Language selection

Search

Patent 2626383 Summary

Third-party information liability

Some of the information on this Web page has been provided by external sources. The Government of Canada is not responsible for the accuracy, reliability or currency of the information supplied by external sources. Users wishing to rely upon this information should consult directly with the source of the information. Content provided by external sources is not subject to official languages, privacy and accessibility requirements.

Claims and Abstract availability

Any discrepancies in the text and image of the Claims and Abstract are due to differing posting times. Text of the Claims and Abstract are posted:

  • At the time the application is open to public inspection;
  • At the time of issue of the patent (grant).
(12) Patent: (11) CA 2626383
(54) English Title: MASS SPECTROMETRY WITH MULTIPOLE ION GUIDES
(54) French Title: SPECTROMETRIE DE MASSE AVEC GUIDES D'IONS MULTIPOLAIRES
Status: Expired
Bibliographic Data
(51) International Patent Classification (IPC):
  • H01J 49/26 (2006.01)
  • H01J 49/10 (2006.01)
  • H01J 49/40 (2006.01)
  • H01J 49/42 (2006.01)
(72) Inventors :
  • WHITEHOUSE, CRAIG M. (United States of America)
  • ANDRIEN, BRUCE A., JR. (United States of America)
  • GULCICEK, EROL E. (United States of America)
(73) Owners :
  • PERKINELMER HEALTH SCIENCES, INC. (United States of America)
(71) Applicants :
  • ANALYTICA OF BRANFORD, INC. (United States of America)
(74) Agent: SMART & BIGGAR
(74) Associate agent:
(45) Issued: 2011-07-19
(22) Filed Date: 1999-05-29
(41) Open to Public Inspection: 1999-12-02
Examination requested: 2008-04-24
Availability of licence: N/A
(25) Language of filing: English

Patent Cooperation Treaty (PCT): No

(30) Application Priority Data:
Application No. Country/Territory Date
60/087,246 United States of America 1998-05-29
09/235,946 United States of America 1999-01-22

Abstracts

English Abstract

A mass spectrometer (40) is configured with individual multipole ion guides (60, 62) configured in an assembly in alignment along a common centerline (5) wherein at least a portion of each multiple ion guide (60, 62) mounted in the assembly resides in a vacuum region (72, 73) with higher background pressure. Said multiple ion guides (60, 62) configured in a higher pressure vacuum region (72, 73) are operated in mass to charge selection and ion fragmentation modes. Individual sets of RF, +/- DC and resonant frequency waveform voltage supplies provide potentials to the rods of each multiple ion guide allowing the operation of ion transmission, ion trapping, mass to charge selection and ion fragmentation functions independently in each ion guide (60, 62). The presence of background pressure maintained sufficiently high to cause ion to neutral gas collisions along a portion of each multiple ion guide linear assembly allows the conducting of Collisional Induced Dissociation (CID) fragmentation of ions by axially accelerating ions from one multiple ion guide into an adjacent ion guide, analoguous to a triple quadruple ion function.


French Abstract

Spectromètre de masse (40) configuré avec des guides d'ions multiples (60, 62) qui sont configurés dans un ensemble aligné le long d'un axe central commun (5) où au moins une parie de chaque guide d'ions multiples (60, 62) montés dans l'ensemble réside dans une région de vide (72, 73) avec une pression ambiante plus élevée. Lesdits guides d'ions multiples (60, 62), configurés dans une région de vide à plus haute pression (72, 73), sont activés en masse afin de charger les modes de sélection et de fragmentation des ions. Des séries individuelles de radiofréquences, de courant continu +/- et les fournitures de tensions des formes d'onde à fréquence résonnante créent des potentiels aux tiges de chaque guide d'ions multiples qui permettent la transmission et le captage des masses ioniques pour charger indépendamment les fonctions de sélection et de fragmentation des ions dans chaque guide d'ions multiples (60, 62). La présence d'une pression ambiante maintenue à un niveau suffisamment élevé pour provoquer la collision des ions avec un gaz neutre le long d'une partie de chaque ensemble linéaire de guides d'ions multiples permet d'effectuer une fragmentation des ions induite par collision, par accélération sur le plan axial d'ions d'un guide à ions multiple à un autre guide adjacent, de manière analogue à une fonction d'ions triples quadripôles.

Claims

Note: Claims are shown in the official language in which they were submitted.




