been incorporated in
commercially available mass
analyzers and that have been described in the literature are configured as
individual ion guide
assemblies isolated in a vacuum pumping stage or contained in a surrounding
enclosure. The
3
CA 02318855 2004-04-29
ion guide surrounding enclosure, generally located in a lower pressure vacuum
region, is
configured to minimize the higher pressure collision cell background pressure
from entering
the surrounding lower vacuum pressure chamber. Commercially available triple
quadrupoles,
shown as prior art in Figure 20 generally are configured with three multipole
ion guides in
one vacuum pumping stage. The elevated pressure within the collision cell is
maintained by
leaking collision gas into the enclosure surrounding the collision cell
multipole ion guide. Gas
leaks out of the collision cell through the enclosure entrance and exit
apertures configured
along the uiple quadrupole centerline. One aspect of the -present invention is
the
configuration of multiple quadrupole ion guides positioned in a common region
of higher
vacuum pressure higher pressure run in ion mass to charge selection and CID
fragmentation
operating modes. A further aspect of the invention is the configuration o~
multiple
quadrupole ion guides in a vacuum region of elevated pressure wherein each
quadrupole can
be.operated in mass to charge selection and/or ion fragmentation modes to
achieve MS/MSn
mass analysis functions.
Conventional triple quadrupole mass analyzers interfaced to .API sources must
be configured
with sufficient vacuum pumping speed in the mass analyzer vacuum stage region
to maintain a
vacuum level that prevents ion collisions with the background gas. The low
pressure vacuum
must be maintained while gas leaks into the chamber from the collision cell
and the ion
source, Vacuum pressure in the collision cell enclosure is generally
maintained at 5 to 8
millitorr and the analyzer vacuum stage is maintained in the low 10 5 to 14'6
tort range:
.Figure 20 is a diagram of the multipole ion guide configuration of atypical
triple quadrupole
mass analyzer 150 interfaced to an Atmospheric Pressure Ion source. Individual
multipole ion
guide assemblies 158,154,155 and 156 are configured, along the same centerline
axis in a three
stage vacuum pumping system. Orifice plate 164 provides a leak from
atmospheric pressure
region 160 into first vacuum stage 151. Ions produced in atmospheric pressure
region 160 are
transferred into vacuum through a supersonic free jet expansion formed on the
vacuum side of
orifice 169 . A portion of the ions introduced into vacuum continue through
the orifice in
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WO 99/38193 PCT/US99/01335
skimmer, mufti ole ion ide 158 the orifice in electrode 161, mufti ole ion
p ~ ' p guide I54, the
orifice in electrode 166, multipoel ion guide 155, the orifice in electrode
167, multipole ion
guide 156, the orifice in electrode 168 to detector 165. The pressures in
vacuum stages 15I,
152 and 153 are typically maintained at 1 torr, 5 millitorr and < 1 x 10 5
torr respectively
while the pressure inside collision cell 157 is maintained at 5 to 8
millitorr. 'Triple
quadrupoles are configured to perform MS or a single MS/MS sequence mass
analysis
function. In an MS/MS experiment, ions start at or near atmospheric pressure,
are
transported through multiple vacuum stages to a low pressure vacuum region
where'rnass to
charge selection occurs in multipole ion guide 154 with little or no ion to
neutral collisions.
Mass to charge selected ions are then are accelerated into a region of
elevated pressure in
collision cell multipole ion guide I55. The resulting fragment ion population
are directed the
low pressure region in quadrupole 156 where mass to charge separation is
conducted with few
or no ion to neutral collisions prior to detection by ion detector 165. A
similar analytical ion
sequence occurs in prior art hybrid quadrupole, quadrupole TOF mass analyzers
where third
quadrupole 156 is replaced by a TOF mass analyzer residing in a fourth vacuum
pumping
stage.
The placement of a multipole ion guide collision cell in a low pressure vacuum
stage increases
the cost and complexity of an API MS/MS mass analyzer. One aspect of the
invention is the
configuration of multiple quadrupole ion guides in a higher pressure vacuum
pumping stage of
an API source using the background pressure formed by the gas Leak from
atmospheric
pressure to perform CID ion fragmentation. Mass to charge selection and CID
ion
fragmentation is performed in the second vacuum stage of an Atmospheric
Pressure Ion
Source mass analyzer, eliminating the need for a separate collision cell with
its additional gas
loading on the vacuum system. The configuration of multiple quadrupoles in the
second
vacuum stage reduces the system vacuum pumping speed requirements and its
associated costs
for API quadrupole and hybrid mass analyzers. Another aspect of the invention
is the
configuration of multiple quadrupole ion guides that have pole dimensions
considerably
CA 02318855 2004-04-29
reduced in size from quadrupole assemblies typically found in commercially
available triple
quadrupoles or hybrid quadrupole TOF mass analyzers. The smaller pole
dimensions and
reduced quadrupole length minimizes the ion transmission time along each
quadrupole
assembly axis. This increases the analytical speed of the mass spectrometer
for a range of mass
analysis functions. The reduced quadrupole size require less space aad power
to operate,
decreasing system size and cost without decreasing performance. Another aspect
of the
invention is the configuration of a multipole ion guide that extends
continously into multigle
vacuum stages into the multiple quadrupole assembly positioned in the higher
pressure region
of an API MS instrument. Multiple vacuum pumping stage ion guides are desuibed
in U.S.
Patent Number 5,652,427. As will be described below, configuring a multiple
vacuum stage
quadrupole ion guide with additional quadrupole ion guides enables operation
over a wide
range of mass analysis functional sequences.
Individual quadrupole ion guide assemblies require individual RF, +/- DC and
supplemental
resonant frequency voltage supplies to achieve ion mass to charge selection;
C1D ion
fragmentation and trapping functions. Quadrupole ion guides have been
configured with
segments where common RF voltage from a single RF supply is applied to all
segments of the
ion guide assembly or rod set. Typically, an RP only entrance, and exit
segment will be
configured in a quadrupole rod set to minimize fringing field effects on ions
entering or
leaving the quadrupole. The RF voltage is applied to the entrance and exit
sections through
capacitive coupling with the primary RF supplied to the central rod segment.
Offset
potentials, that is the common DC voltage applied to all four poles of a given
segment, can be
set individually on each segment to accelerate ions from oae ion guide segment
to the next
within a quadrupole ion guide assembly. The offset potential applied to
segments of an ion
guide, can be set to trap ions within an ion guide as well. In the prior art,
electodes are
positioned between individual multipole ion guides when multiple ion guide
assemblies are
configured in a, mass analyzer. Referring to the prior art triple quadrupole
example
diagrammed inFigure 20.. each quadrupole ion guide is separated from an
adjacent ion guide by
6
CA 02318855 2004-04-29
an electrode. Electrodes are configured to minimize the fringing field effects
as ions pass from
one ion guide assembly to the next. They minimize any capacitive coupling
between different
ion guide sets avoiding beat frequency distortions of the RF fields. The
electrodes also serve
the additional purpose of providing a reduced orifice between vacuum pumping
stages or
between a collision cell and the vacuum stage in which it resides to minimize
gas conductance.
When conducting MSIMS experiments, i.e. the collision cell is maintained at a
pressure .of 5 to
8 millitorr, ions transferred from one quadrupole to another in the prior art
must pass
through a background pressure gradient. The collisional effects that occur in
the friri~gmg field
region between multipole ion guides may cause ion losses due to scattering
effects. ,
Referring to Figure 20, multipole ion guide 158 is separated from quadrupole
assembly 154 by
vacuum partitition and electrode 161. Quadrupole 154 is diagrammed with RF
only segments or
sections 162 and 170 and analytical segment 163. Multipole ion guide 158 may
be
configured as a quadrupole, hexapole or octapole and may have a different RF
voltage supply
from that of quadrupole 154. .The RF frequency, amplitude, phase and different
RF related
electric fields produced by a difference in the number of poles between ion
guide 158 and
quadrupole 154 create fringing fields that can negatively effect the
efficiency of ion transport
from ion guide 158 into quadrupole 154. The effect on ion trajectories of exit
fringing fields
of multipole ion guide 158 and the entrance fringing fields of quadrupole 154
are reduced by
electrode I61 and RF only segments 162. Electrodes 166 and 167 serve the
similar functions of
reducing fringing field effects and acting as a vacuum partitions. Collision
cell multipole ion
guide may be configured with four, sax or eight poles and have R,F fields at
its entrance and
exit ends that differ from the RF and DC fields of the adjacent quadrupole ion
guides. Ion
losses occur at each transfer from one multipole ion guide assembly to the nem
due.to ion
collisional scattering, fringing field effects and ion collisions with the
electrodes. One aspect
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WO 99/38193 PCT/US99/01335
of the invention is the configuration of multiple quadrupole assemblies along
a common axis
with no electrode partitions in between. Each quadrupole assembly configured
according to
the invention can individually conduct mass selection and CID fragmentation of
ions. One or
more multiple vacuum stage quadrupole can be configured, according to the
invention in a
multiple quadrupole assembly. Ijames, Proceedings of the 44th ASMS Conference
on Mass
Spectrometry and Allied Topics, 1996, p 795, proposes a linear combination of
four
quadrupole ion guides operated in RF only ion transport and trapping mode with
ion pulsing
into a TOF mass analyzer. Two of the quadrupoles in the proposed assembly
extend
continuously into two vacuum pumping stages. The extended abstract does not
teach
applying different RF potentials to quadrupoles one through four. Nor does it
teach
conducting mass to charge selection or CID fragmentation operation with the
proposed
multiple quadrupole assembly as is included as aspects of the present
invention.
Separate RF voltage supplies providing RF voltage to individual multipole ion
guide
assemblies in the present invention can be operated with a common frequency
and phase to
minimize RF fringing field effects. Each quadrupole assembly can have
different RF
amplitude applied during mass to charge selection and/or ion CID fragmentation
operation.
Eliminating the electrodes between quadrupole ion guide assemblies increases
ion transmission
efficiency and allows ions to be directed forward and backward between
quadrupole ion guide
assemblies. Efficient bidirectional transport of ions along the axis of a
multiple quadrupole
assembly allows a wide range analytical functions to be run on a single
instrument. A
equivalent array of analytical functions would require more than one prior art
mass analyzer
to achieve. One aspect of the invention includes RF quadrupoles configured
between each
analytical quadrupole assembly to minimize any fringing fields due to
interquadrupole
differences in RF amplitude, +/- DC voltage and resonant frequency voltages.
The RF only
seg~iients, configured with individual RF supplies, also serve to minimize RF
or resonant
frequency coupling between analytical quadrupole ion guide assemblies. In
another aspect of
the invention, the RF only quadrupoles may be configured as RF only segments
of each
l
CA 02318855 2004-04-29
quadrupole assembly capacitively coupling to the adjacent quadrupole ion guide
RF supply.
In yet another aspect of the invention, the junctions between individual
quadrupole assemblies
are located in the higher pressure vacuum region where little pressure
gradient exists at the
junction between quadrupole assemblies. Ion collisions with the background gas
serve to
damp stable ion trajectories to the quadrupole centerline where fringing
field' effects between
quadrupoles are minimized. This collisional damping of ions trajectories by
the background
gas serves to maximize ion transmission in the forward and backward direction
between
individual quadrupole ion .guide assemblies.
Triple quadrupoles, three dimensional ion traps, hybrid quadrupole-T~Fs,
hybrid magnetic
sector and Fourier Transform (FTMS) mass analyzers can perform MS1MS analysis.
Ion traps
and FTMS mass analyzers can perform MS/MSa analysis, however, ion CI17
fragmentation is
performed with relatively low energy resonant frequency excitation. CID
fragmentation in
~ple quadrupoles and hybrid quadrupole-TOF mass analyzers is achieved by
acceleration of
ions along the quadrupole axis referred to herein as DC acceleration CID
fragmentation. Ions
are generally accelerated with a few to -tens of eV in quadrupole DC
acceleration CID
fragmentation. Hybrid or tandem magnetic sector mass analyzers can perform
high energy
DC acceleration ion fragmentation with ions accelerated into gas phase
collisions with
hundreds or even thousands of eV. Single mass range mass to charge selection
in triple
quadrupoles .is achieved by applying RP and +/ DC to the non collision cell
quadrupole
assemblies 154 and 156 in Figure 20. Single or multiple range mass to charge
selection in three
dimensional- ion traps is achieved using RF voltage amplitude scanning coupled
with resonant
frequency ejection of unwanted ions. Triple quadrupoles operate with
a,continuous ion beam
delivered from an API source. Ion traps must analyze ions provide in a
continuous ion beam
in batch-wise manner: The space charge of trapped ions in a three dimensional
ion trap
imposes performance restrictions not encountered in triple quadrupole
operation. The effects
of space charge in an ion trap potentially limit its utility in quantitative
analysis applications.
The mass to charge selection resolution in quadrupole ion guides operated in
low vacuum
CA 02318855 2004-12-15
pressures is limited in part. by the ion .transit time. Each mass analyzer
type perforcas ion
mass to charge selection and CID tation~through a different means each with
its~own
advantages and disadvantages depending on the analytical problem to be solved.
Quadrupoles and three dimensional ion trap mass analyzers and recently hybrid
quadrupole-
TOF mass analyzers have become the most widely used mass analyzer types
interfaces with
Atmospheric Pressure Ion Sources such as Electrospray (ES) and Atmospheric
Pressure
Chemical Ionization (APCI) sources. FTMS instruments p~eovide very high
resolution and
mass accuracy but price and operational complexity have limited the number of
units
currently in use.. It is one aspect of the present invention to combine the
functional
capabilities of triple quadrupoles, three dimensional ion traps and hybrid
quadrupole-TOP
mass analyzers into a single instrument. The invention includes but is not
limited~to resonant
frequency CID ion fragmentation, DC acceleration CID fragmentation even for
energies ovei
one hundred eV,. RF anti +/ DC mass to charge selection, single csr multiple
mass range RF
amplitude and resonant frequency ion ejection, mass to charge selection, ion
trapping in
qnadrupole ion guides and TOF mass analysis. The invention enables mass
specuometric .
anal~ical functions that can not be performed any prior art mass analyzer
type. Por example,
MSIMSn where n > 1 can be performed on a hybrid quadrupole-TOP's configured
according
.to the invention, using DC acceleration fragmentation for each CID step or
combinations of
resonant frequency excitation and DC aaeleration-C~ ion station. Ion trapping
vrich
mass to charge selection of CID ion fragmentation can be performed in each
individual .
quadrupole assembly without stopping a continuous ion beam. These techniques,
according
to the invention, as described below increase the duty cycle and sensitivity
of a hybrid
quadrupole-TOP during MSIMS dents. ..
The' hybrid quadrupole-TOP configured according to the inventions is ~ a lower
cost beach top
instrument that includes all the performance capability as described in U.S..
Patent Numbers
5,652,427, 5,689,111, 6,011,259 and 6,621,073.
CA 02318855 2004-12-15
Emulation and improved performance of prior art API triple
quadrupole, three dimensional ion trap, TOF arid hybrid quadrupole-TOF mass
analyzer
functions can be achieved with the hybrid quadrupole-TOF mass analyzer
configured
according to the invention. The assemblies of multiple quadrupole ipn guide
configured
according to the invention can be interfaced to all mass analyzer types
tandelm an hybrid
instruments and most ion source types that produce ions from gas, liquid or
solid phases.
Summary of the Invention
The invention, as described below. includes a number of embodiments. Each
embodiment
contains at least one multipole ion guide located in and operated in higher
background
pressure vacuum regions where multiple collisions between ions and neutral
background gas
occur. Although the invention can be applied to multipole ion guides with any
number of
poles, the description will primarily refer to quadrupole ion guides. Tn one
embodiment of
the invention, the quadrupole ion guide is configured in a vacuum region with
background
pressure maintained sufficiently high to cause collisional damping of the ions
traversing the
ion guide length. The quadrupole ion guide, positioned in the higher pressure
vacuum region,
can be operated in trapping mode, single pass ion transmission mode, single or
multiple mass
to charge selection mode andlor resonant frequency CID ion fragmentation mode
with or
without stopping a continuous primary ion beam. In one embodiment of the
invention, a
high pressure quadrupole ion guide is operated to achieve single or multiple
mass to charge
range selection by ejected unwanted ions traversing or trapped in the ion
quadrupole volume.
Unwanted ion ejection is achieved by applying resonant or secular frequency
waveforms to
the ion quadrupole rods over selected time periods with or without r amping or
stepping of
the RF amplitude. In yet another embodiment of the invention ion, +/ DC
potentials are
applied to the poles of the quadrupole ion guide during mass to charge
selection. The +/- DC
potential is applied to the quadrupole rods or poles while ramping or stepping
the RF
amplitude and applying resonant frequency excitation waveforms to eject
unwanted mass to
charge values. In another embodiment of the invention, at least one quadrupole
ion guide
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positioned in a higher pressure region and operated in mass to charge
selection and/or ion
Cm fragmentation mode is configured as a segmented or sectioned multipole ion
guide. The
segmented ion guide may include two or more sections where the RF voltage is
applied to all
segments from a common RF voltage supply. In one embodiment of the invention
at Ieast
one segment of the segmented quadrupole is operated in RF only mode while at
least one
other segment is operated in mass to charge selection and/or Cm ion
fragmentation mode.
Individual DC offset potentials can applied to each segment independently
allowing trapping
of ions in the segmented quadrupole assembly or moving of ions from one
segment to the an
adjacent segment. size
In another embodiment of the invention a segmented multipole ion guide is
configured such
that at least one segment extends continuously into multiple vacuum stages. A
portion of the
multiple vacuum stage multipole ion guide is positioned in a vacuum region
where the
pressure in the ion guide volume is maintained sufficiently high to cause
multiple ion to
neutral collisions as the ions traverse the segmented ion guide length. The RF
voltage is
applied from a common RF voltage supply to all segments or sections of the
multiple vacuum
stage multipole ion guide. At least one section of the segmented multiple
vacuum stage
multipole ion guide can be operated in trapping mode, single pass ion
transmission mode,
single or multiple mass to charge selection mode and/or resonant frequency CID
ion
fragmentation mode with or without stopping a continuous primary ion beam. In
one
embodiment of the invention, one or more segments of the multiple vacuum
pumping stage
ion guide are operated in RF only mode while at least one segment is operated
in mass to
charge selection or Cm ion fragmentation mode. Mass to in at least one segment
of the
multiple vacuum stage segmented ion guide can be achieved by applying RF and
+/- DC
potentials to the ion guide poles. Alternatively, ejection of unwanted ions in
mass to charge
selection mode can be achieved by applying resonant frequency waveforms with
or without
stepping the RF amplitude. The range of frequency components required to eject
unwanted
ion mass to charge values can be reduced by adding +/- DC voltage to the rods
with or
f
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without varying the RF amplitude during ion mass to charge selection
operation. In one
embodiment of the invention, individual offset potentials can be applied to
different segments
of the multiple vacuum stage multipole ion guide. Offset potentials can be set
on individual
ion guide segments to trap ions within the volume defined by the surrounding
segmented ion
guide poles or to move ions from one segment to the next. The vacuum pr~sure
along at least
one segment of the multiple vacuum stage ion guide varies along the axial
length of said
segment.
The invention can be configured with several types of ion sources, however,
the embodiments
of the invention described herein comprise mass analyzers interfaced to
atmospheric pressure
ion sources including but not limited to Electrospray, APCI, Inductively
Coupled Plasma
(ICP) and Atmospheric Pressure MALDI. In the embodiments described, the
primary source
of background gas in the multipole ion guides configured in higher pressure
vacuum regions is
the Atmospheric Pressure Ion source itself. This configuration avoids the need
to add
additional collision gas to a separate collision cell positioned in a lower
pressure vacuum
region. Elimination of a separate collision cell in an API mass analyzer,
reduces the vacuum
pumping speed requirements, system size and complexity. Reduced size and
complexity
lowers the mass analyzer cost without decreasing performance or analytical
capability. As
will become clear from the description given below, a mass analyzer configured
and operated
according to the invention has increased performance and analytical range over
the prior art.
In another embodiment of the invention, individual multipole ion guide
assemblies are
configured along a common centerline where the junction between two ion guides
is
positioned in a higher pressure vacuum region. Ion collisions with the
background gas on
both sides the junction between two axially adjacent multipole ion guides
serve to damp stable
ion radial trajectories toward the centerline where fringing fields are
minimized. Forward and
reverse direction ion transmission transmission efficiency between multipole
ion guides is
maximized by minimizing the fringing fields effects between at junction
between two ion
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PCT/US99/01335
guides. In anther aspect of the invention, no electrode is configured in the
junction between
two adjacent quadrupole ion guides configured along the common quadrupole
axis. The two
adjacent quadrupole assemblies, configured according to the invention have the
same radial
cross section pole dimensions and pole elements are axially aligned at the
junction between the
two quadrupole ion guides. Each quadrupole assembly has an independent set of
RF, resonant
frequency, +/- DC and DC offset voltage supplies. In another aspect of the
invention,
common RF frequency and phase is maintained on adjacent and axially aligned
poles of
adjacent axially aligned quadrupole ion guides. The RF amplitude, resonant
frequency
waveforms, +/- DC amplitude and the DC offset potentials applied to the poles
of adjacent
quadrupole ion guides can be independently adjusted for each quadrupole ion
guide assembly.
Adjustment of relative DC offset potentials allows ions with stable
trajectories to move in the
forward or reverse direction between the two quadrupoles high transmission
efficiency due to
minimum fringing field effects. In another aspect of the invention, at least
one segmented
quadrupole ion guide assembly is configured in axial alignment with another
quadrupole ion
guide where the junction between the two quadrupole ion guide assemblies is
positioned in a
region of higher background pressure. The junction between the adjacent
quadrupole ion
guides may or may not be configured with an additional electrode. In another
aspect of the
invention at least one quadrupole ion guide that extends continously into
multiple vacuum
pumping stages is configured in axial alignment adjacent to another quadrupole
ion guide
assembly. It is another aspect of the invention that at least one section of
at least one
quadrupole in the above listed axially aligned quadrupole combinations is
operated in mass to
charge selection and/or CID ion fragmentation mode. Mass to charge selected
ions traversing
one quadrupole assembly can be accelerated from one quadrupole into an
adjacent quadrupole
through an offset voltage amplitude difference sufficient to cause CID ion
fragmentation. The
background gas present in the region of the junction between the two adjacent
quadrupole ion
guides serves as the collision gas for ions axially accelerated from one
quadrupole ion guide
into the next. Forward or reverse direction ion acceleration with sufficient
offset voltage
amplipltude differential applied can be used to fragment ions through
Collisional Induced
14
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Dissociation.
At least one section of each quadrupole ion guide configured in a multiple
quadrupole axially
aligned assembly is configured to operate in ion trapping or single pass
transmission mode,
single or multiple mass to charge selection mode and resonant frequency Cm ion
fragmentation modes. MS/MSn analytical functions can be achieved by running
mass to
charge selection in conjunction with DC acceleration CID ion fragmentation. DC
acceleration fragmentation is achieved by accelerating mass to charged ions in
the forward or
reverse direction between adjacent. ion guides. Alternatively ions can be
fragmented using
resonant frequency excitation CID fragmentation in the volume defined within
an ion guide
segment in at least one quadrupole ion guide. Combinations of mass to charge
selection with
DC acceleration and resonant frequency excitation CID fragmentation can be run
in the
axially aligned multiple quadrupole ion guide assembly configured in a higher
pressure
vacuum region to achieve a wide range of MS/MSn analytical functions. In one
aspect of the
invention, the final mass analysis step in an MS/MSn analysis sequence can be
conducted using
a quadrupole mass analyzer. A dual quadrupole ion guide assembly can be
configured
according to the invention as part of a triple quadrupole mass analyzer.
Alternatively, a three
quadrupole ino guide assembly can be configured according to the invention
encompassing the
entire triple quadrupole mass analyzer MS and MS/MS functionality with
continuous ion
beams.
In another embodiment of the invention, a multiple quadrupole ion guide
axially aligned
assembly where at least one junction between two adjacent ion guides is
located in a higher
pressure vacuum region, is configured with a TOF mass analyzer. At least one
quadrupoie ion
guide in the multiple quadrupole assembly is configured to be operated in mass
to charge
selection and/or CID ion fragmentation mode. In on aspect of the invention,
TOF mass
analyzer is configured and operated to conduct the last mass analysis step in
any MS/MSn
analytical sequence. Single step MS/MS analysis can be achieved by first
conducting a mass to
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charge analysis step and second an ion fragmentation step with resonant
frequency excitation
or DC acceleration CID within the multiple quadrupole ion guide assembly
configured
according to the invention. The mass to charge analysis of the resulting
product ions is
conducted in the Time-Of-Flight mass analyzer. The mass to charge selection
and ion
fragmentation steps in the MS/MS analysis can be conducted with or without ion
trapping
and without stopping the primary in beam. MS/MSn analysis, where n > 1, can be
achieved
by conducting sequential mass to charge selection and ion fragmentation steps
using the
multiple quadrupole ion guide assembly configured according to the invention.
Different
methods for conducting mass to charge selection and ion fragmentation can be
combined in a
given MS/MS° sequence wherein the final mass to charge analysis step is
conducted using the
TOF mass analyzer. In one embodiment of the invention, an API source is
interfaced to the
multiple quadrupole-TOF hybrid mass analyzer configured according to the
invention.
In yet another embodiment of the invention, a segmented ion guide wherein at
least one
segment extends continuously into multiple vacuum pumping stages is configured
with a TOF
mass analyzer. At least one segment of the multiple vacuum pumping stage
segmented
multipole ion guide is configured to conduct ion mass to charge selection and
CID
fragmentation with or without trapping of ions. In one embodiment of the
invention at least
one multiple vacuum stage segmented quadrupole ion guide is included in a
multiple
quadrupole ion guide assembly configured with a TOF mass analyzer. MS/MSn
analytical
functions can be achieved by conducting one or more ion mass to charge
selection and CID
fragmentation steps in the multiple quadrupole ion guide assembly prior to
conducting mass
to charge analysis of the product ion population using the Time-Of Flight mass
analyzer. In
one embodiment of the invention, the size of the quadrupole assembly is
reduced resulting in
decreased cost and size of a benchtop API multiple quadrupole-TOF mass
analyzer. In one
aspect of the invention, the multiple quadrupole-TOF hybrid mass analyzer can
be operated
whereby ion mass to charge selection and fragmentation can be conducted in a
manner that
can duplicate and improve the performance of triple quadrupole MS and MS/MS
mass analysis
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routines. Alternatively, the same multiple quadrupole-TOF hybrid mass analyzer
can be
operated whereby ion trapping, single or multiple steps of ion mass to charge
selection and ion
fragmentation can be conducted in a manner that can duplicate and improve the
performance
of three dimensional ion trap MS and MS/MSn mass analysis routines. The same
multiple
quadrupole-TOF mass analyzer configured according to the invention can r ~n MS
and
MS/MSn routines that can not be conducted by any mass spectrometer described
in the prior
art.
,l'.
In another embodiment of the invention, multiple quadrupole ion guide
assemblies configured
and operated according to the invention, are configured in hybrid mass
analyzer that include
Fourier Transform, three dimensional ion trap or magnetic section mass
analysis. In one
aspect of the invention, segmented multipole ion guides that extend
continuously into
multiple vacuum pumping stages are configured with Fourier Transform, three
dimensional
ion trap or magnetic sector mass analyzers.
High ion transmission efficiencies can be achieved in segmented multiple
vacuum pumping
stage multipole ion guides or multiple quadrupole ion guide assemblies
configured according
to the invention. Ions can traverse between multiple ion guides configured
with the junction
between adjacent axially aligned quadrupole ion guides located in a higher
pressure vacuum
region while remaining in stable radial trajectories. Consequently minimum
loss of desired
mass to charge value ions occur during trapping in or traversing through the
multiple
quadrupole ion guide assembly configured according to the invention. In one
embodiment of
the invention, the individual RF voltage supplies applying potentials to each
individual
quadrupole assembly of the multiple quadrupole assembly have variable
amplitudes but the
same frequency and phase RF output. Consequently, ions whose m/z values have
stable
trajectories traversing the multiple quadrupole ion guide assembly length can
selectively
remain in a stable trajectory through the entire multiple quadrupole ion guide
assembly
length. Ions with low axial translational energies can be efficiently
transported through
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multiple segmented or non segmented quadrupole ion guides enabling higher
resolution in
mass selection or mass analysis operation. Ions can also be trapped in
selected sections of each
segmented or non segmented quadrupole ion guide and transferred when required
to improve
duty cycle and achieve a wide range of mass analysis operations. An important
feature of
multipole ion guides or individual segments of a segmented ion guide operated
in trapping
mode is that ions can be released from one end of an ion guide or segment
simultaneously
while ions are entering the opposite end of the ion guide or individual
segment. Due to this
feature, a segmented ion guide receiving a continuous ion beam can selectively
release only a
portion of the ions located in the ion guide into an axially aligned adjacent
ion guide or other
mass analyzer such as TOF. In this manner ions are not lost in between mass
analysis steps.
Ions can also be transferred back and forth between multipole ion guide
assemblies or between
segments within multipole ion guide assemblies allowing the performing of an
array of mass
analysis operations that are not possible with prior art mass analyzer
configurations.
Brief Description of the Figures
Ion Guide Mass Selection TOF
Figure 1 is a diagram of an Electrospray ion source orthogonal pulsing Time-Of
Flight mass
analyzer with an ion reflector configured with three independent multipole ion
guides
configured along a common axis. The third multipole ion guide extends
continuously from
vacuum stage two into vacuum stage three.
Figure 2 is a diagram of the configuration of electronic voltage and control
modules for the
three multipole ion guide assembly and surrounding electrodes diagrammed in
Figure 1.
Figure 3 is a diagram of a alternative embodiment of an Electrospray ion
source TOF mass
analyzer with orthogonal pulsing configured with two segmented multipole ion
guides.
f
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Figure 4A is a diagram of an Electrospray ion source TOF mass analyzer with
orthogonal
pulsing configured with two multipole ion guides, the second of which extends
continuously
into two vacuum pumping stages.
Figure 4B is a diagram of an Electrospray ion source, orthogonal pulsing Ti ~
e-Of-Flight mass
analyzer with a linear flight tube geometry, configured with a three segment
multipole ion
guide which extends continuously into two vacuum pumping stages.
Figure 4C is a diagram of an Electrospray ion source, orthogonal pulsing Time-
Of Flight mass
analyzer configured with a three segment multipole ion guide which extends
continuously
into 3 vacuum pumping stages.
Figure 5 is a diagram of an API TOF mass analyzer with orthogonal pulsing
configured with
three multipole ion guide assemblies the second of which extends from vacuum
stage two into
vacuum stage three the third of which is configured in the orthogonal pulsing
region of the
TOF mass analyzer.
Figure 6 is a diagram of an API source TOF mass analyzer with orthogonal
pulsing configured
with a two multipole ion guide assemblies the first of which is configured as
a three segment
ion guide that extends into the second and third vacuum pumping stages which
is configured
in the third vacuum stage.
Figure 7 is a diagram of and API TOF mass analyzer with orthogonal pulsing
which includes
a segmented ion guide assembly located in vacuum stage two and a second and
third multipole
ion guide assembly located in vacuum stage three.
Figure 8 is a portion of the stability diagram for a quadrupole ion guide.
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Figure 9 is a diagram of the cross section of a quadrupole ion guide
configured with round
rods.
Figure 10 is a diagram of an Electrospray ion source quadrupole mass analyzer
configured
with three quadrupole ion guides with the second quadrupole ion guide
extending
continuously from the second into the third vacuum pumping stage.
Figure 11 is a diagram of an API source quadrupole mass analyzer configured
with three
quadrupole ion guides. The third quadrupole ion guide is positioned in low
vacuum pressure
vacuum stage three operated with a different RF amplitude and phase compared
with the RF
applied to quadrupoles one and two.
Figure 12 is a diagram of an API source quadrupole mass analyzer configured
with a three
segment multipole ion guide assembly located in the higher pressure second
vacuum pumping
stage with its exit end extending into a second ion guide positioned in low
pressure vacuum
stage three.
Figure 13 is a diagram of an API source quadrupole mass analyzer configured
with a three
segment segmented multipole ion guide assembly with the third segment
extending
continuously from the second into the third vacuum pumping stage and a second
and third
ion guide and detector located in vacuum stage three.
Figure 14 is a diagram of an Atmospheric Pressure Chemical Ionization Source
quadrupole
mass analyzer configured with a single segment multipole ion guide that
extends continuously
from the second into the third vacuum pumping stage.
Figure 15 is a diagram of an Glow Discharge Ionization Source quadrupole mass
analyzer
configured with a three segment multipole ion guide where the third segment
extends
CA 02318855 2004-04-29
continuously from the second into the third vacuum pumping stag.
Figure 16 is a diagram of an API source quadrugole mass analyzer configured
with a
quadrupole located in the higher pressure region of the second vacuum pumping
stage and a
detector located in lower pressure vacuum pumping stage 3.
Figure 17 is a diagram of an API source quadrupole mass analyzer configured
with a three
segment ion guide located in the higher pressure region of vacuum stage two
and a detector
located in lower pressure vacuum stage three.
Figure 18 is a diagram of an API source quadrupole mass analyzer configured
with a
quadrupole located in the higher pressure region of the second vacuum pumping
stage and a
detector also located in vacuum pumping stage two.
Figure 19. is a diagram of an API source quadrupole mass analyzer configured
with a three
segment ion guide located in the higher pressure region of vacuum stage two
and a detector
also located in vacuum stage two.
Figure 20 is a diagram of a prior art multipole ion guide configuration of a
typical triple
quadrupole mass analyzer interfaced to an Atmospheric Pressure Ion source.
Detailed Description of the Invention and the Preferred Embodiments
A multipole ion guide which extends continuously from one vacuum pumping stage
into at
least one additional vacuum pumping stage configured in a mass analyzer
apparatus has been
described in U.S. patent number 5,652,427. Ion trapping within a multipole ion
guide
coupled with release of at least a portion of the ions trapped within the
multipole ion guide
followed by pulsing of the released ions into the flight tube of a Time-Of
Flight mass analyzer
flight tube is described in U.S, patent number 5,689,111. The operation of a
multipole ion
guide configured in an API TOF mass analyzer to achieve MS and MSIMSn
analytical
capability has been described in U:S. Patent No. 6,011,259. The inventions
described
in the following sections include new embodiments of multipole ion guides, new
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WAD 99/38193
configurations multiple ion guide assemblies and their incorporation into mass
analyzers with
new methods of operating said ion guides and mass analyzers. The inventions
improve the
performance and analytical capability of the mass analyzers in which they are
configured
while in some embodiments reducing the size and cost of said instruments when
compared to
prior art configurations.
Multipole ion guides have been employed for a wide range of functions
including the
transport of ions in vacuum and for use as ion traps, mass to charge filters
and as a means to
fragment ion species. A conventional multipole ion guide consists of a set of
parallel
electrodes, poles or rods evenly spaced at a common radius around a center
point. Sinusoidal
voltage or alternating current (AC or RF) potentials and +/- DC voltages are
applied to the
ion guide rods or electrodes during operation. The applied AC and DC
potentials are set to
allow a stable ion trajectory through the internal volume of the rod length
for a selected range
of mass to charge (m/z) values. These same AC and DC voltage components can be
set to
cause an unstable ion trajectory for ion mass to charge values which fall
outside the operating
stability window. An ion with an unstable trajectory will be rejected from the
ion guide
volume before the ion traverses the ion guide length. Multipole ion guides are
typically
configured with an even set of poles, 4 poles (quadrupole), 6 poles
(hexapole), 8 poles
{octapole) and so on. Odd number multipole ion guides have also been described
but have not
been commonly used in commercial instruments. Quadrupoles, hexapoles and
octapoles
operating with RF or AC only voltages applied only have been used in ion
guides in mass
spectrometer instruments. Where m/z selection is required, quadrupoles can
achieve higher
mass to charge selection resolution than hexapoles or octapoles. Quadrupole
ion guides
operated as mass analyzers have been configured with round rods or with the
more ideal
hyperbolic rod shape. For a given internal rod to rod spacing (r~, the
effective entrance
acceptance area through which an ion can successfully enter the multipole ion
guide without
being rejected or driven radially out of the center volume, increases with an
increasing
number of poles. A multipole ion guides configured a higher numbers of poles,
operated in
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RF only mode, can transfer a wider range of ion mass to charge values in a
stable trajectory
than a multipole ion guide configured with a lower number of poles. Due xo the
performance
differences in multipole ion guides with different numbers of poles, a
suitable choice of ion
guide will depend to a large measure on its application. The term triple
quadrupole is
conventionally used to describe a configuration of three multipole ion guide
axially aligned
and separated by electrodes in a single vacuum pumping stage with MS/MS
operating
capability. The collision cell in such "triple quadrupoles" is often a
hexapole or octopole
operated in RF only mode.
The multipole ion guides described in the invention can be configured with any
number of
poles. Where an assembly of individual ion guides are configured, a mixture of
quadrupole
and hexapole or octapoles may be preferred for optimal performance. Multipole
ion guide
rod assemblies have been described which are configured with non parallel and
conical rods
that can produce an asymmetric electric field on the z or axial direction
during operation.
This axial electric field can aid in pushing the ions through the length of
the ion guide more
rapidly than can be achieved with a parallel set of rods for a given
application, usually
involving high background pressure. Although, adding an axial field can aid in
ion movement
through the multipole ion guide assembly, the rod geometry configured to
provide an axial
field can compromise mass to charge selection resolution and increase the
complexity and cost
of fabrication. To aid in the clarity of the description, the inventions
described below are
configured with parallel rod or electrode assemblies. Axial fields within a
given multipole ion
guide assembly are configured in some embodiments using RF only entrance and
exit pole
sections or segments.
Single section or segmented multipole ion guide assemblies can be configured
such that at least
one segment to extends from one vacuum pumping stage continuously into at
least one
adjacent vacuum pumping stage. Individual multipole ion guides with like cross
sectional
geometries can be configured as axially aligned assemblies with at least one
junction between
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ion guides located in a higher pressure vacuum pumping region where multiple
ion to neutral
gas collisions occur. The higher background vacuum pressure region can be used
effectively to
achieve analytical functions such as collisional induced dissociation (CID) of
ions in the same
vacuum pumping stage where ion mass to charge selection is also performed.
Segmented or
non segmented multipole ion guides which extend continuously from one vacuum
pumping
stage into another in an atmospheric pressure ion source mass spectrometer
instrument can
efficiently transport ions over a wide range of background pressures.
Multipole ion guides can
deliver ions from an atmospheric pressure ion source to a mass analyzers
including but not
limited to TOF, FTMS, Quadrupoles, Triple Quadrupoles, magnetic sector or
three
dimensional ion .traps. Alternatively, assemblies of segmented or non
segmented multipole
ion guides configured with at least portion of the multiple ion guide assembly
positioned in a
higher vacuum pressure region can be operated directly as a mass analyzer with
MS and
MS/MS analytical capability.