We claim:


1. An apparatus for analyzing chemical species, comprising:

(a) an ion source for producing ions from a sample substance;
(b) at least two vacuum pumping stages;

(c) a detector located in one of said at least two vacuum pumping stages;

(d) at least one multipole ion guide each comprising at least two multipole
ion guide
segments for transporting said ions, each said multipole ion guide being
located in a plurality
of vacuum stages such that each said multipole ion guide begins in one vacuum
pumping
stage and extends into at least a second vacuum stage of said at least two
vacuum stages;

(e) a region comprising neutral gas molecules wherein at least a portion of at
least one
of said at least two multipole ion guide segments is positioned, and wherein
the neutral gas
pressure is high enough that collisions occur between said ions traversing
said ion guide and
said neutral gas molecules; and

(f) RF and DC voltage sources that supply DC voltages and RF voltages with
substantially the same RF frequency and phase to any one of said at least one
multipole ion
guide, and

(g) means to control the amplitudes of said RF voltages and said DC voltages
supplied
to one of said at least two multipole ion guide segments independently of said
RF voltages
and said DC voltages supplied to others of said at least two multipole ion
guide segments.


2. An apparatus according to claim 1, wherein said ion source operates at
substantially
atmospheric pressure.


3. An apparatus according to claim 1, further comprising a mass to charge
analyzer
located in at least one of said at least two vacuum pumping stages.


4. An apparatus according to claims 1, further comprising at least one
resonant
frequency waveform source for supplying a resonant frequency waveform to at
least one of
said at least two multipole ion guide segments.


66



5. An apparatus according to claim 1, wherein each of said at least two
multipole ion
guide segments further comprises an exit end where ions exit said each ion
guide segment,
said apparatus further comprising at least one electrostatic lens comprising
one or more
electrodes configured at said exit end of at least one of said at least two
multipole ion guide
segments, and DC lens voltage supplies for applying DC voltages to said
electrodes.


6. An apparatus according to claim 1, wherein said RF and DC voltages comprise

trapping voltages, whereby said ions are trapped in at least one of said at
least two multipole
ion guide segments of said multipole ion guide; and releasing voltages,
whereby said trapped
ions are released following said trapping of said ions in at least one of said
at least two
multipole ion guide segments of said multipole ion guide.


7. An apparatus according to claim 5, wherein said RF and DC voltages and said
DC
lens voltages comprise trapping voltages, whereby said ions are trapped in at
least one of said
at least two multipole ion guide segments of said multipole ion guide; and
releasing voltages,
whereby said trapped ions are released following said trapping of said ions in
at least one of
said at least two multipole ion guide segments of said multipole ion guide.


8. An apparatus according to claims 6 or 7, further comprising at least one
timing
control device for controlling the timing of said application of said trapping
and releasing
voltages.


9. An apparatus according to claim 1, wherein at least one of said multipole
ion guide
segments is configured as a quadrupole.


10. An apparatus according to claims 1 or 9, wherein at least one of said
multipole ion
guide segments is configured with more than four poles.


11. An apparatus according to claim 10, wherein at least one ion guide segment
comprises
an inner radius that is different from other ion guide segments of said at
least one multipole
ion guides.


12. An apparatus according to claim 1, wherein at least two of said at least
two ion guide
segments comprise the same number of poles, the same pole diameters, and the
same


67



circumferential orientation.


13. A method for analyzing chemical species, utilizing: an apparatus
comprising an ion
source; at least two vacuum stages; a multipole ion guide comprising at least
two multipole
ion guide segments for transporting said ions, said multipole ion guide being
located in a
plurality of vacuum stages, wherein at least a portion of said multipole ion
guide is positioned
in a region wherein the neutral gas pressure is high enough that collisions
occur between said
ions traversing said ion guide and said neutral gas molecules; RF and DC
voltage sources that
supply DC voltages and RF voltages with substantially the same RF frequency
and phase to
said multipole ion guide, said method comprising:

(a) producing ions from said chemical species in said ion source;

(b) directing said ions from said ion source into said multipole ion guide;

(c) controlling the amplitudes of said RF voltages and said DC voltages
supplied to
one of said at least two multipole ion guide segments to be independent of
said RF voltages
and said DC voltages supplied to others of said at least two multipole ion
guide segments,

(d) directing said ions to collide with said neutral gas molecules in said
region,
whereby the kinetic energy of said ions is reduced due to collisional cooling;
and,

(e) detecting at least a portion of said ions with said detector.


14. A method according to claim 13, further comprising the step of conducting
mass to
charge analysis of said ions in at least a first one segment of said at least
two multipole ion
guide segments.


15. A method according to claim 14, wherein said mass to charge analysis of
said ions
comprises applying a combination of RF and DC voltages to said at least a
first one segment
so as to create combined RF and DC electric fields within said at least a
first one segment,
whereby ions with mass to charge values outside a selected range are ejected
from said at
least a first one segment due to unstable motion in said combined RF and DC
fields.