An important feature of multipole ion guides is that ions can be released from
one end of an
ion guide assembly or segment simultaneously while ions are entering the
opposite end of the
ion guide assembly or individual segment. Due to this feature, a multipole ion
guide receiving
a continuous ion beam operataing in trapping mode can selectively release only
a portion of
the ions located in the ion guide into another ion guide, ion guide segment or
another mass
analyzer which performs mass analysis on the released ions. In this manner
ions from a
continous ion beam are not lost in during discontinuous between mass analysis
steps. One
preferred embodiment of the invention is the configuration of a hybrid API-
quadrupole-TOF
mass analyzer comprising an API source, an assembly of three quadrupole ion
guides with two
quadrupole mass analyzers operated in mass to charge selection and ion
fragmentation modes
and a Time-Of flight mass analyzer. With a multiple quadrupole ion guide
assembly
configured in such a hybrid API-quadrupole-TOF mass analyzer, a wide range of
MS and
MS/MSn analytical functions can be high duty cycle with high duty cycle, mass
to charge
resolution and mass measurement accuracy.
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In the following description of the invention, three primary configurations-
are shown with
alternative embodiments described for each configuration. The first embodiment
is the
configuration of a multiple quadrupole ion guide Time-Of Flight hybrid mass
spectrometer
apparatus. Although the hybrid instrument as described includes a TOF m ~s
analyzer, an
FTMS, magnetic sector, three dimensional ion trap or quadrupole mass analyzer
can be
substituted for the TOF MS. The second embodiment is the configuration of an
assembly of
individual quadupole ion guides with at least one~junction between ion guides
located in a
higher pressure vacuum region to achieve the MS and MS/MS analytical functions
of prior art
configurations of triple quadrupole mass analyzers. The third embodiment
described is the
configuration of a quadrupole ion guide positioned in a higher vacuum
background pressure
region and operated in mass to charge selection mode. The third embodiment can
be operated
to achieve the API MS functions of prior art configurations of low vacuum
pressure single
quadrupole mass analyzers. The small size higher pressure quadrupole ion guide
can be
configured as a smaller an lower cost when compared to prior art API MS
intruments.
A preferred embodiment of the invention is diagrammed in Figure 1. A linear
assembly 8 of
three independent quadrupole ion guides is configured in a four vacuum pumping
stage hybrid
API source-multiple quadrupole-TOF mass analyzer. Referring to Figures 1 and
2, multiple
quadrupole ion guide assembly 8 comprises three independent quadrupole ion
guide
assemblies 60, 61 and 62, positioned along common axis 5. Alternatively,
quadrupole ion
guide assemblies 60, 61 and 62 pole ion guide can be configured with six,
eight or more rods or
poles, however, the ion mass to charge selection resolving power that can be
achieved using
multipole ion guides decreases as the number of poles increases. Higher ion
mass to charge
selection resolution can be achieved with quadrupoles (four poles) when
compared with
hexapoles (six poles), octapoles (eight poles) or ion guides with more than
eight poles or odd
numbers of poles. Consequently, quadrupoles have been commonly used as mass
analyzers.
Hexapoles and octapoles which have a broader m/z stability window and a larger
effective
CA 02318855 2000-07-24
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entrance acceptance area, when compared to quadrupoles, are often used in RF
only mode to
efficiently transport and trap ions in low and higher pressure vacuum regions.
The multipole
ion guides diagrammed in the preferred embodiments presented will be described
as
quadrupoles as this configuration can achieve increased ion mass to charge
selection resolution
compared with the performance of multipole ion guides with higher numbers of
poles.
However, for some functions and methods of invention, multipole ion guides
configured with
six or more poles can be readily substituted for the quadrupole ion guides
used in the
embodiments diagrammed.
Quadrupole ion guide assembly 60 comprises four parallel electrodes, poles or
rods equally
spaced around a common centerline 5. Each pole comprises two sections. Each
electrode of
section 1 has a tapered entrance end contoured to match the angle of skimmer
26. Power
supply 63 applies RF, AC and DC potentials to both segments of segmented
quadrupole 60.
Quadrupole assembly 60, 61 and 62 are configured along common axis 5 where the
junctions 7
and 10 between each independent quadrupole assembly are positioned in higher
pressure
vacuum stage 72. Vacuum stages 71, 72, 73 and 74 are typically maintained at
pressures 1 to 2
torr, 1 to 10 millitorr, 1 to 8 x 10-5 torr and 1 to 5 x 10-~ torr
respectively. Ions experience
several collisions with the neutral background gas molecules as they traverse
the volume
defined by quadrupoles 60, 61 and 62 in vacuum stage 72. Unlike the prior art,
no electrodes
are configured in junctions 7 and 10 between independent quadrupole assemblies
60, 61 and
62. To avoid fringing field effects and maximize ion transmission between
quadrupole
assemblies, quadrupole ion guide assemblies 60, 61 and 62 are configured with
the same radial
cross section geometries with poles aligned. In addition, independent RF
generators
configured in power supplies 63, 64 and 65 are sychronized to apply the same
RF frequency
and phase to axially aligned adjacent quadrupole electrode. As will be
described below
individual quadrupole ion guide assemblies 60 and 62 can be independently
operated in mass
to charge selection and ion fragmentation modes to achieve MS/MSn functions
with Time-Of
Flight mass analysis. Segmented ion guides are configured such that the same
RF voltage
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supply applies voltage to all segments of the ion guide assembly. Junction 6
between segments
1 and 2 is configured to of maximize capacitive coupling between adjacent
axially aligned
poles. RF is typically capacitively coupled to each quadrupole section in a
segmented ion
guide. This allows different DC offset potentials to be applied to different
sections of a
segmented ion guide to affect ion movement through the segmented multiple ion
guide.
Typically sections positioned at a quadrupole entrance end are operated in RF
only mode to
minimize fringing field effects when the analytical section of the segmented
quadrupole is
operated in mass to charge selection mode. Junctions 7 and 10 between
quadrupole'assemblies
60 and 61 and 61 and 62 respectively are configured according to the invention
to eliminate or
minimize capacitive coupling between independently operating quadrupole
assemblies. Beat
frequency or constructive of destructive interference between waveforms
between quadrupole
assemblies 60 and 62 during ion mass to charge selection and fragmentation
operation is
prevented by eliminating capacitive coupling between the two quadrupole
assemblies.
Quadrupole assembly 61 with independent RF and DC power supply 64 prevents or
minimizes capacitive coupling between quadrupole assemblies 60 and 62 while
maximizing
ion transfer efficiency along the multiple quadrupole assembly axis 5.
Alternatively,
quadrupole 61 can be configured as a single flat electrode with an aperture
centered on
centerline 5 with DC applied to isolate quadrupole assemblies 60 and 62. The
preferred
embodiment is the configuration of quadrupole 61 having the same radial cross
section as
quadrupoles 60 and 62 with poles axially aligned.
In an ideal quadrupole ion guide the pole shapes would be hyperbolic but
commonly, for ease
of manufacture, round rods are used. A cross section of a quadrupole with
round rods 104,
105, 106, and 107 is diagrammed in Figure 9. The same AC and DC potentials are
applied to
opposite pole sets (104, 106 and 105, 107) for most quadrupole operating
modes. Adjacent
poles have the same primary RF frequency and amplitude but a phase difference
of 180
degrees. When the offset or common DC potential is subtracted, adjacent poles
generally have
the same amplitude but opposite polarity DC potentials applied. In addition to
the primary
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RF electrical component resonant frequency AC voltage can be applied to the
quadrupole
rods to achieve m/z selection and ion fragmentation functions. A common DC
offset can be
applied to all rods 104, 105, 106, and 107 as well. The primary RF, opposite
polarity DC,
common DC and resonant frequency potentials can be applied simultaneously or
in part to
the poles of a segmented quadrupole ion guide to achieve a range of analytical
functions.
When an ion guide is segmented into sections, each pole or rod is broken up
into electrically
insulated sections which, when assembled, align as a single continuous rod.
Each segment
within a rod assembly is electrically insulated from its adjacent segments.
The insulation is
configured between each rod section to minimize space charge effects which
could distort the
electric fields within the region bounded by the rods. Junctions 7 and 10
between quadrupole
assemblies 60 and 61 and 61 and 62 respectively are configured to minimize
space charge
effects and RF field distortion to maximize stable ion transmission efficiency
between
individual quadrupole ion guides 60, 61 and 62 multiple quadrupole ion guide
assembly 8.
In the embodiment shown in Figure 1, segmented quadrupole assembly 60,
quadrupole
assembly 61 and the entrance end of multiple vacuum stage quadrupole assembly
62 are
positioned in second vacuum pumping stage 72 where the operating background
pressure is
greater than 1 x 10~ torr. At background pressures greater than 1x10 torr,
typically
maintained in the 1 to 10 millitorr range, ions traversing the multiple
quadrupole assembly
length will encounter collisions with the neutral background gas. One or more
quadrupole
assemblies of multiple quadrupole ion guide assembly 8 can be operated in mass
to charge
selection mode. Mass to charge selection operation can be achieved by applying
a
combination of RF and DC potentials, applying specific resonant frequencies at
sufficient
amplitude to reject unwanted ion m/z values, ramping the RF frequency or
amplitude with or
without +/- DC ramping or combinations of these techniques. Those portions
multiple
quadrupole assembly 8 located in the higher pressure region of vacuum stage 72
can also be
configured to operate in ion transfer, ion trapping, and Collisional Induced
Dissociation
fragmentation modes as well as m/z selection mode or with combination of these
individual
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operating modes. Operating a portion of multipole ion guide in higher
background pressure
in an API MS system can improve ion transmission efficiencies as was described
in U.S.
patents 5,652,427 and 4,963,736. In m/z analysis or m/z selection operating
mode, ion
collisions with the background gas slow down the selected ion m/z trajectories
in the radial
and axial directions as the ions traverse the multipole ion guide length in
single pass or
multiple pass ion trapping mode. Ions spending increased time in the multipole
ion guide are
exposed to an increased number of RF cycles. In this manner higher m/z
selection resolution
can be achieved for shorter multipole ion guide lengths than can be attained
using a ''~
quadrupole mass analyzer with the more conventional method of operating in low
background pressure single pass non trapping mode. Operating multipole ion
guides in mass
selection mode in higher pressure background gas allows the configuration of
smaller more
compact systems with reduced vacuum pumping speed requirements. A smaller
multipole ion
guide configuration reduces the cost of driver electronic and the higher
pressure operation
reduces the vacuum system costs. An instrument configured with a segmented
multipole ion
guide, a portion of which is configured in a higher vacuum pressure region can
achieve
improvement in the API MS system performance at lower cost when compared to an
instrument which includes one or more quadrupole mass analyzer operating at
background
pressure maintained low enough to avoid or miniriiize ion collisions with
neutral background
gas.
Electrospray probe 15 in Figure 1 can be configured to accommodate solution
flow rates to
probe tip 16 ranging from below 25 nl/min to above 1 ml/min. Alternatively,
the API MS
embodiment diagrammed in Figure 1 can be configured with but is not limited to
Atmospheric Pressure Chemical Ionization (APCI), Inductively Coupled Plasma
(ICP), Glow
Discharge (GD) source, multiple probes in one source, or combinations of
different probes in
one source. Ion sources which operate in vacuum or partial vacuum such as but
not limited
to Chemical Ionization (CI), Electron Ionization (E1), Fast Atom Bombardment
(FAB), Flow
FAB, Laser Desorption {LD), Matrix Assisted Laser Desorption Ionization
(MALD~,
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Wt, 99/38193 PCTNS99/01335
Thermospray (TS) and Particle Beam (1'B) can also be configured with the
hybrid mass
analyzer configuration diagrammed in Figure 1. Sample bearing solution can be
introduced
into ES probe 15 using a variety of liquid delivery systems. Liquid delivery
systems may
include but are not limited to, liquid pumps with or without auto injectors,
separation
systems such as liquid chromatography or capillary electrophoresis, syringe
pumps, pressure
vessels, gravity feed vessels or solution reservoirs. ES source 12 is operated
by applying
potentials to cylindrical electrode 17, endplate electrode 18 and capillary
entrance electrode 19.
Counter current drying gas 21 is directed to flow through heater 20 and into
ES source
chamber 12 through endplate nosepiece 24 opening 22. Orifice 57 into vacuum as
shown in
Figure 1 is the bore through dielectric capillary tube 23 with entrance
orifice 13. The
potential of an ion being swept through dielectric capillary tube 23 into
vacuum is described
in U.S. patent number 4,542,293. Ions enter and exit the dielectric capillary
tube with
potentials roughly equivalent to the entrance and exit electrode potentials
respectively. The
use of dielectric capillary 23 allows different potentials to be applied to
the entrance and exit
ends of the capillary during operation. This effectively decouples the API
source from the
vacuum region both physically and electrostatically allowing independent
tuning optimization
of both regions. To produce positive ions, negative kilovolt potentials are
applied to
cylindrical electrode 17, endplate electrode 18 with attached electrode
nosepiece 24 and
capillary entrance electrode 19. ES probe 12 remains at ground potential
during operation.
To produce negative ions, the polarity of electrodes 17, 18 and 19 are
reversed with ES probe
12 remaining at ground potential. Alternatively, if a nozzle or conductive
(metal) capillaries
are used as orifices into vacuum, kilovolt potentials can be applied to ES
probe 12 with lower
potentials applied to cylindrical electrode 17, endplate electrode 18 and the
orifice into
vacuum during operation. With conductive orifices or capillaries, the entrance
and exit
potentials are equal, so the API source potentials are no longer decoupled
from the vacuum
region potentials. Heated capillaries can be configured as the orifice into
vacuum used with or
without counter current drying gas.
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With the appropriate potentials applied to elements in ES source chamber 12,
Electrosprayed
charged droplets are produced from a solution or solutions delivered to ES
probe tip 16. The
charged droplets Electrosprayed from solution exiting ES probe tip 16 are
driven against the
counter current drying gas 21 by the electric fields formed by the relative
po~ ntials applied to
ES probe 15 and ES chamber 12 electrodes I7, 18, and 19. A nebulization gas 48
can be applied
through a second layer tube surrounding the sample introduction first layer
tube to assist the
Electrospray process in the formation of charged liquid droplets. As the
droplets evaporate,
,;.
ions are formed and a portion of these ions are swept into vacuum through
capillary~orifice
57. If a heated capillary is configured with heater 25 as an orifice into
vacuum with or
without_counter current drying gas, charged droplet evaporation and the
production of ions
can occur in the capillary as charged droplets traverse the length of
capillary orifice 57 towards
first vacuum pumping stage 71. A portion of the ions entering first stage
vacuum 71 are
directed through the skimmer orifice 27 and into second vacuum stage 72.
Ions produced at or near atmospheric pressure from sample bearing liquid in
atmospheric
pressure ion source 12 are delivered into vacuum through dielectric capillary
tube 23 carried
along by the neutral background gas. Vacuum partition 53 includes a vacuum
seal with
dielectric capillary 23. The neutral background gas forms a supersonic jet as
it expands into
vacuum through capillary exit orifice 14 and sweeps the entrained ions along
through multiple
collisions during the expansion. The hybrid mass analyzer diagrammed in Figure
1 is
configured with four vacuum pumping stages to remove background neutral gas as
the ions of
interest traverse from the API source through each vacuum stage during
operation. The cost
and size of an API/MS instrument can be reduced if it is configured with
multiple vacuum
pumping stages and the pumping speed required for each stage is minimized.
Typically, three
to four and in some cases more than four pumping stages are employed in API/MS
instruments. With the development of multiple vacuum stage (interstage)
turbomolecular
vacuum pumps, three and even four stage vacuum systems require only one rotary
and one or
two turbomolecular pumps to achieve satisfactory background pressures in each
stage.
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WO 99138193 PCT/US99/01335
Multipole ion guides operated in the AC or RF only mode have been configured
in API/MS
instruments to transport ions efficiently through second and/or third vacuum
pumping stages
72 and 73. In the four vacuum pumping stage embodiment diagrammed in Figure 1,
a rotary
vacuum pump is used to evacuate first vacuum stage 71 through pumping port 28
and the
background pressure is maintained in first vacuum stage 71 is maintained
typically between
0.2 and 2.5 torr. A portion of the free jet expansion and the entrained ions
pass through
skimmer orifice 27 and into second vacuum pumping stage 72. Skimmer 26 forms a
part of
vacuum partition 52 dividing first and second vacuum pumping stages 71 and 72.
Background
pressures in second vacuum stage 72 can typically range from 10~ to 2 x 10-1
torr depending
on skimmer orifice 27 size and the pumping speed employed in second vacuum
stage 72
through vacuum pumping port 29.
Ions entering second vacuum stage 72 through skimmer orifice 27 enter
segmented multipole
ion guide 8 where they are trapped radially by the electric fields generated
from the multipole
rod assembly. The locally higher pressure at the entrance region 9 of
segmented multipole ion
guide 8 damps the ion trajectories as they pass through the fringing fields of
the at the entrance
end 9 of multipole ion guide 8. This locally higher pressure region at
entrance region 9 results
in a high capture efficiency for ions entering multipole ion guide 8. Ion m/z
values that fall
within the operating stability window will remain radially confined within the
internal
volume described by the rods of segmented multipole ion guide 8. If segment 1
of multipole
ion guide 8 is operated in RF only mode, a broad range of m/z values can be
efficiently
transferred into ion guide segment 2 when the appropriate relative bias
voltages are applied
between segments 1 and 2. Similarly, when the appropriate relative bias
voltages are applied
between multipole ion guide segments 2, 3 and 4. ions traversing multipole ion
guide segment
2 can pass into segment 4. Ions pass into third vacuum pumping stage 73 while
traversing the
len Fgth of segment 4 of segmented multipole ion guide 8. Multipole ion guide
segment 4 passes
through but is electrically insulated from vacuum partition 32. Third vacuum
stage 73 is
evacuated through vacuum pumping port 30. Ions exit segmented multipole ion
guide
f
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l
assembly 8 at exit end 10 and pass through electrostatic lenses 33, 34, and 35
into pulsing
region 37 of Time-Of-Flight mass analyzer 40. Lens 33 is configured as part of
vacuum
partition 36 between pumping third and fourth vacuum stages 73 and 74.
Time-Of Flight mass analyzer 40 is configured in fourth vacuum stage 74 and
this vacuum
stage is evacuated through pumping port 31. Fourth vacuum stage 74 is
typically maintained
in the low 10-6 to 10 ~ torr vacuum pressure region. TOF pulsing region 37 is
bounded by
,f
electrostatic lenses 41 and 42. Ions which exit from multipole ion guide 8
move into~TOF
pulsing region 37 can be pulsed into the TOF mass analyzer or can continue
through pulsing
region 40 passing through orifice 55 in lens 54. By applying appropriate
voltages to lens 54,
channeltron detector 38, conversion dynode 39 and Faraday cup 56, ions passing
through
orifice 55 can be directed to impact on conversion dynode 39 or be collected
in Faraday cup
56. In the mass analyzer embodiment diagrammed in Figure 1, ions entering TOF
pulsing
region 37 can be either TOF mass analyzed, detected by channeltron detector 38
or detected
with Faraday cup 56. Ions enter TOF pulsing region 37 when lenses 41, 42 and
43 are set at
the approximately the same potential. In the TOF configuration diagrammed in
Figure 1,
TOF flight drift region 58 is maintained at kilovolt potentials when the
appropriate voltage is
applied to lens 60. Negative voltage is applied to lens 60 for positive
polarity ions and positive
voltage is applied for negative polarity ions TOF during operation. With TOF
drift region 58
maintained at kilovolt potentials, a voltage value at or near ground can be
applied to pulsing
lenses 41, 42 and 43 when ions are entering and pulsing region 37. Positive
ions are pulsed
into TOF drift region 56 by raising the potential of pulsing lens to 41 some
positive voltage,
raising 42 to approximately half that positive voltage, and leaving lens 43 at
ground potential.
The positive ions are accelerated out of pulsing region 37 and to entrance 49
of TOF drift
region 58. The velocity of ions traversing drift region 58 remains constant
until ions enter ion
reflector 50 at entrance point 51. Ions entering ion reflector 50 are
initially decelerated and
then re-accelerated beginning at point 45, exiting the reflector at point 44.
Once again, the
velocity of the ions traversing drift region 58 is constant until the ions
through flight tube lens
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60 grid at point 46. Ions are post accelerated from point 46 onto the surface
of multichannel
plate detector 47 where they are detected. Negative ions are pulsed from
pulsing region 37
and directed to the surface of detector 47 in a similar manner by reversing
the voltage
polarities. Limited by the flight time of the highest m/z value ion being
detected, ions can
typically be pulsed from pulsing region 37 at a pulsing rate of up to 20,000
times per second.
The full mass spectrum pulsed ion signals detected can be added to produce
over 100 spectra
per second saved to disk. Signal from detector 47 can be recorded with data
acquisition
systems using Analog to Digital (A/D) converters or Time to Digital converters
(TDC).
Tirne-Of Flight mass analyzer 40 has the capability of detecting full mass
spectra of all m/z
value ions traversing pulsing region 37. The TOF mass analysis step, initiated
with
orthogonal pulsing of ions into drift region 58, is decoupled from many
trapping, nontrapping,
mass selection or ion fragmentation steps which occur prior to the resulting
ion population
entering pulsing region 37. Using the embodiment diagrammed in Figure 1, full
mass spectra
is generated at maximum resolution and sensitivity and if required, at rapid
spectra acquisition
rates.
Provided that the ion population delivered to pulsing region 37 is properly
focused with a
minimum off axis component of energy, a range of analytical functions can be
achieved
upstream of pulsing region 37 without modifying optimal tuning of TOF mass
analyzer 40.
The hybrid mass analyzer embodiment diagrammed in Figure 1 is configured to
allow a
variety of MS and MS/MSn experiments to be conducted using a number of
different
techniques. Several combinations of m/z selection and ion fragmentation and
mass analysis
can be performed sequentially or simultaneously using the embodiment
diagrammed in Figure
1. At least five types of collisionally induced ion fragmentation can be
performed. These
include:
''' 1. ion acceleration through higher pressure gas in the capillary to
skimmer region,
2. single or multiple ion resonant frequency excitation fragmentation a
multipole
ion guide segments 1, 2 or 4 with or without trapping.
l
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PCT/US99/01335
'WO 99/38193
3. ion acceleration from one segment to another in multipole in guide 8 with
or
without trapping
or,
4. higher energy ion acceleration into multipole ion guide 8 from ion guide
exit
lenses 36 and 34.
5. overfilling of an ion guide segment until Cm fragmentation occurs.
At least four types of single or multiple ion mass to charge value selection
techniques~can be
used with multipole ion guide 8 including:
1. Resonant frequency rejection of unwanted ion m/z values with or without
trapping in a given ion guide segment.
2. Applying AC and DC potentials to the rods of an ion guide segment to
achieve
ion m/z selection with or without trapping.
3. Scanning RF amplitude or frequency to remove unwanted ion m/z values from
an ion guide segment with or without trapping.
4. Controlling the release of trapped ions into TOF pulsing region 37 as
described
in U.S. patent 5,689,111.
Combinations of m/z selection and fragmentation techniques can be selected to
optimize
performance for a given analytical application. Some examples of combining
techniques to
achieve optimal MS or MS/MS~' are given below.
Mass selection can be performed with trapping with and without cutting off the
ions
primary ion beam from entering a given segment where ion mass to charge
selection or Cm
fragmentation is being conducted. Electrospray ion source 12 delivers a
continuos ion beam
into vacuum. By trapping and release of ions in multipole ion guide 8, a
continuous ion beam
from ES source 12 can be efficiently converted into a pulsed ion beam into TOF
pulsing
region 37 with very high duty cycle as is described in U.S. patent 5,689,111.
Segmented
CA 02318855 2004-04-29
multipole ion guide 8 can be operated in non trapping or trapping mode where
all segments or
only selected segments are operated in trapping or non trapping triodes.
Specific examples of
segmented ion guide operating modes will be described below as a means to
achieve MS,
MS/MS and MSIMSa analytical functions. Iii the simplest. case, segmented ion
guide 4 can be
operated as a non segmented ion guide by applying the same AC and DC
potentials to all
segments of each pole. Single segment MS and MS/MSn TOF operating sequences
are
described in U.S. Patent No. 6,011,259 dated January 4, 2000 and need not be
repeated here.
Instead techniques using multiple segment ion guide operation will be
described.
MS TOF Punctions
:Consider conducting an MS experiment with and.without ion fragmentation. If a
specific range of ion mass to charge is of interest, one or more multipole ion
guide segments
can be operated in m/z selection mode. Narrowing the mlz charge range of ions
entering
TOP pulsing region 37 can improve the duty cycle and TOF system performance in
trapping
and in non trapping mode. Narrowing the rauge~ of m/z values pulsed into TOF
drift region
58 allows an increase in TOF pulse .rate and duty cycle in non trapping ion
guide operation. If
a broad range of ion m/z values are pulsed into TOF drift region 58, the pulse
rate is limited
by the flight time of the heaviest ion m/z. If the next TOF pulse occurs
before the all ions
from the previous pulse impact on detector 47 then ions from the previous
pulse will arrive
during acquisition of the subsequent pulse causing chemical noise in the mass
spectrum
acquired. Restricting the range of m/z ions entering TOF drift region 58
allows the setting of
a maximum TOF pulse rate while eliminating chemical noise contributions from
adjacent
pulses. preventing unwanted ion mlz values from entering TOF drift region 58
also allows
more. efficient detector response for those ion m/z values of interest. When
an ion impacts a
channel of a multichannel plate detector, that channel requires a certain
recovery time ~rom its
ch 'age depletion. This charge depletion recovery time can be as long as one
millisecond
during which any ion impacting on this channel would not be detected or would
result in
reduced secondary electron yield. For example, the arrival of ions from a
strong solvent peak
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CA 02318855 2000-07-24
PCT/US99/01335
WO 99!38193
signal at low m/z value may be of no interest in a particular analytical
experiment but ma~~
deaden a significant number of detector channels in TOF each pulse prior to
the arrival of
higher m/z value ions in the same pulse. The impact of the solvent peak m/z
ions on the
detector may reduce the full signal from subsequently arriving ions. Rejecting
undesired m/z
value ions from the multipole ion guide prior to TOF pulsing to limit the io~
population
pulsed into flight tube drift region 56 to only those m/z values of analytical
interest for a
given application, helps to improve the TOF sensitivity, consistency in
detector response and
~f~
improves detector life.
Non trapping or trapping mass to charge selection can be conducted in
multipole ion
guide segment 1, 2 or 4. Consider an example where it is desirable to restrict
the m/z range of
ions entering TOF pulsing region 37 to the range from 300 to 500 m/z. This can
be achieved
by a number of methods, a few of which are described in the following
examples;
1. Multipole ion guide segment 1 is operated in non trapping RF only mode,
operate
segment 2 with a low mass cutoff of 300 m/z by applying the appropriate DC an
AC
amplitudes, segment 3 is operated in non trapping RF only mode and segment 4
is operated in
trapping mode with a high mass cutoff of 500 m/z with multiple resonant
frequency ejection
while retaining an m/z stability window for m/z values below 500 m/z. Ions are
trapped in
segment 4 and released into TOF pulsing region 37 by gating ions with lens 33,
a combination
of 33 and 34 or by switching values of the ion guide offset potentials. Such
ion trapping and
release techniques are described in U.S. patent 5,689,111. Ions trapped in
segment 4 are
prevented from moving back into segment 2 by applying the appropriate relative
offset
potentials to the poles of segments 2 and 3. In this manner, ions moving
through segmented
multipole ion guide 8 which have m/z values above 500 and below 300 will be
rejected before
entering TOF pulsing region 37.
2. Multipole ion guide segment 1 is operated in non trapping RF only mode to
maximize ion transmission into segment 2. RF and DC amplitude values are
applied to
segment 2 to pass a m/z range approximately 300 to 500. Segment 4 is operated
in RF only
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CA 02318855 2000-07-24
WO 99/38193 PCT/US99/OI335
trap and release mode where the ion gate release and TOF pulse delay timing is
set to pulse
m/z -values ranging from 300 to 500 into TOF drift region 58 pulsing at a rate
of 10,000 Hz.
3. Multipole ion guide segment 1 is operated in non trapping RF only mode to
maximize ion transmission into segment 2. A range of resonant frequencies are
added to the
RF of segment 1 to reject ions above m/z 500 and below m/z 300. Segment 4 is
operated in
RF only trap and release mode Pulsing at a rate of 10,000 Hz.
Other combinations of multipole ion guide segment operation can be performed
to
achieve the desired m/z range values released into TOF drift region 58. Based
on analytical
objectives, the choice of m/z selection or fragmentation in each multipole ion
guide segment
should be made to maximize performance, particularly ion transmission
efficiency. The
application of RF and DC to achieve mass selection in quadrupoles may decrease
the effective
entrance acceptance aperture, reducing ion transmission efficiency for the
m,/z values of
interest. If mass to charge selection can be achieved with resonant frequency
rejection of
unwanted ions the quadrupole is operating essentially in RF only mode so that
the effective
segment entrance acceptance area is not reduced. Mass to charge selection with
resonant
frequency rejection of unwanted ions also allows the selection of distinct
multiple ion m/z
values where ion m/z values falling between selected ion m/z values may be
rejected. If a
narrow m/z selection was desired say 1 m/z unit wide for an MS/MS experiment
rather than
the 200 m/z range given above, then the m/z selection technique which yields
the highest
transmission efficiency would be selected. Resonant frequency rejection or
combined RF and
DC m/z selection techniques with trapping to achieve higher resolution m/z
selection can be
applied uniformly or in combination to single or multiple segments of
multipole ion guide 8.
Ion trapping during m/z selection allows the ion population in a given segment
to be exposed
to more RF cycles before being released to an adjacent segment, effectively
increasing m/z
selection resolution. Ion collisions with the background neutral gas pressure
in second
vacuum stage 72 aids in maintaining stable trajectories in segments 1 through
4 for ions which
fall in the ion guide stability window. Trapping ions in a given segment
allows time for ions
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CA 02318855 2000-07-24
'~O 99/38193 PCT/US99/01335
which fall outside the stability window, established by the voltages applied
to the segment
poles, to be rejected from the multipole _ion guide even in the presence of
ion to neutral gas
collisions.
Although different RF frequencies can be set on each segment of multipole ion
guide 8,
applying the same RF frequency to segments 1 through 4 minimizes the fringing
fields
between segments and maximizes the efficiency of ion transfer from one segment
to the next.
Ion m/z values falling within the stability region can move freely from one
multipol~'ion
guide segment to the next when the same RF frequency is applied to all
segments. The RF
amplitude may be set to different values for each ion guide segment to achieve
a range of
analytical functions. However, reduction in cost of electronics can be
achieved if the same
RF frequency and amplitude is applied to each ion guide segment. Tradeoffs
between system
cost and performance flexibility can be decided based on specific analytical
applications
requirements. In the most flexible embodiment, each segment of multipole ion
guide 8 will
have it own independently controlled, DC, RF and resonant frequency supplies
connected to
the poles of each segment. A wide range of analytical functions can be
achieved by
independently controlling the RF frequency, amplitude, offset DC amplitude, +/-
DC
amplitude and resonant frequency amplitude and frequency spectrum. The
amplitude and
frequency components independently set by random wave form generator can be
used to
apply simple or complex AC wave forms to the poles of a given segment to
achieve a range of
simultaneous or sequential mass to charge selection and/or CID fragmentation
analytical
functions. Minimally, each multipole ion guide segment would have an
independent DC
offset supply or supplies where the DC offset value for a given segment can be
rapidly
switched during an analytical sequence.
Conversion dynode 39 with detector 55 has been configured to detect ions which
traverse
pulsing region 37 and are not pulsed into TOF drift region 58. Segments 2 or 4
of segmented
multipole ion guide 8 can be operated in non trapping mass to charge selection
scan mode
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CA 02318855 2000-07-24
Wfl 99/38193 PCT/US99/01335
with ions detected by detector 55. Alternatively ions can be fragmented with
resonant
frequency excitation in segment 2 while mass to charge scanning segment 4.
Ions exiting
segment four pass through TOF pulsing region 37 and through aperture 55 of
lens 54 where
they are detected on detector 38. Alternatively, ions can be detected using
Faraday cup 56.
Detector 38 and Faraday cup 56 can be used as diagnostic tools or in some
analytical
applications. The use of TOF as a full mass spectrum detector will yield
higher analytical
duty cycle and hence sensitivity than analytical techniques utilizing scanning
modes with
segments of multipole ion guide 8.
MS/MSn TOF Functions
The mass analyzer embodiment diagrammed in Figure 1 comprises a four segment
multipole
ion guide where segments 1, 2 and 3 and the entrance end of segment 4 are
located in the
second vacuum pumping stage 72. By setting the appropriate skimmer orifice 27
size and
vacuum pumping speed through vacuum port 29, the background pressure in second
vacuum
stage 72 can be maintained between lx 10~ to over 500 millitorr with
reasonable vacuum
pumping speeds. For many of the operational sequences described below a
background
pressure should be maintained where multiple collisions between ions and
background gas
occurs as ions traverse the on guide length but the mean free path is
sufficiently large that ions
can be rejected from multipole ion guide 8 with ion m/z selection with AC and
DC or
resonant frequency rejection within an experimentally useful time frames. The
optimal
background pressure will be a function of the multipole ion guide geometry
including pole to
pole spacing and individual segment lengths and the range of MS/MSn functions
that the
instrument will be required to perform. For purposes of discussion, consider
that the
background pressure in second vacuum stage 72 is maintained at pressure
between one and ten
millitorr. One to ten millitorr is a typical operating pressure found in of
three dimensional
quadrupole traps and the multipole ion guide collision cells of triple
quadrupoles. The
background gas in three dimensional ion traps is typically helium and the
background gas
introduced~nto the collision cell of a triple quadrupole is typically Argon.
The background
CA 02318855 2000-07-24
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gas in second vacuum stage 72 will be the composition of countercurrent drying
gas 21 from
ES source 12. This is typically nitrogen. The composition of the background
gas in second
vacuum stage 2 can be controlled and maintained quite uniform at all times
during MS
operation. The pressure in ES source I2 atmospheric chamber is maintained
close to
atmospheric pressure and the temperature in capillary bore 57 is steady state
wring MS
operation so that the choked gas flux through capillary orifice 57 is
consistent for during MS
operation. In the embodiment diagrammed in Figure 1, skimmer orifice 27 is
typically
positioned inside the supersonic free jet zone of silence upstream of the
normal shock:
Consequently, the gas flux into second vacuum stage 72 is consistent over time
during MS
operation. The background pressure consistency in second vacuum stage 72 is
primarily
determined by the consistency of vacuum pumping speed through vacuum port 29.
The use
of turbomolecular vacuum pumps to evacuate second stage 72 provides consistent
pumping
speeds over extended time periods. With the ability to monitor turbomolecular
pump RPM,
the consistency of pumping speed can be monitored both through vacuum gauge
reading and
pumping speed verification. With a consistent composition and pressure for the
neutral
background gas in second vacuum stage 72, consistent and repeatable results
can be obtained
for a wide range of experimental sequences performed.
The background pressure present in second vacuum stage 72, ions is
sufficiently high to be
used for ion fragmentation through Cm processes but not so high that m/z
selection
performance or ion transmission efficiency is compromised. The configuration
of segmented
multipole ion guide 8 combined with TOF mass analysis diagrammed in Figure 1
allows for
performing all MS and MS/MS functions of triple quadrupoles, all MS and MS/MSn
functional sequences of three dimensional ion traps and can perform several MS
and MS/MSn
functions that are not possible with either triple quadrupoles or three
dimensional quadrupole
ion traps. The embodiment shown in Figure 1 is a hybrid mass analyzer which
can perform a
wide range of mass analysis analytical functions than is available
individually from
commercially available triple quadrupoles and ion trap mass spectrometers.
Examples of some
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MS/MSn functions that can be performed with the hybrid TOF embodiment
diagrammed in
Figure 1 will be described below.
MS/MS Hybrid TOF Functions
Four primary MS/MS operating modes are used in triple quadrupoles which
employs DC ion
acceleration into an RF only collision cell to achieve Cff~ fragmentation.
These four modes
include:
1. transmitting a selected m/z range in quadrupole 1, fragmented the selection
ions in the RF only collision cell while scanning quadrupole 3,
2. neutral loss scan, where quadrupole 1 and 3 are scanned simultaneously with
a
fixed m/z offset,
3. scanning quadrupole 1 while setting quadrupole 3 to pass a selected m/z
range,
and
4. Setting both quadrupole 1 and 3 to pass different m/z values without
scanning
to monitor selected fragmentation events.
The embodiment of a hybrid TOF shown in Figure 1 produce full spectrum
fragment ion data
at higher sensitivity and resolution for all four types of triple quadrupole
operating modes
listed above. First, some, segmented ion guide TOF operational sequences to
achieve MS/MS
data with fixed m/z range selection in the first quadrupole of a triple
quadrupole and m/z
scanning of quadrupole 3 will be described below. As full TOF mass spectrum
acquisition is
performed on the fragment ions, the same segmented ion guide TOF MS/MS
operational
sequence can accommodate triple quadrupole operating modes 1 and 4 above.
MS/MS analysis requires the steps of 1 mass to charge selection, 2
fragmentation of the
selection m/z ion and 3 mass analysis of the first generation fragment or
product ions. The
mass to charge analysis step in any given MS/MS sequence will be performed
with TOF mass
analyzer 40. The mass to charge selection and ion fragmentation steps will be
performed in
segmented multipole ion guide 8 with additional ion fragmentation, when
required,
I
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WO 99/38193 PCTNS99/01335
performed in the capillary to skimmer region. An MS/MS experimental sequence
can be
conducted which results in fragment ions similar to those produced in a triple
quadrupole
MS/MS experiment. Alternatively, using a different experimental sequence,
fragment ion
populations can result which are similar to those produced in an ion trap
MS/MS experiment.
First consider a triple quadrupole MS/MS experiment where a single parent ion
species is
selected using the first quadrupole, the selected m/z range ions are
fragmented using CID in
the triple quadrupole collision cell and the third quadrupole is scanned to
detect the first
generation fragment ions. Effectively replacing quadrupole three, TOF mass
analyzer 40 is
used with considerably higher duty cycle in the embodiment shown in Figure 1
to
simultaneously detect a full spectrum of the first generation fragment ions
produced. The
initial ion mass to charge selection and fragmentation steps are performed in
segmented ion
guide 8 using the following technique.
1. Segment 1 is operated in RF only non trapping and non mass selection mode
(no
resonant frequency excitation) passing a wide m/z range of ions. Segment 1 has
the
same RF amplitude and frequency as that applied to segment 2.
2. RF and DC voltages are applied to segment 2 which is operated close to the
Mathieu
stability for a selected m/z range of ions. Ions whose mass to charge values
fall
outside the Mathieu stability region will be rejected as they traverse the
length of
segment 2. The DC offset potential applied to segments 1 and 2 allow ions to
pass
from segment 1 into segment 2 with maximum ion transmission but no
fragmentation.