16. A method according to claim 14, said apparatus further comprising at least
one
resonant frequency waveform source, wherein said mass to charge analysis
comprises
applying resonant frequency excitation waveforms to said at least a first one
segment

68



whereby ions with mass to charge values outside a selected range experience
resonant
excitation sufficient to result in their ejection from said at least a first
one segment.

17. A method according to claim 13, further comprising the step of conducting
fragmentation of said ions in at least a second one segment of said at least
two multipole ion
guide segments of said multipole ion guide, wherein at least a portion of said
at least a second
one segment is located in said region wherein the neutral gas pressure is high
enough that
collisions occur between said ions and said neutral gas molecules.


18. A method according to claim 14, further comprising the step of conducting
fragmentation of said ions in at least a second one segment of said at least
two multipole ion
guide segments of said multipole ion guide, wherein at least a portion of said
at least a second
one segment is located in said region wherein the neutral gas pressure is high
enough that
collisions occur between said ions and said neutral gas molecules.


19. A method according to claim 18, wherein said first one segment and said
second one
segment are the same segment.


20. A method according to claims 17 or 18, said apparatus further comprising
at least one
resonant frequency waveform source, wherein said fragmentation of said ions
comprises
applying resonant frequency excitation waveforms to said at least a second one
segment,
whereby ions with mass to charge values of one or more selected ranges
experience resonant
excitation sufficient to result in their fragmentation due to collisions with
said neutral gas
molecules within said portion of said at least a second one segment.


21. A method according to claims 17 or 18, wherein said fragmentation
comprises
applying different DC voltages to each of said at least two multipole ion
guide segments such
that ions are accelerated from a first one of said segments into a second one
of said segments,
wherein at least a portion of said second segment is located in said region
wherein the neutral
gas pressure is high enough that collisions occur between said ions and said
neutral gas

molecules.

22. A method according to claims 13, 14, 17, 18 or 19, further comprising the
steps of
trapping said ions in at least one segment of said at least two multipole ion
guide segments of


69



said multipole ion guide, and releasing said trapped ions from said at least
one segment.


23. A method according to claim 22, wherein the step of trapping said ions in
at least one
segment of said at least two multipole ion guide segments comprises applying
DC trapping
voltages to said at least one segment.


24. A method according to claim 22, said apparatus further comprising at least
one
electrostatic lens positioned at the exit end of at least one of said at least
two multipole ion
guide segments, wherein the step of trapping said ions in at least one segment
of said at least
two multipole ion guide segments comprises applying DC trapping voltages to
said at least
one exit lens.


25. A method according to claim 22, wherein any of said steps of directing
said ions to
collide with said neutral gas molecules; conducting mass to charge analysis of
said ions; or
conducting fragmentation of said ions, is performed during said trapping said
ions.


26. A method according to claim 25, wherein the steps of mass to charge
selection and
fragmentation of said ions are performed 'n' times, resulting in MS/MS<n >
analysis, wherein
'n' is two or greater.


27. A method according to claims 13, 14, 17, 18 or 19, said apparatus further
comprising
a mass to charge analyzer located in at least one of said at least two vacuum
pumping stages,
said method further comprising the final step of performing mass to charge
analysis of at
least a portion of said ions with said mass to charge analyzer.


28. A method according to claim 22, said apparatus further comprising a mass
to charge
analyzer located in at least one of said at least two vacuum pumping stages,
said method
further comprising the final step of performing mass to charge analysis of at
least a portion of
said ions with said mass to charge analyzer.


29. A method according to claim 25, said apparatus further comprising a mass
to charge
analyzer located in at least one of said at least two vacuum pumping stages,
said method
further comprising the final step of performing mass to charge analysis of at
least a portion of
said ions with said mass to charge analyzer.





30. A method according to claim 26, said apparatus further comprising a mass
to charge
analyzer located in at least one of said at least two vacuum pumping stages,
said method
further comprising the final step of performing mass to charge analysis of at
least a portion of
said ions with said mass to charge analyzer.


71

Description

Note: Descriptions are shown in the official language in which they were submitted.



CA 02626383 2011-01-04
60412-4222D

Mass Spectrometry with Multipole Ion Guides

This application is a divisional application of Canadian National Phase
application
No.2332534, filed on 29th May, 1999.

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 operated in higher pressure vacuum regions.