3. Segments 3 and 4 of multipole ion guide 8 are operated in RF only mode with
an RF
frequency applied which equals that of segments 1 and 2. The RF amplitude
applied
to segments 3 and 4 may or may not match that of segments 1 and 2 depending on
m/z range of the product ions. The DC offset potential applied between
segments
2, 3 and 4 serve to accelerate ions from segment 2 through segment 3 and into
segment 4 with sufficient energy to cause CID fragmentation of the ion species
selected in segment 2. The background pressure in segment 3 and entrance end
62
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of segment 4 (I to 10 millitorr in this example) serves initially as the
collision gas
and then as the ion kinetic energy damping gas for the parent and fra_ gment
ion
population traversing the length of segment 4. Potentials applied to exit lens
33
serve to trap and release ions from segment 4. Trapped ions which are released
or
gated from segment 4 pass into TOF pulsing region 37 where they are pulsed
into
TOF drift region 58 and mass to charge analyzed. Ton trapping in segment 4
causes
ions to take multiple passes back and forth through ion guide segment 4.
before
being gated out. As trapped ions move back toward entrance end 62 of segment 4
they pass through the higher pressure background gas in the entrance end 62
where
collisional damping of ion kinetic energy occurs. Even for high ion energy
acceleration into segment 4 to cause CID fragmentation, the resulting fragment
ion
kinetic energy spread can be damped to create an a monoenergetic ion
population in
segment 4 with close to thermal energy spread. The mean kinetic energy of ions
traversing segment 4 is determined by the DC offset potential applied to the
poles of
segment 4.
This sequence of mass selection, DC acceleration CID fragmentation and TOF
mass analysis
of the fragment ions, produces a result similar to an MS/MS experiment run on
a triple
quadrupole mass analyzer. The hybrid TOF embodiment shown in Figure 1 acquires
full
fragment ion spectrum without scanning and is configured with a segmented
multipole ion
guide with no electrostatic lens elements in between segments. This embodiment
results in
higher sensitivity MS/MS experimental sequences with higher resolution and
mass accuracy
performance when compared to triple quadrupole operation. CID of parent ions
is achieved
in both hybrid TOF and triple quadrupoles by DC acceleration of ions into an
RF only
collision cell. Due to the collisional damping of ion kinetic energy in
segments 1 and 2, the
ionfenergy of the parent ion beam is determined by the DC offset potential of
segment 2. The
ion collisional energy is then set by the relative DC offset potentials
applied to segments 2, 3
and 4. The background pressure in third vacuum stage 73 is maintained at 10-5
torr or lower
f
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WO 99/38193 PCT/US99/01335
so that ions exiting ion guide segment 4 at exit end 11 experience no further
collisions with
background gas as they move into TOF pulsing region 37. Ion molecule
collisions in this
region would cause scattering and defocusing of the ion beam being transferred
into TOF
pulsing region 37 reducing TOF performance. The poles of segment 4 extend
continuously
from the higher background pressure of second vacuum stage 72 into third
vacuum stage 73.
Stable trajectory ions traversing segment 4 are transferred from a higher to a
lower
background pressure and in reverse direction from lower to higher background
pressure with
very high efficiency. Ions with stable trajectories are transferred through
the four segments of
segmented ion guide 8 in the MS/MS sequence described above with little or no
ion loss
between segments.
Alternatively, the same MS/MS function can be achieved by mass to charge
selecting with
segment 1, fragmenting the selected ions by DC acceleration from segment 1 to
segment 2,
passing of the fragment ions into segment 4 where they are trapped and gated
into TOF
pulsing region 37. Segment 4 can also be operated in non trapping mode where
ions traverse
segment 4 with a single pass on the way to TOF pulsing region 37. A second
alternative is to
operate segments 1 and 2 in mass selective mode with selected m/z ions
accelerated through
segment 3 and into segment 4 by setting the appropriate DC offset potentials.
A second
technique can be employed to achieve mass to charge selection in segments 1 or
2 prior to
CID fragmentation. Mass selection of one or more discrete m/z ranges can be
achieved by
applying a spectrum of resonant frequencies to reject unwanted ion m/z values
from segment
1 and/or 2 while retaining selected m/z value ions. Combinations of RF, DC and
resonant
frequency ion ejection can be configured in segments 1 and 2 to achieve m/z
range selection
prior to CID ion fragmentation from DC acceleration of ions from one ion guide
segment to
another.
Segments 1 and 2 can also be operated in ion trapping mode during m/z
separation. This
technique will be employed in MS/MSn experimental sequences as will be
described below but
CA 02318855 2000-07-24
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can also be used in an MS/MS sequence. To achieve ion trapping in segment 2,
the DC offset
potential applied to segment 3 is raised relative to the DC offset potential
applied to segment
2. The DC offset potential of segment 3 can pulsed low to gate ions from
segment 2 into
segment 3. Segment 3 may be operated in non trapping or trapping mode. In
trapping mode,
ions can be gated into segment 4 at a rate which is independent of the rate
that ions are gated
into TOF pulsing region 37. The ion residence time in segment 4 can serve to
damp out the
pulsatile characteristics of the ion gating into segment 4. The trapping of
ions in segment 2
will cause ions to traverse the length of ion guide segment 4 with more than a
single pass. Ions
traversing segment 2 with multiple passes experiences more RF cycles and hence
higher m/z
selection resolution can be achieved even in the presence of higher background
pressure which
may tend to delay ion ejection from segment 2. Similarly, ion trapping an m/z
selection can
be achieved in segment 1 by raising the DC offset potential of segment 2 above
the offset
potential applied to the poles of segment 1. The DC offset of segment 1 can
track the DC
offset potential applied to segment 2 effectively preventing ions from moving
between
segments 2 and 4 during ion trapping cycles.
The segmented ion guide TOF can be operation can be configured to simulate
triple
quadrupole MS/MS operating modes, such as in neutral loss scans, in which
quadrupole 1 is
scanned during data acquisition. In the segmented ion guide TOF operating
sequence, full
TOF spectra of fragment ions are acquired from which Reconstructed Ion
Chromatographs
(RIC) can be generated to match triple quadrupole like neutral loss type MS/MS
data. To
achieve this superset of data neutral loss data, the hybrid segmented ion
guide, TOF
embodiment shown in Figure 1 can be configured to operate as follows;
1. segment 1 is operated in non trapping RF only mode with DC offset
potentials
applied that allow ions to pass into segment 2 at low energies with no ~ CID
fragmentation.
2. segment 2 is operated in non trapping ion m/z selection mode with the
application
of RF and DC potentials, resonant frequency excitation potentials or a
combination
I
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of both. To simulate the scanning of the first quadrupole of a triple
quadrupole
mass analyzer, the m/z selection window of segment 2 is periodically stepped
to a
new value until the desired m/z range is covered. The m/z window stepping in
segment 1 is synchronized with the TOF spectra acquisition so that the parent
ion
mass range of any given first generation daughter ion spectrum is known.
3. segment 3 is operated in trapping RF only mode. The DC offset potentials
are
applied to segments 2, 3 and 4 to accelerate ions from segment 2 into segment
4 with
sufficient energy to cause the desired amount of CID ion fragmentation in
segment
4. Ions gated from segment 4 into TOF pulsing region 37 are pulsed into TOF
drift
region 58 and mass analyzed.
Consider a neutral loss scan over the parent mass to charge range from 400 to
800. If the
parent m/z window is 4 m/z wide, the m/z window selected by segment 2 would
need to be
covered in 100 steps to cover the m/z range from 400 to 800. If the TOF mass
analyzer is
pulsed at a rate of 10,000 times per second with 1,000 pulses added for each
mass spectra saved
to memory, then 10 mass spectra per second would be recorded. Under these TOF
data
acquisition conditions, a full simulated neutral loss scan would take 10
seconds to acquire. If
TOF spectra were acquired at a rate of 40 spectra per second, total
acquisition time for each
full simulated neutral loss scan would be 2.5 seconds, approaching typical
scan speeds used in
triple quadrupole neutral loss scans. The TOF full spectrum data acquired in
the above list
operating technique data contains more analytical information than the
combined information
from a triple quadrupole neutral loss scan or the case where the first
quadrupole is scan with
the third quadrupole m/z range selection fixed. Hence either triple quadrupole
experiment
can be simulated with the above listed segmented ion guide TOF operating
sequence.
Variations in the above sequence can be used to achieve the same ends. For
example, m/z
range selection can be conducted in segment 1 or segment 1 and 2 in trapping
or non trapping
mode. Segment 4 can be operated in trapping or non trapping mode. In trapping
mode, the
trapping voltage applied to lens 33 can be held low when the m/z range in
segments 1 or 2 is
47
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WO 99/38193 PCT/US99/01335
switched. Trapped ions from the previous m/z window are then allow to clear
the trap. A
small delay time may be added after a m/z range selection step to allow the
segment 4 trap to
fill prior to resuming TOF pulsing.
In the above simulated triple quadrupole neutral loss scan operating mode, DC
ion
acceleration is employed to achieve Cm first generation ion fragmentation.
Alternatively,
resonant frequency excitation CID fragmentation can be employed in multipole
ion guide
segments 1 through 4 or combinations of DC ion acceleration and resonant
frequency
excitation. The preferred fragmentation technique will depend on the
analytical information
desired. Resonant frequency excitation can be used to fragment selected ions
without adding
internal energy to non selection m/z values, particularly fragment product
ions. When DC
ion acceleration CID is use, the internal energy of all accelerated ions is
increased including
that of the produced fragment ions. Resonant frequency excitation has the
disadvantage that
to achieve increased fragmentation energy the amplitude of the resonant
frequency will be
increased. 'To contain the ions being excited the RF amplitude must be
increased
proportionally which increases the low m/z cutoff. Typically, when operating
ion traps in
MS/MS mode, the bottom one third or more of the m/z scale may be ejected to
achieve
sufficient resonant frequency excitation fragmentation of the parent ion or
ions of interest.
Both DC ion acceleration and resonant frequency excitation can be combined
simultaneously
or sequentially to achieve optimal MS/MS or MS/MSn performance. Consequently,
the
hybrid segmented ion guide TOF embodiment diagrammed in Figure 1 can be
configured to
achieve all triple quadrupole and ion trap MS/MSn functions and conduct
additional
experiments not possible using either a triple quadrupole or an ion trap.
MS/MSn Hybrid TOF Functions with a Continuous Primary Ion Beam
A tide range of MS/MSn functions can be achieved using the hybrid TOF
embodiment
shown in Figure 1. To simplify the description of the operational sequences
required to
achieve specific MS/MSn functions the techniques used can be divided into two
groups, those
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' WO 99/38193 PCT/US99/01335
that require cutting of the continuous ion source generated primary ion beam
and those that
require no break in the primary ion beam during operation. First some MS/MSn
techniques
which accept a continuos ion beam from electrospray ion source 12 will be
describe below.
Consider running an MS/MS2 experiment with the embodiment shown in Fig~re 1.
The
simplest functional sequence is an extension of the MS/MS case described above
where DC
accelerated ion fragmentation occurs between segments 1 and 2. Specifically
segmented
multipole ion guide TOF hybrid is operated in the following mode.
1. Segment 1 is operated in mass to charge selection mode. Selected mass to
charge ions
are accelerated into segment 2 with sufficient DC offset potential applied
between
segments 1 and 2 to cause CID fragmentation of the m/z selected ions.
2. Segment 2 is operated in mass to charge selection mode where one or more
first
generation product ions is selected. The m/z selected ions are then
accelerated
through segment 3 and into segment 4 by applying the appropriate relative DC
offset potentials to segments 2, 3 and 4 to cause CID fragmentation of the
selected
first generation fragment ions.
3. Segment 4 is operated in RF only trapping mode from which ions are gated
into
TOF pulsing region 37. The second generation fragments ions are subsequently
pulsed into TOF drift region 60 and mass to charge analyzed.
Ion mass to charge selection operation in segments 1 and 2 may employ AC and
DC mass
filtering, resonant frequency rejection of unwanted m/z ions or a combination
of both as was
described above. Ion fragmentation may be achieved using resonant frequency
excitation
instead of or in conjunction with DC ion acceleration fragmentation in
segments 2 and 4.
Resonant frequency excitation can occur simultaneously with ion m/z selection
in segment 2.
Segment 2 can alternatively be operated in trapping mode by applying the
appropriate relative
DC offset potentials to the poles of segment 2 to trap ions in segment 2 or
release ions from
segment 2 into segment 4. In all MS/MSn experiments, the relative capillary to
skimmer
49
CA 02318855 2004-04-29
potential can be raised to increase the internal energies of ions in the
primary ion beam to
facilitate ion fragmentation in segmented ion guide 8.
MS/MS2 can alternatively be achieved by mixing DC ion acceleration and
resonant frequency
excitation ion fragmentation techniques by operating segmented multipole ion
guide 8 in the
following mode.
1. Segment 1 is operated in RF only ion pass mode. Ions are pass from segment
1 to
segment 2 with low energy and causing ao fragmentation.
2. Segment 2 is operated in mass to charge selection mode and ions are
accelerated from
segment-1 through segment 3 and into segment 4 with sufficient energy to cause
=Cm fragmentation of the m/z selected ions.
3. Segment 4 is operated in trapping, m/z selection and resonant frequency
excitation
fragmentation of the selected first generation ion. Second generation fragment
or
' product ions are gated into TOF pulsing region 37 and subsequently TOF mass
analyzed.
Quasi MS/MSn experiments can be achieved with a continuos incoming ion beam
using
techniques described in U.S. Patent No. 6,011,259 dated 3anuary 4, 2000. In
the techniques
described, true m/z selection does not take place prior to ion fragmentation.
Instead two
spectra are acquired sequentially, the first with the or a combination of
parent or fragment
ions and the second with the next generation fragment ions, the first TOF mass
spectrum
acquired is subtracted from the second to give a spectrum the MS/MSp
fragments. This
method. requires multiple component resonant frequency excitation CID ion
fragmentation.
Using.this technique, an MS/MS~ experiment could be conducted as described
below.
Mass spectrum 1 is acquired with the following segmented ion guide operating
conditions.
1. Segment 1 is operated in mass to charge selection mode. The resulting ion
population is accelerated into segment 2 with sufficient energy to cause CID
' fragmentation.
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CA 02318855 2000-07-24
I~VO 99/38193 PCT/US99/01335
2. Two component resonant frequency excitation is applied to the poles of
segment 2,
to induce CID fragmentation of the selected second and third generation ions.
The
product ions are passed through segment 3 to segment 4 without further
fragmentation.
3. Segment 3 is operated in trapping or nontrapping RF only mode witk~ ions
passed
into TOF pulsing region 37. Ions are subsequently pulsed into drift region 58
of
TOF mass analyzer 40 and mass to charge analyzed.
A second TOF mass spectrum is generated with three component resonant
frequency y
excitation applied to segment 2 or a single resonant excitation frequency
applied to the poles
of segment 4 to fragment the third generation product ion having the selected
resonant
frequency. The first mass spectrum acquired is subtracted from the second mass
spectrum
resulting in a mass spectrum containing fourth generation fragment or product
ions and their
specific parent ion.
An alternative MS/MSn analysis technique can be used which may use either a
continuos or
non continuous primary ion beam depended in the specific analytical
application. With this
technique, ions are moved from one segment to an adjacent segment in blocks.
All ions
trapped in one segment are transferred to the next sequential segment before
accepted a group
to ions from the previous segment. Each segment can independently perform
single or
multiple m/z selection and /or resonant frequency excitation CID ion
fragmentation or ions
can fragmented using DC acceleration CID as ions are transferred between
segments. The
steps of an MS/MS3 analysis using this technique are listed below.
1. Segment 1, is operated in RF only mode with m/z selection using
multifrequency
resonant frequency ejection of unwanted ions. The relative DC offset
potentials
applied to the poles of segments 1 and 2 are set to accelerate ions from
segment 1
into segment 2 with sufficient kinetic energy to cause DC acceleration CID ion
fragmentation. The primary beam remains on at all times and ions continuously
enter segment 1.
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2. The relative DC offset potentials applied to segments 2 and 3 are set to
trap ions in
segment 2 for a given time period. Segment 2 is operated in m/z selection mode
and
selected m/z value first generation fragment ions are trapped in segment 2 for
the
given time period.
3. The DC offset potentials applied to segment 3 are then switched low to pass
ions
from segment 1 through segment 3 and into segment 4 for a time period of a
duration long enough to substantially empty segment 2 of trapped ions. Ions
are
accelerated from segment 2 through 3 and~into 4 with sufficient kinetic energy
to
cause DC acceleration CID ion fragmentation. After the ion transfer period,
the
DC offset potential applied to the poles of segment 3 is switched high
trapping ions
in segment 2 and preventing trapped ions in segment 4 from re-entering segment
2
in the reverse direction.
4. Segment 4 is initially operated in m/z selection mode while ions are being
transferred into segment 4 from segment 2 through segment 3. The potential
applied to lens 33 is initially set to trap and hold ions in segment 4. After
the DC
offset potential applied to segment 3 is raised to cut off ion flow from
segment 2, the
potentials applied to the poles of segment 4 are switched such that segment 4
is
operated in RF only mode with resonant frequency excitation CID fragmentation
of the selected m/z value second generation fragment ions trapped in segment
4. If
an MS/MS3 experiment is desired, the resulting third generation product or
fragment ions trapped in segment 4 are released, by switching the voltage
applied to
lens 33, in gated ion packets into TOF pulsing region 37 and subsequently TOF
mass analyzed. Alternatively, additional sequential m/z selection and CID
fragmentation steps can be continued with the ions trapped in segment 4, prior
to
releasing ions into TOF pulsing region 37, if higher order MS/MS° steps
are
"'~ required. TOF spectra of a portion of the products ions can be acquired at
each
MS/MS step or at the end of the MS/MSn sequence. While MS/MS steps are being
conducted with ions trapped in segment 4, selected first generation product
ions
l
sz
CA 02318855 2004-04-29
continue to accumulate in segment 2.
5. When all n generation product ions trapped in segment 4 have been gated
into TOF
pulsing region 37 and subsequently TOF mass analyzed, the DC offset applied to
segment 3 is lowered and steps 3 and 4 above are repeated.
MS/MSn Hybrid TOP Punctions with a Non-Continuous Primary Ion Beam
Several segmented ion guide TOF functional sequences are possible to achieve
MS/MSn
operation with a non-continuous primary ion beam. U.S. Patent No. 6,011,259
describes the configuration of multipole ion guide TOF mass analyzer where the
multipole
ion guide is operated in trapping mode with sequential mlz ion selection and
resonant
frequency excitation steps prior to TOF mass analysis: The addition of
multiple segments to a
multipole ion guide configured in a higher background pressure region allows
variations of the
single segment two dimensional trap TOF MS/MSn sequences with a non-continuous
primary
ion beam. Unlike three dimensional ion traps or FTMS mass analyzers, the
segmented ion
guide TOF hybrid configuration cari achieve MS/MSn functionality with ability
to conduct
higher energy DC acceleration ion fragmentation at each. ion m/z selection and
fragmentation
step. Alternatively, segmented ion guide 8 can be configured to conduct
resonant frequency
excitation fragmentation or combinations or both CID fragmentation techniques
during an
MS/MSn experiment to optimize performance for a given analysis. One example of
a
MSIMSn experiment conducted with ion DC acceleration ion fragmentation using
the
segmented ion guide TOF hybrid shown in Pigure 1 is described below.
1. Segment ~1 is operated in RF only non mass selection mode with ions being
passed
into segment 2 with no fragmentation.
2. Segment 1 is operated in trapping or non trapping mass to charge selection
mode and
the resulting ion population is accelerated through segment 3 into segment 4
with
sufficient kinetic energy to cause CID fragmentation.
3. Segment 3 is operated iu trapping mass to charge selection mode and a
selected m/z
range of first generation ions is collected in multipole ion segment 4 with no
ion
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CA 02318855 2000-07-24
WO 99/38193 PCT/US99/OI335
gating into pulsing region 37. After collecting selected m/z first generation
fragment ions for a specified time period or with occasional TOF monitoring of
the
segment 4 ion population to prevent saturation, the primary ion beam is
prevented
from entering segment 1 of segmented ion guide 8 by decreasing the potential
on
capillary exit 14 relative to the potential applied to skimmer 26. Ions
exiting
capillary 23 are prevented from passing through skimmer opening 27 due to the
retarding electric field applied in the capillary to skimmer region.
4. Ions trapped in segment 4 are then DC accelerated in the reverse direction
through
segment 3 into segment 2 by applying the appropriate relative DC offset
potentials
to segments 2, 3 and 4 to cause Cm of ions accelerated into segment 2. Ions
accelerated in the reverse direction into segment 2 are prevented from
entering
segment 1 by increasing the relative DC bias potentials of segments 1 and 2.
If a
short MS/MSn analysis time is required, ions may be prevented from entering
segment 1 to decrease the time required to empty segment 2 of ions at each
MS/MS
step. Alternatively ions may be allowed to enter segment 1 as an extension of
segment 2 to increase the segment 1 volume. Ions are prevented from exiting
segment 1 in the reverse direction through entrance end 9 by applying a DC
retarding field between skimmer 26 and the poles of segment 1. The neutral gas
molecules from the free jet expansion continuing to enter second vacuum stage
2
through skimmer aperture 27, serve to damp reverse ion axial trajectories
which
aids in preventing trapped ions from being lost through entrance ion guide
entrance
end 9. The potentials applied to segment 2 and segment 1 just prior to
receiving the
ion population from segment 4 are switched such that segments 1 and 2 are
operated
in m/z selection mode.
5. A selected m/z range of second generation fragment ions is collected in
segment 2.
,'~ The resulting population of second generation fragment ions is re-
accelerated
through segment 3 into segment 4 with sufficient kinetic energy to cause CID
fragmentation of the selected second generation ion population.
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CA 02318855 2000-07-24
'WO 99!38193 PC'T/US99/01335
6. Segment 4 is again operated in trap mode. If the experiment is to end at
third
generation ions, the resulting ion population in segment 3 can be TOF mass
analyzed. If n generation product ions beyond MS/MS3 are required, step 4 or
steps
4 and 5 are repeated to produce MS/MSn generation fragment or product ions and
so on. The trapped ion population can be sampled at each MS/MS step and TOF
mass analyzed consuming only a small portion of the trapped ion population.
TOF
mass analysis is conducted after the last MS/MS°th step until the
entire ion
population is emptied from multipole ion guide 8.
7. The voltage applied to capillary exit end 14 is raised to allow ions in the
primary ion
beam to again pass through skimmer aperture 27 and into segmented ion guide 8
at
entrance end 9.
8. Sequence 1 through 7 is repeated. Any number of MS/MS° steps can be
configured
in this manner with TOF mass analysis.
Another example of MS/MSn analysis utilizing a mixture of resonant frequency
excitation
fragmentation and DC ion acceleration CID fragmentation is described below
with non-
continuous primary ion beam operation.
1. Operate segment 1 in non m/z selection RF only mode to pass ions into
segment 2
without CID fragmentation.
2. Segment 2 is operated in mass selection mode with trapping or non trapping,
passing
selected m/z ions through segment 3 and into segment 4 with no DC acceleration
fragmentation.
3. Segment 3 is operated in trapping mode with resonant frequency excitation
fragmentation of the m/z selected parent ions. A supplemental set of resonant
frequencies is simultaneously applied to reject undesired first generation
fragment
ions while retaining selected m/z value ions. The internal energy of the m/z
selected first generation fragment ions does increase in segment 4 during
parent ion
Cllr fragmentation. First generation m/z selected fragment ions are
accumulated in
CA 02318855 2004-04-29
segment 4 for a set time period or until,a desired ion population density is
reached,
checked by short duration TOF ion sampling.
4. When segment four has been filled to the desired ion density level, the
primary ion
beam is prevented from passing through skimmer aperture 27 by lowering the
potential applied to the capillary exit electrode.
5. The selected first generation fragmentation ions are accelerated in the
reverse
direction from segment 4 through segment 3 into segment 2 with sufficient
kinetic
energy to cause CID fragmentation:
b. Prior to receiving the first generation ions and second generation fragment
ions, the
v potentials applied to the poles of segment 1 are switched to operate in mass
selection
.:: mode for mass selection of second generation fragment ions.
7. If further MS/MS fragmentation is desired, steps 2 through 6 can be
repeated or .
TOF mass analysis can be performed on the entire ion population trapped in
multipole ion guide 8.
8. When TOF mass analysis is completed and multipole ion guide 8 has been
emptied,
the primary ion beam is again allowed to pass through skimmer aperture 27 and
.
into segment 1 of multipole ion guide 8. Steps 1 through 7 can be repeated to
continue an MS/'MS~ analysis.
As is described in U.S. 'Patent No. 6,011,259 higher energy CID fragmentation
can be
achieved by accelerating ions back into multipole ion guide 8 from exit end 11
in the low
pressure .region of third vacuum pumping. stage 73. Ions gated into the gap
between lenses 33
and 34 are raised in potential by rapidly increasing voltage applied to lenses
33 and 34. The
potential applied to lens 33 is then decreased to accelerate ions back into
multipole ion guide
8. The reverse direction DC accelerated ions impact the background gas in
multipole ion
guide 8 as they traverse the length of ion guide 8 or individual segments 1
through 4. In a
similar manner, segment 3 or a combination segment 3 and 4 can be used to
reverse accelerate
ions into segment 2 in a repetitive manner to rapidly increase the internal
energy of an ion
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PCTNS99/01335
population. ion acceleration from segment 3, however, occurs in the presence
of background
collision gas so ion terminal velocities achievable may be Iower than can
those velocities
attained by accelerated ions from the collision free region at ion guide exit
end 11. Unlike a
three dimensional or FTMS systems which can conduct MS/MSn experiments, the
segmented
ion guide TOF hybrid shown in Figure 1 can deliver a broader range of
collisi~nal energies to
achieve ion fragmentation. The control MS/MSn function sequences is simplified
by direct
computer control of DC and AC voltage switches and power supplies.
,;.
Rapid switching of DC offset potentials can be achieved by switching between
two power
supplies DC power supplies set at the appropriate potentials. The poles of
each segment are
connected to a set of AC and DC power supplies through switches. The primary
RF applied
to the poles of each may be connected through capacitive coupling directly
from individual
RF supplies. The DC voltage components are added after the RF coupling
capacitor and the
resonant frequency AC can be capacitively coupled into the each pole by
connecting after the
RF coupling capacitor. The state of each switch can be controlled through a
computer
program which can simultaneously change the status all switches required to
achieve a change
of instrument state. RF and DC power supply amplitudes and frequencies can be
set through
interfaces such as Digital to Analog converters using the same computer
control program.
With such a computer controlled system, MS/MSn experimental sequences are
achieved by
programming specific sets of switch, control signal and delay patterns.
Control sequences can
be user selected before initiating a data acquisition run and state changes
can be programmed
to occur during the run based on data received. Data dependent software
decisions may be
used for example to select the largest peak in a parent mass spectrum. The
largest amplitude
parent peak is then m/z selected and subsequently fragmented.
Segment 3 of multipole ion guide 8 serves to decouple segments 2 and 4
electrically and
functionally. Ions can be trapped in segment 2 and released when the DC offset
potentials
applied to segment 3 are increased to trap ions and lowered to pass ions from
segment 2 into
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WC3~ 99/38193 PCT/US99/01335
segment 3. Figure 2 shows an alternative embodiment of a segmented multipole
ion guide
TOF hybrid instrument where multipole ion guide 204 is comprised of 3
segments. Segment
3 of ion segmented ion guide 8 has been removed to simplify operational
sequences and cost of
electronic components. Most MS/MS" sequences described for the embodiment
shown in
Figure 1 can be run with the three segment multipole ion guide embodiment
shown in Figure
2. The segmented ion guide TOF hybrid instrument shown in Figure 2 is
comprised of
Electrospray ion source 212, four vacuum pumping stages 208, 209, 210 and 211,
segmented
ion guide 204 and TOF mass analyzer 261. In the embodiment shown, TOF mass
analyzer
214 is configured with steering lens set 262 to adjust the position of ion
impact on detector
212. Segmented multipole ion guide 204 is comprised of first segment 201,
second segment
202 and third segment 203. The poles of segments 201 and 202 are joined but
electrically
insulated from each other at joint 206. Similarly, the poles of segments 202
and 203 are joined
but electrically insulated from each other at joint 207. Segment 203 extends
continuously
from second vacuum pumping stage 209 into 210. Each multipole ion guide
segment 201, 202
and 203 can be operated independently in single or multiple m/z range
selection and/or
resonant frequency excitation modes.
The background pressure in second stage 209 is maintained above 0.1 millitorr
to allow
collisional damping of stable trajectory ion energies and to enable Cm
fragmentation of ions
in each multipole ion guide segment. The local pressure at entrance en 213 of
segment 201 is
be higher due to the free jet expansion and aid in increasing the ion guide
capture efficiency at
entrance of multipole ion guide 204. By setting the appropriate relative DC
offset potentials
between segments, ions can be transferred in either direction from one
multipole ion guide
segment to another with or without causing Cm fragmentation. With the
elimination of the
short segment in between segments 202 and 203, segment 203 requires more
closely tied
opezration with segment 202. For example segment 202 can not be operated in
ion trap and
release mode without varying the relative offset potentials between segments
202 and 203.
This to some extent simplifies instrument operation and cost by reducing
variables and
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CA 02318855 2000-07-24
WO 99/38193 PCT/US99/01335
components, the tradeoff is reduced overall system functional flexibility.
System flexibility and to some extent complexity can be increased to achieve
additional
functionality by increasing the number of segments in the segmented ion guide
308 as shown
in Figure 3. Segmented ion guide 308 is comprised of 8 segments 300
through~307 insulated
from each other by electrically insulting junctions 310 through 316
respectively. First and
second segments 300 and 301 can be operated using techniques described for
segments 1 and 2
in Figure 1. Segments 302, 303, 304, 305 have been configured between segments
301' and 306
and located in second vacuum stage 317. The DC offset applied segments 302
through 305
operating in RF only mode can be set to cause a more sustained and higher
energy DC
acceleration to achieve ion fragmentation in either direction along segmented
ion guide 308.
Alternatively, segments 302 through 305 can be operated as a single segment in
m/z selection
or resonant frequency excitation ion fragmentation mode. Combining segment 302
through
305 operation in m/z selection mode allows the conducting of MS/MS3
experiments with
continuos primary ion beam 209 to maximize sensitivity. Increasing the number
of in
rnultipole ion guide segments configured in vacuum stage 2 allows an increased
ion transfer
rate through multipole ion 308 even at higher background pressures in second
vacuum stage
317. A low voltage DC offset gradient applied between segments 300 through 306
would
move help to move ions in the axial direction without increasing ion internal
energy through
more energetic collisions with the background gas. Segment 307 has been added
at exit end
318 of multipole ion guide 308 to serve as an alternative means to trap ions
in segment 306 and
gate ions from multipole ion guide 308 into TOF pulsing region 320. Trapping
with DC
offset potentials applied to the poles of segment 307 compared with using
retarding potentials
applied to lens 321 reduces any defocusing effects which may occur due to exit
end fringing
field effects. Segment 307 is operated primarily in RF only ion transfer mode
which reduce or
eliminate asymmetric DC fringing field effects at exit end 318 of multipole
ion guide 308.
Segment 306 may be operated in m/z selection mode with AC and DC applied to
the poles.
Segment 307 effectively decouples the fringing fields created by segment 306
from the ion
59
CA 02318855 2004-04-29
focusing and acceleration region exit end 318 of multipole ion guide '308.
Segment 307 allows
the focusing of ions into TOP pulsing region 320 to be optimized independent
of the segment
306 operating conditions: The embodiment shown in Figure 3 offars a high
degree of
flexibility in conducting a of MSIMSn experiments including a range of m/z
selection arid ion
fragmentation techniques.
Figure 4 an embodiment of the invention in which three segment multipole ion
guide
multipole ion guide 408 is configured in a hybrid API TOF mass analyzer. Three
segment
multipole ion guide 408 extends continuously from higher background pressure
vacuum stage
411 into' lower background pressure vacuum stage 412. Segment 402 can be
operated in RF
only mode to transfer ions into TOF gulsing region 415 or as a two dimensional
trap
configured with full MSIMSn function capability when coupled with TOF mass
analysis as is
described in U.S. Patent No. 6,011,258 dated 3anuary 4, 2000. The embodiment
in Figure 4
includes two additional segments from the embodiment described in U.S. Patent
No.
6,011,25 9. Segments 401 and 403 can be operated in a mode which serves to
decouple the
'effects of segment 408 operating modes from effecting the trajectories of
ions~entering or'
exiting multipole ion guide 408 at entrance and exit ends 416 and 417
respectively. For
~cample segment 401 can be operated is R only mode to efficiently uaasfer ions
froiri
entrance region 416 into segment 408. 'The kinetic energies and trajectories
of ions entering
multipole: ion guide 408 at entrance end 416 are damped by the collisional
interaction with the
background gas. Ions traversing segment 401 eater segment 408 closer to
centerline 418 where
the defocusing effects of DC fringing fields will have little effect on ion.
transmission
efficiency. The DC offset potentials applied to segment 403 can be switched.
to trap ions in
segment 402 or gate ions from segment 402 into TOF pulsing region415.: Ions
traversing
pulsing region 402 are pulsed into TOF drift region 414 and mass analyzed. A
linear TOF
fligl#t tube geometry is shown in Figure 4 as an alternative embodiment to
flight tube
geometry which includes an ion reflector geometry.
CA 02318855 2004-12-15
Segment 403 operating in RF only mode establishes consistent ion trajectories
from multipole
ion guide exit region 417 into TOF pulsing region 415 by shielding differences
in fringing
fields at the exit end of segment 2 which can occur during different operating
modes' of
segment 402. Segment 401 can also be operated in mJz selection andlor
fragmentation mode
and parent or product ions can be transferred forward or in reverse between
segments 401 and
402. Consequently, ions can be fragmented with DC ion acceleration between
segments 401
and 402 complementing resonant frequency C1D functions described in previous
embodiments and in U.S. Patent Number 6,011,259. Ions traversing segment
403 may be accelerating back into segment 402 to cause CID ion fragmentation
in that portion
of segment 402 which extends into vacuum stage 411: . Pulsing ions in the
reverse direction
from segment 403 into 402 can be accomplished by switching the DC potentials
applied to the
poles of segtrient 403 and lens 418 in a synchronous manner to initially raise
the ion energy of
the ions in exit region 417 and accelerating the ions into segment 402. Some
DC field
penetration into segment 403 from lens 418 and the poles of segment 402 will
occur with
voltage differences applied between the two elements to aid accelerating the
ions from segment
403 into 402. The embodiment diagrammed in Figure 4 allows full MSlMS°
functionality in a
cost effective configuration with some tradeoffs in functional flexibility due
to the reduced
number of multipole ion guide segments.
Aa alternative embodiment of a three segment multipole ion guide Figure 4b in
which
segmented multipole ion guide 448 is configured to extend into first vacuum
pumping stage
450. Ions produced in Electrospray ion source 452 move into first vacuum
pumping stage 450
through capillary 453. Ions exiting capillary 453 at exit end 454, enter.the
first multipole ion
guide segment 441 where they are radially confined by the RF fields applied to
the poles on
segment 441. Ions with mlz values which fall within the stability window
determined by the
electric fields applied to the poles of segment 441 move through segment 441
and can be
transferred into segment 442. MSIMS~' functions with TOF mass to charge
analysis can be
achieved using techniques similar to those described for the three segment ion
guide shown in
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Figure 4. Alternatives to segmented ion guide 448 may include extending
segment 442 into
vacuum stage 450. Additional multipole ion guide segments can be added the
that portion of
multipole ion guide 448 which extends into vacuum stage 454. This
configuration allows mass
to charge selection and ion fragmentation functions at higher background
pressures which
may be preferable to lower pressure operation for analysis. Additional
variations to
configuration of the segmented multipole ion guide are shown in Figures 5
through 7.
The segmented multipole ion guide embodiment shown in Figure 5 is configured
to extend
into TOF pulsing region 507. Ions traversing the length of multipole ion guide
508 pass
through segments 501, 502 and 503 and are transferred into segment 507. The
relative DC
voltages applied to the poles of segments 503 and 504 and lens 507 trap ions
in segment 504.
Ions trapped in segment 504 are pulsed into TOF drift region 510 by cutting
off the RF
voltage component and applying an asymmetric DC potential to the poles of
segment 504 to
accelerate ions radially through the gap between two poles. Full MS/MSn
functions with
TOF mass to charge analysis can be achieved with the embodiment shown in
Figure 5.
Segments 501, 502 and 503 can be operated individually or in complementary
fashion to
achieve m/z selection and/or ion CID fragmentation of ions prior to TOF mass
to charge
analysis. The ions trapped in segment 6 prior to pulsing may be traveling in
either direction
axially along the length of segment 6. As segment 6 is residing in a low
pressure region, few
ion collisions will occur with the background gas. Consequently, no ion axial
ion velocity
damping will occur in segment 6 prior to pulsing into TOF drift region 510. To
increase the
number of ions which have the required trajectory to impact the detector in
the TOF tube,
ions must be pulsed from segment 506 during the initial first pass or ions
must be transferred
into segment 6 with very low axial kinetic energy. The latter has the
disadvantage that the
pulsing region fill time might be quite long resulting in the slowing down of
the TOF pulse
rate's Radial ion motion in segment 6 due to the RF field prior to pulsing can
contribute to
spatial and energy spread of ions pulsed into TOF drift region 510. An
additional constraint
which must be considered when operating with a two dimensional trap configured
as the
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pulsing region is that a multichannel plate detector commonly used in TOF
analyzers has a
limited instantaneous charge depletion dynamic range, typically on the order
of 100. If too
many ions of like m/z value arrive at the detector within a 2 nanosecond time
window, the
detector output may reach saturation resulting in signal amplitude distortion.
Reducing ion
accumulation time in segment 506 prior to pulsing the trapped ions into
TOF,drift region 510
can help to avoid detector saturation. Configuring steering lens set 511 may
help in
optimizing ion pulsed ion trajectories to impact on the TOF detector.
;;.:
An alternative embodiment of a hybrid API source multipole ion guide TOF is
diagrammed
in Figure 6. Referring to Figure 6, an additional multipole ion guide 610 has
been configured
between segmented multipole ion guide 608 and TOF pulsing region 611.
Multipole ion
guide 610 can be operated as a collision cell when gas is added to region 612
surrounded by
partition 614 or in m/z selection mode. Segments 601, 602 and 603 comprising
segmented ion
guide 608 can be operated individually or collectively in m/z selection and/or
CID ion
fragmentation modes to achieve MS/MSn functions with TOF mass to charge
analysis. Each
segment of multipole ion guide 608 can be operated in single pass or ion
trapping mode. In
addition, ions can be m/z selected to fragmented with CID in ion multipole ion
guide 610.
Multipole ion guide 608 extends continuously into lower pressure vacuum stage
615 where
ions exiting from segment 603 are not subjected to collisional scattering from
background gas
collisions. Ion transfer efficiency into multipole ion guide 610 is not
effected by the
background pressure in vacuum stage 613. The configuration of second and
distinct CID ion
fragmentation region 612 comprising multipole ion guide 610 allows for the
introduction of a
different collision or reactive background gas than is present in second
vacuum stage 613. The
embodiment shown in Figure 6 allows studies of gas phase ion neutral reactions
or the use of
different gases for CID fragmentation of ions with full MS/MSn operating mode
capability.
Multipole ion guide can be operated in single pass or trap mode releasing ions
continuously or
by gating into TOF pulsing region 611. An additional RF multipole ion guide
may be
configured in vacuum stage 615 between multipole ion guide 610 and TOF pulsing
region 611
63
CA 02318855 2005-04-21
to .reduce the pressure betareea Cm region 612 and fourth vacuum stage 618
which is
maintained at low pressure., Multipole ion guide 608 may also be conftgured.to
extend into
poles of ion guide 610 to improve ion transmission efficiency as is described
in U.S. Patent
6,121,607 which issued on September 19, 2000.
The dual multipole ion guide erabodiment shown in Pigure 6 allows for some
specialized
operating modes but may reduce ovexall functional flexibility when. compared
with earlier
embodiments describe.. ~ . ' . , ,
Figure 7 shows an alternative embodiment for a multipole ion guide hybrid TOP
mass
analyzer which can be operated in MS/MSn analysis mode, Segmented multipole
ion guide
708, conf"tgured with segments 701, 702 and 703, is positioned in second
vacutun_ stage 710: A
second multipole ion guide 704 located in vacuum stage 711 is surrounded by
gas partition
713. Gas partition 713 allows the addition of collision gas into region 713 to
raise the pressure
.in region 713 when it is desirable to 'operate ion guide 704 as a collision
cell. A third
~nultipole ion guide 714 is positioned in vacuum stage 711 to efficiently
transfer ions from
.multipole ion guide 704 info pulsing region 712 allowing sufficient vacuum
pumping between
higher pressure collision.region 713 and lower pressure TOP pulsing region
712. Multipole
ion guide may be operated in single pass o1' ion trapping mode with gating
into TOP pulsing
.region.712. Separating multipole ion guides 703 and 704 into distihct vacuum
stages allows
increased fle~cibility in tnultipole ion guide geometries particularly for
multipole ion guide
708. .Multipole ion guides which estead into, more than one vacuum stage are
configured with
relatively small inner dianieters.(small r~ to minimize the neutral gas
conductance from one
vacuum. stage to the next. Minimizing gas conductance reduces vacuum pumping
costs for a .
:r .
given background pressure target. The poles of multipole ion guides 708, 704
and~714 begin
and end vacuum stages'710 and 711 respectively so there are no vacutun pumping
constraints
im,~osed on either multipole ion guide geometry. The inner radius (r~ of ion
guide 708, 704
or 714 are not constrained due.to vacuum pumping requirements in the
embodiment shown ,
in Figure 7.
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CA 02318855 2000-07-24
~'NO 99/38193 PCT/US99/01335
Analogous to previously described embodiments, the background pressure in
vacuum stage 7
is maintained sufficiently high to insure that collisions between background
gas and ions occur
as ions traverse the length of multipole ion guide 708. The background
pressure in vacuum
stage 710 allows Cm ion fragmentation of ions traversing multipole ion guide
708 using
resonant frequency excitation or intersegment DC ion acceleration techniques.
Each segment
in multipole ion guide 708 can be operated independently or in conjunction
with other
segments in m/z selection or Cm ion fragmentation operating modes. Voltages
appl ed to
vacuum partition and electrostatic lens 707 can be set to pass ions from
segment 703 into
multipole ion guide 704 or can be set to trap ions in multipole ion guide
segment 703. Each
segment in multipole ion guide 708 can be operated in trapping or nontrapping
mode by
setting the appropriate relative DC offset potentials to the poles of adjacent
segments.
Similarly multipole ion guide 704 can be operated in m/z selection or resonant
frequency
excitation Cm ion fragmentation mode when collision gas is present in region
713. Ions can
also be DC accelerated into multipole ion guide 704 with sufficient kinetic
energy to cause
CID fragmentation. Combinations m/z selection and CID ion fragmentation steps
conducted
with multipole ion guides 708 and 704 can be configured to achieve a variety
of MS/MSn
analytical functions with TOF mass analysis. As with the embodiment shown in
Figure 6,
collision gas or reactant gas can be introduce into region 713 which is
different than the
background gas in vacuum stage 710. Selected ion-molecule reactions can be
studied by added
the appropriate reactant gas into region 713 with multipole ion guide 708
delivering m/z
selected and/or fragmented product ions into multipole ion guide 704. The
resulting ion
population flowing through or trapped in multipole ion guide 704 is
subsequently TOF mass
analyzed.
The embodiments shown in Figures 1 through 7 are some examples of
configurations of
multipole ion guide TOF hybrid mass analyzers where mass to charge selection
and selection
and ion fragmentation occurs in a higher pressure region. The invention is not
limited to the
CA 02318855 2000-07-24
Wf~ 99/38193 PCT/US99/01335
specific embodiments shown and techniques described. For example, instead of a
segmented
ion guide, individual ion guides maybe positioned in the higher background
pressure region
and used to conduct m/z and ion fragmentation steps in an MS/MSn analysis.
This
arrangement would allow different RF frequencies to be applied to each
separate multipole ion
guide potentially increasing flexibility, however, system cost and complexity
would increase
proportionally as well. The four vacuum pumping stage embodiment shown can be
re-
configured as a two, three or five stage vacuum system with m/z selection
and/or CID
fragmentation conducted with multipole ion guides' in a higher background
pressure vacuum
region. Different ion sources can be configured with the multipole ion guide
TOF hybrid
instrument. Even ion sources which operate in vacuum can be configured with
multipole ion
guides operating at higher background vacuum pressures. With ion sources that
operate in
vacuum, gas may be added to the vacuum region containing the multipole ion
guide to operate
in higher pressure m/z selection and ion fragmentation modes. The invention
can be applied
to variations of TOF mass analyzer geometries. For example, the TOF mass
analyzer may be
configured with an in lice pulsing region, a curved field ion reflector or a
discrete dynode
multiplier. In alternative embodiments, the portions of a segmented multipole
ion guides or
individual multipole ion guides located in a higher pressure regions can also
be configured to
operate in ion transfer, ion trapping, and any of the fragmentation modes
already discussed as
well as m/z analysis or m/z selection mode or combinations of these individual
operating
modes. To one skilled in the art, all the fragmentation, CID, mass selection,
and MS/MS
methods discussed in the embodiments described in Figures 1 through 7 can be
implemented
in alternative embodiments of the invention.
Ion Guide Higher Pressure MS/MSn Quadrupole
As has already been stated with API source and a Time-Of flight mass analyzer
an important
feature of multipole ion guides is that ions can be released from one end of
an ion guide or
segment simultaneously while ions are entering the opposite end of the ion
guide or individual
segment. Due to this feature, a segmented ion guide receiving a continuous ion
beam can be
66
CA 02318855 2000-07-24
CVO 99/38193 PCT/US99/01335
selectively release only a portion of the ions located in the ion guide into a
mass analyzer
which performs mass analysis on the released ions. In this manner ions are not
lost in
between mass analysis steps. Another specific embodiment of this aspect of the
invention is
the configuration of an API source with segmented multipole ion guide where
the multipole
ion guide which may or may not be combined with additional quadrupole miss
analyzers or
multipole ion guide collision cells. In this embodiment of the invention, a
quadrupole
segmented ion guide is itself configured as an MS or MS/MSn mass analyzer with
a portion of
the segmented ion guide length operated in pressures above 10~ torr. If
required, the'electron
multiplier detector may be configured and operated lower background pressure
region in the
embodiments shown. Segmented multipole ion guides configured as mass analyzers
or as a
portion of a mass analyzer can achieve an increased performance and analytical
capability for a
lower cost and complexity than separate multipole ion guides configured in
series.
Figure 10 shows an embodiment of the invention where a five segment quadrupole
segmented
ion guide is configured as a mass analyzer in an API MS instrument. Multipole
ion guide 1008
is configured with segments 1001,1002, 1003, 1004 and 1005 with electrically
insulated
junctions 1018, 1019, 1020 and 1017 separating each segment respectively.
Through to
vacuum partition 1023 in second vacuum stage 1016, Electrospray source 1012
and segmented
multipole ion guide 1008 configuration is similar to the embodiment described
in Figure 1.
Second vacuum stage 1016 is operated with a background maintained above of
10'~ torr. A
common RF frequency with, in some cases, different RF amplitudes can be
applied to all
segments in multipole ion guide 1008 to maximize intersegment ion transfer
efficiency. In the
embodiment diagrammed in Figure 10, the TOF mass analyzer has been replaced by
additional multipole ion guide segment 1005. Multipole ion guide segment 1005
is located in
third vacuum stage 1017 which is maintained at a background pressure below 10-
4 torr. As
segment 1005 is a quadrupole mass analyzer and may be operated in scanning or
selected ion
monitoring mode. The embodiment shown in Figure 10 can perform all analytical
functions
performed by traditional triple quadrupole configurations as well as
additional MS/MS
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CA 02318855 2000-07-24
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analytical functions. The four basic MS/MS mode traditional triple quadrupole
analytical
functions as listed in a previous section are repeated below for convenience.
Triple
quadrupoles can operated with the following techniques;
1. transmitting a selected m/z range in quadrupole 1, fragmented the selection
ions in the RF only collision cell while scanning quadrupole 3,
2. neutral loss scan, where quadrupole 1 and 3 are scanned simultaneously with
a
fixed m/z offset,
3. scanning quadrupole 1 while setting quadrupole 3 to pass a selected m/z
range,
and
4. Setting both quadrupole 1 and 3 to pass different m/z values without
scanning
to monitor selected fragmentation events.
All the above analytical techniques can be achieved with the embodiment shown
in Figure 10
by using the following configuration.
1. Operate segment 1001 in single pass (non trapping) RF only mode with the
applied
RF amplitude set to pass the desired range of m/z values.
2. Operate segment 1002 in single pass (non trapping) m/z selection mode. For
functions 2 and 3 above segment 2 will be scanned repetitively in m/z
selection
mode at the desired scan speed and over the desired range of ion m/z values.
The
relative DC offset potentials applied to segments 1002, 1003, 1004 1005 are
set to
accelerate mass to charge selected ions through segments 1003 and 1004 and
into
segment 1005 with sufficient energy to cause CID fragmentation of accelerated
ions
in segments 1003 and 1004. The background pressure in the entrance end of
segment 1004 can be maintained sufficiently high to damp axial ion
trajectories
after fragmentation to achieve an ion beam with low energy spread. In this
manner,
the ion energy of ions entering segment 1005 is determined by the relative DC
offset
potentials of applied to segments 1004 and 1005.
3. Segment 1005 is operated in mass to charge selection mode. The ion mass to
charge
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CA 02318855 2000-07-24
5~V0 99/38193 PCT/US99/01335
value selection range may be fixed as in triple quadrupole MS/MS techniques 3
and
4 listed above or scanned as is required in techniques 1 and 2 above. The m/z
selection scanning ramps of segments 1002 and 1005 can be synchronized to
achieve
neutral loss scans, technique 2 above, or monitoring of selected fragmentation
events, technique 4 above.
4. Detecting ions passing from segment 1005 through lens 1006 by accelerating
the ions
into conversion dynode 1007 and detecting the resulting products with electron
multiplier 1024. '''
The embodiment shown in Figure 10 is capable of conducting additional
analytical functions
not possible with traditional triple quadrupole geometries where both
analytical quadrupoles
1 and 3 are operated in a low vacuum region to minimize ion collisions with
the background
gas. For example non-trapping continuous ion beam MS/MS2 analysis can be
achieved by
operating segment 1001 in mass to charge selection mode and accelerating the
selected ions
into segment 1002 with sufficient energy to cause Cm fragmentation in segment
2. Segment
1001 can be operated in static or scanning m/z selective mode. Alternatively,
MS/MS2
analysis can be conducted with resonant frequency excitation CID ion
fragmentation if it is
desirable to not increase the internal energy of product ions. This can be
achieved in scanning
or non scanning modes as follows;
1. Operate segment 1001 in single pass (non trapping) RF only mode with the
applied
RF amplitude set to pass the desired range of m/z values.
2. Operate segment 1002 in single pass (non trapping) m/z selection mode. For
functions 2 and 3 above segment 2 will be scanned repetitively in m/z
selection
mode at the desired scan speed and over the desired range of ion m/z values.
3. The relative DC offset potentials applied to segments 1002, 1003 and 1004
are set to
accelerate mass to charge selected ions through segment 1003 and into segment
1004
without causing DC acceleration CID fragmentation. Segment 1004 is operated in
resonant frequency excitation fragmentation mode to fragment the m/z value
ions
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CA 02318855 2000-07-24
W~ 99/38193 PCT/US99/01335
selected by segment 1002. The first generation fragment ions produced in
segment
1004 pass into segment 1005 with the appropriate relative DC offset
_potentials set to
optimally pass ions through maximum m/z selection resolution. The background
pressure in the entrance end of segment 1004 can be maintained sufficiently
high to
damp axial ion trajectories after fragmentation to achieve an ion beam with
low
energy spread. In this manner, the ion energy of ions entering segment 1005 is
determined by the relative DC offset potentials of applied to segments 1004
and
1005.
3. Segment 1005 is operated in mass to charge selection mode. The ion mass to
charge
value selection range may be fixed as in triple quadrupole MS/MS techniques 3
and
4 listed above or scanned as is required in techniques 1 and 2 above. The m/z
selection scanning ramps of segments 1002 and 1005 can be synchronized to
achieve
neutral loss scans, technique 2 above, or monitoring of selected fragmentation
events, technique 4 above.
4. Detecting ions passing from segment 1005 through lens 1006 by accelerating
the ions
into conversion dynode 1007 and detecting the resulting products with electron
multiplier 1024.
Due to the common RF frequency, ions can be transferred efficiently from
segment 1004 to
1005 with low energy to achieve higher resolution mass to charge selection.
Ions can be
temporarily trapped in any segment of multipole ion guide 1008 to increase the
ion resident
time to achieve higher resolution m/z selection or resonant frequency
excitation CID
fragmentation. The scan speeds can be matched to the ion trap and release
rates, for example
with discrete m/z value scan steps to improve MS/MSn performance. If a higher
pressure
detector is used, the entire segmented multipole ion guide 1008 can be
configured in one
higher background pressure vacuum stage. Elimination of a vacuum pumping stage
will
reduce instrument cost, size and complexity while imposing little or no
reduction in system
flexibility or performance. Configuring segmented multipole ion guide 1008 in
a single
CA 02318855 2000-07-24
'WO 99/38193 PCT/US99/01335
vacuum pumping stage eliminates any size constraint on the internal diameter
to minimize
neutral gas conductance between multiple vacuum pumping stages. Alternatively,
multipole
ion guide 1008 can also be configured to extend into first vacuum stage 1025
in a two or three
vacuum stage system. Additional alternative embodiments for triple quadrup 1e
like mass
anal zers confi red with a mufti ole ion ide operated in mass to charge
selection mode in
Y ~ P
a higher pressure vacuum region are shown in Figures l I through 13.
.;~
Figure 11 is a diagram of an alternative embodiment of the invention in which
three segment
multipole ion guide 1108 is configured with a separate multipole ion guide
1104. The
embodiment shown in Figure 11 is a variation of the embodiment shown in Figure
10 where
quadrupole 1104 can be configured with poles of a different geometry than
those of segmented
multipole ion guide 1108 comprised of segments 1101, 1102 and 1103. Multipole
ion guide
1004 can be operated with a different RF frequency than that applied to
multipole ion guide
1108. Full triple quadrupole MS and MS/MS function analysis can be achieved
with the
embodiment of the invention diagrammed in Figure 11 using the techniques
described in the
above sections.
An alternative embodiment is shown in Figure 12 in which segmented multipole
ion guide
1208 is configured in higher vacuum pressure stage 1210 and extends into the
rod volume
described by separate multipole ion guide 1204. Multipole ion guide segment
1203 extends
into exit lens 1205 through which ions can be efficiently transferred, even at
low energies, into
multipole ion guide 1204. Full tripled quadrupole MS and MS/MS functions can
be achieved
by operating segments 1201, 1202, 1203 and quadrupole 1204 in scanning and
static m/z
selection and CID fragmentation modes as described in the above sections.
An alternative embodiment of the invention is shown in Figure 13 in which an
additional
multipole in guide collision cell 1312 has been added to a three vacuum
pumping stage
multipole ion guide mass analyzer. Three segment multipole ion guide 1308 is
configured in
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CA 02318855 2000-07-24
WO 99/38193 PCTNS99/OI335
higher vacuum pressure vacuum stage extending into lower pressure vacuum stage
1315. Mass
to charge selected an/or fragment ions are transferred from multipole ion
guide 1308 into
multipole ion guide 1310 which in configured in collision region 1312
surrounded by gas
partition 1313. Multipole ion guide 1304 serves as the final quadrupole mass
analyzer before
ions are detected with detector 1305. Analogous to the added multipole ion
guide in the API
TOF hybrid embodiment shown in Figure 6, collision or reactive gas can be
introduced into
region 1312 which is different than the background gas in vacuum stage 1314.
Added
multipole ion guide 1310 positioned in independent collision region 1312
allows increased
experimental flexibility in MS/MSn analysis. Continuous beam MS/MS3
experiments can be
achieved with the embodiment shown in Figure 13 operating with DC acceleration
or
resonant frequency excitation CDR ion fragmentation techniques.
Ion Guide Higher Pressure Quadxupole
One aspect of the present invention incorporates a non-segmented or segmented
ion guide
into a high pressure mass analyzer. Segmented multipole ion guides configured
as mass
analyzers or as a portion of a mass analyzer can achieve an increase
performance and analytical
capability.
Figure 14 shows a high pressure operation non-segmented multipole ion guide or
mass
analyzer 1400 which extends continuously from pumping stage two 1401 where the
pressure is
greater than 1x10'' torr, substantially at a pressure where ions traversing
the multipole ion
guide length will encounter collisions with the neutral background gas, into
pumping stage
three 1402 where the detector 1403 is located. The mass analyzer can be
configured with four,
six, eight or more rods or poles, however, the m/z selection resolving power
which can be
achieved using multipole ion guides decreases as the number of poles
increases, consequently,
quad'rupoles have been commonly used as mass analyzers. Thus, for the mass
analyzer
diagrammed in this embodiment a quadrupoles will be the configuration
presented. The
quadrupole multipole ion guide assembly 1400 diagrammed in Figure 14 is
composed of four
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parallel poles or rods equally spaced around a common centerline 1404. In an
ideal
quadrupole mass analyzer the pole shapes would be hyperbolic but commonly, for
ease of
manufacture, round rods are used. A cross section of a quadrupole with round
rods 104, 105,
106, and 107 is diagrammed in Figure 9. The same AC and DC potentials are
applied to
opposite rods sets (104, 106 and 105, 107) for most quadrupole operating
modes. Adjacent
rods have the same AC and DC amplitude but opposite polarity. In addition, a
common DC
offset can be applied to all rods 104, 105, 106, and 107.
In this embodiment of the invention the non-segmented quadrupole mass analyzer
begins in
pumping stage two 1401 where the pressure greater than 1 x 10~ torr,
substantially at a
pressure where ions traversing the multipole ion guide length will encounter
collisions with
the neutral background gas. The multipole ion guide mass to charge analysis or
selection
operation can be achieved by applying a combination of RF and DC potentials,
select resonant
frequency to reject unwanted ion m/z values, scanning the RF frequency or
amplitude values
or combinations of these methods. In m/z analysis or m/z selection operating
mode ion
collisions with the background gas slows down the selected ion m/z
trajectories in the radial
and axial directions as the ions traverse the multipole ion guide length in
single pass. Ions
spending increased time in the multipole ion guide are. exposed to an
increased number of RF
cycles. In this manner higher m/z selection resolution can be achieved for
shorter multipole
ion guide lengths than can be attained using a quadrupole mass analyzer with
the more
conventional method of operating in low background pressure. Operating
multipole ion
guides in analytical mode with higher pressure background gas in an API MS
system allows
the configuration of smaller more compact systems with reduced vacuum pumping
speed
requirements. A smaller multipole ion guide configuration reduces the cost of
driver
electronics and the higher pressure operation reduces the vacuum system costs.
Such a system
can achieve improvement in the API MS system performance when compared to an
instrument which includes a quadrupole mass analyzer operated at background
pressure
maintained low enough to avoid or minimize ion collisions with neutral
background gas.
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Atmospheric Pressure Chemical Ionization (APCI) source 1405 can be configured
where
solvent is delivered to the APCI nebulizer 1417 tip 1406 at flow rates below
500 nl/min to
above 2 ml/min. This embodiment could be reconfigured with any of the
following
alternative sources but is not limited to Electrospray (ES), Inductively
Coupled Plasma (ICP),
Glow Discharge (GD) source, multiple similar probes in one source, or
combinations of
different probes in one source. Sample bearing solution can be introduced into
the APCI
source 1405 with liquid delivery systems. Liquid delivery systems may include
but are not
limited to, liquid pumps with or without auto injectors, separation systems
such as liquid
chromatography or capillary electrophoresis, syringe pumps, pressure vessels,
gravity feed
vessels or solution reservoirs. APCI source 1405 is operated by applying
potentials to
cylindrical electrode 1407 and corona needle 1408, endplate electrode 1409 and
capillary
entrance electrode 1410. Counter current drying gas 1411 is directed to flow
through heater
1412 and into APCI source chamber 1405 through endplate nosepiece 1413 opening
1414.
The orifice into vacuum as shown in Figure 14 is a dielectric capillary tube
1415 with entrance
orifice 1416. The potential of an ion being swept through dielectric capillary
tube 1415 into
vacuum is described in U.S. patent number 4,542,293. To produce positive ions,
negative
kilovolt potentials are applied to endplate electrode 1409 with attached
electrode nosepiece
1413 and capillary entrance electrode 1410 and positive kilovolt potentials
are applied to
cylindrical electrode 1407 and corona needle 1408. APCI nebulizer 1417 and
APCI heater
1418 remains at ground potential during operation. To produce negative ions,
the polarity of
the just mentioned electrodes are reversed. Alternatively, if a nozzle or
conductive (metal)
capillaries are used as orifices into vacuum, kilovolt potentials can be
applied to APCI corona
needle 1408 and cylindrical electrode 1407 during operation. Heated
capillaries can be
configured as the orifice into vacuum used with or without counter current
drying gas.
Unlike an ES source, an APCI source creates sample and solvent molecule vapor
prior to
ionization. The APCI ionization process, unlike Electrospray, requires gas
phase molecule-
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ion charge exchange reactions. Sample solution is introduced through
connecting tube X1420
into APCI probe 1417 and is sprayed with pneumatic nebulization from APCI
inlet probe tip
1406. The sprayed liquid droplets traverse cavity 1421 and flow into APCI
vaporizer 1418. In
the embodiment shown, cavity 1-421 is configured with a droplet separator
ball. Separator ball
1424 removes larger droplets from the sprays produced by the nebulizer
inletprobes to
prevent them from entering vaporizer 1418. Separator ball 1424 can be removed
when lower
solution flow rates are introduced to improve sensitivity. The liquid droplets
are evaporated
in vaporizer 1418 forming a vapor prior to entering the corona discharge
region 1422' around
and / or downstream of corona discharge needle tip 1423. Additional makeup gas
flow may
be added independently or through APCI inlet probe assembly to aid in
transporting the
droplets and resulting vapor through the APCI source assembly. An electric
field is formed in
APCI source 1405 by applying electrical potentials to cylindrical lens 1407,
corona discharge
needle 1408, endplate 1409 with nosepiece 1413 and capillary entrance
electrode 1410. The
applied electrical potentials, counter current gas flow 1411, and the total
gas flow through
vaporizer 1418 are set to establish a stable corona discharge in region 1422
around and / or
downstream of corona needle tip 1423. The ions produced in corona discharge
region 1422 by
atmospheric pressure chemical ionization are driven by the electric field
against counter
current bath gas 1411 towards capillary orifice 1416. Ions are swept into
vacuum through
capillary orifice 1416 and pass through capillary 1415 and into the first
vacuum stage 1425.
If a capillary is configured with a heater 1426 as an orifice into vacuum with
or without
counter current drying gas, additional energy can be transferred to the gas
and ions in the
capillary. This additional energy is some time useful for additional drying or
additional energy
for fragmentation. A portion of the ions entering the first stage vacuum 1425
are directed
through the skimmer 1427 and into the second vacuum stage 1401.
Ions are produced at or near atmospheric pressure from sample bearing liquid
in atmospheric
pressure ion source 1405. The ions are delivered into vacuum through
dielectric capillary tube
1415 carried along by the neutral background gas, which pass through vacuum
partition 1428.
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The neutral background gas forms supersonic jet as it expands into vacuum from
an exit
orifice 1429 and accelerates the entrained ions through multiple collisions
during the
expansion. Vacuum systems incorporating one or more vacuum pumping stages have
been
configured to remove background neutral gas as the ions of interest traverse
from the API
source orifice to the mass analyzer entrance. The cost and size of an APUMS
instrument can
be reduced if multiple vacuum pumping stages are configured and the pumping
speed required
for each stage is minimized. Typically, three to four vacuum pumping stages
are employed in
the lower cost or benchtop API/MS instruments. With the development of
multiple vacuum
stage turbomolecular vacuum pumps, three and even four stage vacuum systems
require only
one rotary and one turbomolecular pump to achieve satisfactory background
pressures in each
stage. Multipole ion guides operated in the AC or RF only mode have been used
extensively
in API/MS instruments to transport ions efficiently through the second 1401
and/or third
1402 vacuum pumping stages. In this embodiment, a rotary vacuum pump is used
to evacuate
the first vacuum stage 1425 through pump port 1430 the background pressure is
maintained
between 0.2 and 2 torr. A portion of the free jet expansion passes through a
skimmer 1427
which is part of the vacuum partition 1431 and into second vacuum stage 1401
where
background pressures can range from 10~ to 101 torr depending on the skimmer
orifice 1432
size and the pumping speed employed in vacuum stage two 1401 through pump port
1433.
Ions are deliverer to pumping stage three 1402 through the mass analyzer ion
guide which
pass through vacuum partition 1434 and this stage is evacuated through pump
port 1435. Ion
then exit the mass analyzer and pass through a exit lens 1436 which focus the
ions into the
detector 1403. Repeller plate 1437 also act to focus ions into the detector.
This high pressure
quadrupole system has three pumping stages. The mass to charge analysis or
selection
operation can be achieved by applying a combination of RF and DC potentials,
select resonant
frequency to reject unwanted ion m/z values, scanning the RF frequency or
amplitude values
or ct~mbinations of these methods. In addition, only the traditional CID
process can be
performed. This CID process fragment all ions that come through the capillary
however due
to different bond strengths of different molecules different amounts of
fragmentation can
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occur.
A farther extension of the embodiment shown in Figure 14 is shown in Figure
15,
demonstrating a segment mass analyzer ion guide 1500 which extends
continuously from
pumping stage two where the pressure is greater than 1x10'' torr,
substantially at a pressure
where ions traversing the multipole ion guide length will encounter collisions
with the neutral
background gas, into pumping stage three where the detector is located. Only
the additional
embodiment will be outlined here however all that has been explained for
Figure 14 i~ directly
transferable to Figure 15. The mass analyzer assembly 1500 which extends
continuously from
the second vacuum stage 1501 into the third vacuum stage 1502. Again a
quadrupole is used as
the mass analyzer as has been discussed previously and the four parallel poles
or rods are
equally spaced around a common centerline 1506. V~hen an ion guide is
segmented into
sections each rod is broken up into sections which when assembled align as a
single
continuous rod. Each segment within a rod assembly is electrically insulated
from its adjacent
segments. The insulation is configured with the rod sections to minimize space
charge effects
which could distort the electric fields within the region bounded by the rods.
As shown in
Figure 15 the four continuous rods are broken in to segments 1503, 1504, and
1505 and are
electrically insulated from adjacent segments at insulating junction 1507 and
1508.
This embodiment is shown with a Glow Discharge (GD) source 1409. This
embodiment
could be reconfigured with any of the following alternative sources but is not
limited to
Electrospray (ES), Inductively Coupled Plasma (ICP), Atmospheric Pressure
Chemical
Ionization (APC~ source, multiple similar probes in one source, or
combinations of different
probes in one source. Gases sample can be introduced through port 1510
substantially at or
below atmospheric pressure. GD source chamber is maintained at this pressure
by a pump
attached to pump port 1514. GD source 1509 is operated by applying potentials
to discharge
needles 1511 and 1512. The orifice into vacuum as shown in Figure 15 is a
nozzle or skimmer
1513. Ions are formed in the GD source 1509 and pass through skimmer 1513 and
into the
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mass analyzer.
Mass selection can be performed, for example, segment 1503 and 1505 can be a
RF only
segment for ion transport, and segment 1504 is configured to operate in mass
selective mode.
The multipole ion guide mass to charge analysis or selection operation can be
achieved by
applying a combination of RF and DC potentials, select resonant frequency to
reject
unwanted ion m/z values, scanning the RF frequency or amplitude values or
combinations of
these methods.
Figure 16 demonstrates a non-segmented mass analyzer ion guide 1600
exclusively housed in
pumping stage two 1602 where the pressure is greater than lxi0'° torr,
substantially at a
pressure where ions traversing the multipole ion guide length will encounter
collisions with
the neutral background gas. To one skilled in the art one can see that this
embodiment can
claim all that was claimed with the embodiment attached to Figure 14 with the
additions that
the mass analyzer 1600 exclusively housed in pumping stage two 1602. An
Electrospray source
1608 is configured on this system however the system could be reconfigured
with any of the
following alternative sources but is not limited to Atmospheric Pressure
Chemical Ionization
(APCn, Inductively Coupled Plasma (ICP), Glow Discharge (GD) source, multiple
similar
probes in one source, or combinations of different probes in one source.
Details of the
Electrospray source 1608 have already been discussed along with ion formation
and
transportation from the Electrospray source 1608 to the entrance of the
skimmer 1609, along
with other variations on this hardware and thus, will not be repeated. A
portion of the free
jet expansion passes through a skimmer 1609 which is part of the vacuum
partition 1610 and
into second vacuum stage 1602 where background pressures can range from 10~ to
10-1 torr
depending on the skimmer orifice size and the pumping speed employed in vacuum
stage two
160f through pump port 1612. Ions travel through the mass analyzer 1600 and
exit the mass
analyzer in stage two. Ion that exit the mass analyzer are focused through a
lens 1604 which is
part of the vacuum partition 1605. Ions are deliverer to pumping stage three
1603 through
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this lens 1604 and are focused into the detector 1606 by repeller plate 1607
and this stage is
evacuated through pump port 1613. This high pressure quadrupole system has
three pumping
stages. The mass to charge analysis or mass selection operation can be
achieved by applying a
combination of RF and DC potentials, scanning the RF frequency or amplitude
values or
combinations of these methods.
Figure 17 demonstrates a segmented mass analyzer multipole ion guide 1700
exclusively
housed in pumping stage two 1702 where the pressure is greater than 1x10'4
torr, sub'Stantially
at a pressure where ions traversing the multipole ion guide length will
encounter collisions
with the neutral background gas. To one skilled in the art one can see that
this embodiment
can claim all that was claimed with the embodiment attached to Figure 15 with
the additions
that the segmented mass analyzer 1700 exclusively housed in pumping stage two
1702. Any of
the following sources can be configured on this system Electrospray (ES),
Atmospheric
Pressure Chemical Ionization (APCI), Inductively Coupled Plasma (ICP), Glow
Discharge
(GD) source, multiple similar probes in one source, or combinations of
different probes in one
source. Details of the source have already been discussed along with ion
formation and
transportation from the source to the entrance of the skimmer 1609, along with
other
variations on this hardware and thus, will not be repeated. A portion of the
free jet expansion
passes through a skimmer 1709 which is part of the vacuum partition 1710 and
into second
vacuum stage 1702 where background pressures can range from 10~ to 101 torr
depending on
the skimmer orifice size and the pumping speed employed in vacuum stage two
1702 through
pump port 1712: Ions travel through the segmented mass analyzer 1700 and exit
the mass
analyzer in stage two 1712. The ions pass through the four continuous rods
that are broken
into segments 1715, 1717, and 1719 and are electrically insulated from
adjacent segments at
insulating junction 1716 and 1718. Ion that exit the mass analyzer are focused
through a lens
1704 which is part of the vacuum partition 1705. Ions are deliverer to pumping
stage three
1703 through this lens 1704 and are focused into the detector 1706 by repeller
plate 1707 and
this stage is evacuated through pump port 1713. This high pressure quadrupole
system has
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three pumping stages. The mass to charge analysis or mass selection operation
can be achieved
by applying a combination of RF and DC potentials, scanning the RF frequency
or amplitude
values or combinations of these methods.
Figure 18 demonstrates a non-segmented mass analyzer multipole ion guide 1800
exclusively
housed in pumping stage two 1802 along with a detector 1806 where the pressure
is greater
than 1x10'4 torr, substantially at a pressure where ions traversing the
multipole ion guide
length will encounter collisions with the neutral background gas. To one
skilled in the art one
can see that this embodiment can claim all that was claimed with the
embodiment attached to
Figure 16 with the additions that the mass analyzer 1800 exclusively housed in
pumping stage
two 1802 along with a Microchannel Plate (MCP) detector 1806. An Electrospray
source 1808
is configured on this system however the system could be reconfigured with any
of the
following alternative sources but is not limited to Atmospheric Pressure
Chemical Ionization
(APCI), Inductively Coupled Plasma (ICP), Glow Discharge (GD) source, multiple
similar
probes in one source, or combinations of different probes in one source.
Details of the
Electrospray source 1808 have already been discussed along with ion formation
and
transportation from the Electrospray source 1808 to the entrance of the
skimmer 1809, along
with other variations on this hardware and thus, will not be repeated. A
portion of the free
jet expansion passes through a skimmer 1809 which is part of the vacuum
partition 1810 and
into second vacuum stage 1802 where background pressures can range from 10~ to
10-1 torr
depending on the skimmer orifice size and the pumping speed employed in vacuum
stage two
1802 through pump port 1812. Ions travel through the mass analyzer 1800 and
exit the mass
analyzer in stage two. Ion that exit the mass analyzer are focused through a
lens 1804 ions are
deliverer to the detector 1806. The ions exit the mass analyzer 1800 through a
lens 1804 and in
this same pumping stage the ions collide with a MCP detector which can be
operated in the
low'inillitorr range or below. This high pressure quadrupole and detector
system has only two
pumping stages which can farther reduce the cost and size of an API/MS
instrument. This
vacuum systems may be configured with one small single stage turbomolecular
pump on stage
CA 02318855 2000-07-24
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two and one rotary pump to achieve the desired background pressures in each
stage and in fact
may be alternatively configured with only rotary pumps. The mass to charge
analysis or mass
selection operation can be achieved by applying a combination of RF and DC
potentials,
scanning the RF frequency or amplitude values or combinations of these
methods.
Figure 19 demonstrates a segment mass analyzer ion guide 1900 exclusively
housed in
pumping stage two 1902 along with a detector 1906 where the pressure is
greater than 1x10'4
torr, substantially at a pressure where ions traversing the multipole ion
guide length'avill
encounter collisions with the neutral background gas. To one skilled in the
art one can see
that this embodiment can claim all that was claimed with the embodiment
attached to Figure
17 with the additions that the mass analyzer 1900 exclusively housed in
pumping stage two
1902 along with a Microchannel Plate (MCP) detector 1906. An Electrospray
source 1908 is
configured on this system however the system could be reconfigured with any of
the
following alternative sources but is not limited to Atmospheric Pressure
Chemical Ionization
(APCI), Inductively Coupled Plasma (ICP), Glow Discharge (GD) source, multiple
similar
probes in one source, or combinations of different probes in one source.
Details of the
Electrospray source 1908 have already been discussed along with ion formation
and
transportation from the Electrospray source 1908 to the entrance of the
skimmer 1909, along
with other variations on this 'hardware and thus, will not be repeated. A
portion of the free
jet expansion passes through a skimmer 1909 which is part of the vacuum
partition 1910 and
into second vacuum stage 1902 where background pressures can range from 10~ to
101 torr
depending on the skimmer orifice size and the pumping speed employed in vacuum
stage two
1902 through pump port 1912. Ions travel through the mass analyzer 1900 and
exit the mass
analyzer in stage two. The ions pass through the four continuous rods that are
broken into
segments 1913, 1915, and 1917 and are electrically insulated from adjacent
segments at
insulating junction 1914 and 1916. Ion that exit the mass analyzer are focused
through a lens
1904 ions are deliverer to the detector 1906. The ions exit the mass analyzer
1900 through a
lens 1904 and in this same pumping stage the ions collide with a MCP detector
which can be
81
CA 02318855 2004-04-29
operated in the low mihitorr range or below. This high pressure quadrupole and
detector
system has only two pumping stages which cau farther reduce the cost and size
of an API/MS
iz~stxument. This vacuum systems may be configured with one small single stage
turbomolecular pump on stage two and one rotary pump to achieve the desired
background
pressures in each stage and in fact may be alternatively configured with only
rotary Pumps.
The mass to charge analysis or mass selection operation can be achieved by
applying a
combination of RF and DC potentials, scanning the RF frequency or amplitude
values or
combinations of these methods.
References Cited:
The following is a list of the references referred to above:
U.S
5,401,962Mar. 28,1995 Ferran, Robert..
5,613,294Mar. 25,1991 ~ Ferran, Robert.
4,234,791Nov. 18,1980
En~e, Christie;
Yost, Richard;
Morrison,
James.
4;963,736Oct.16,1990 Douglas, Donald; Preach, John.
5,179,278Jan.12,1993 Douglas, Donald.
5,689,111Nov. 18, 1997
Dresch, Thomas;
Gulcicek,
Erol; Whitehouse,
Craig.
5,652,427Jul. 29,1997 Whitehouse, Craig; Gulcicek, Erol.
08/694,542Aug. 9, 1996 Whitehouse, Craig; Dresch, Thomas; Andrien,
Bruce.
4,542,293~Sep.17,1985~ Penn, John; Yannashita, Masamichi; Whitehouse,
Craig.
P,gblications: .
K.L~'Duffin, T. Wachs, J.D. ~ienion, " Atmospheric Pressure Ion- Sampling
System for Liquid
Chromatography/ Mass Spectrometry Analyses on a Beachtop Mass Specuometex",
Aualyt.
Chem., vol. 64, pp. 61-68, (1992).
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WO 99/38193 PCT/US99/01335
C.F. Ijames, 44th ASMS Conference Proceedings on Mass Spectrometry, 795, 1996.
Having described this invention with regard to specific embodiments, it is to
be understood
that the description is not meant as a limitation since further modifications
and variations may
be apparent or may suggest themselves. It is intended that the present
application cover all
such modifications and variations, including those as fall within the scope of
the appended
claims.
,;~
83