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.
Gas
Chromatography (GC), Liquid Chromatography (LC), Capillary Electrophoresis
(CE) 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 embodiments
of the invention given below will apply primarily to 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. Mass to charge selective resonant frequency excitation can also be more
readily
applied with quadrupoles than with ion guides having higher numbers of poles.
Quadrupole
ion guides have been configured as the primary elements in single and triple
quadrupole mass
analyzers and as part of hybrid mass spectrometers that include Time-Of-
Flight, Magnetic
Sector, Fourier Transform and three dimensional quadrupole ion trap mass
analyzers.
Conventionally, quadrupole ion guides operated as mass to charge filters, are
configured in
background vacuum pressures that minimize or eliminate ion to neutral
background gas
collisions. A wider range of background pressures have been used when
operating
quadrupoles in non mass to charge selection RF only ion transmission mode. In
some mass
spectrometer instruments, quadrupole ion guides operated in RF only ion
transmission mode
are configured in a region where the background vacuum pressure is maintained
sufficiently

1


CA 02626383 2008-04-24

high to promote collisional damping of ion kinetic energy or Collisional
Induced Dissociation
(CID) fragmentation of ions traversing the ion guide length,
Conventionally, quadrupole mass analyzers with electron multiplier or
photomultiplier
detectors are operated in analytical mass to charge selection mode with
background pressures
typically maintained below 2 x 10-` torr range. However, operation of
multipole ion guides at
elevated background vacuum pressures with ion mass to charge separation have
been
described. Ferran in U.S. Patent Numbers 5,401,962 and 5,613,294 describes a
small
quadrupole array with an electron ionization (El) ion source and a faraday cup
detector
operated as a low mass to charge range gas analyzer, This small quadrupole
array can be
operated in background vacuum pressures as high as 1 x 10-2 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.
Douglas in U. S.
Patent Number 5,179,278 describes a quadrupole ion guide configured to
transmit ions from
an Atmospheric Pressure Ionization (API) source into a three dimensional
quadrupole ion
trap. The quadrupole ion guide described by Douglas 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 rods
or poles of this
quadrupole ion guide can be set to limit 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 multipole ion guide that extends
continuously through
multiple vacuum pumping stages is described by Whitehouse et. al. in U. S.
Patent Number
5,652,427. A portion of the multipole ion guide length is positioned in a
vacuum region with
background pressures greater than one millitorr insuring ion to neutral gas
background
collisions. Dresch et.al. in U.S. Patent Number 5,689,111 describe a hybrid
multipole ion
guide Time-Of-Flight (TOF) mass spectrometer wherein the multipole ion guide
is configured
and operated to trap ions and release a portion of the trapped ions into the
pulsing region of
the TOF mass analyzer. Whitehouse et. al. in U. S. Patent No. 6,011,259
describe a hybrid
mass spectrometer wherein at least one multipole ion guide is configured with
a Time-Of-
Flight mass analyzer. As described, at least one quadrupole ion guide can be
operated in ion
transmission, ion trapping, mass to charge selection and/or CID fragmentation
modes or
combinations thereof coupled with Timme-Of-Flight mass to charge analysis. The
hybrid
quadrupole Time-Of-Plight apparatus and method described, allows a range of
MS/MS" mass
analysis functions to be performed. In an improvement over the prior art, one
embodiment of
the present invention comprises multiple quadrupole ion guides configured and
operated in a
higher pressure vacuum region of a hybrid TOF mass analyzer improving the mass
analyzer
MS/MS" performance and extending the analytical capability of a hybrid TOF
mass analyzer.
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

2


CA 02626383 2011-01-04
60412-4222D

Atmospheric Pressure Sources to mass analyzers. A quadrupole ion guide,
operated in RF
only mode in background pressures greater than 10-4 torr, configured to
transport ions from
an API source to a quadrupole mass analyzer is described by Douglas et. al. 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. The ion collisions with
the neutral
background gas reduces the primary ion beam kinetic energy spread and improves
ion
transmission efficiency through the ion guide and downstream of the ion guide.
Multipole
ion guides operated in elevated background pressures have been used as
collision cells for the
CID fragmentation of ions in triple quadrupoles, hybrid magnetic sector and
TOF mass
analyzers. Multipole ion guides configured as collision cells are operated in
RF only mode
with a variable DC offset potential applied to all rods. Thomson et. al. in U,
S. Patent
No.5,847,386 describe a multipole ion guide assembly configured to create a DC
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 along the
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 with a common RF applied along the collision cell multipole ion
guide length.
French in U.S. Patent No. 4,328,420 describe multipole ion guides configured
with open
structure rod assembles. These open structure rod assemblies operated in RF
only mode, are
configured as collision cells in triple quadrupoles and as a means to reduce
the gas pressure in
analytical quadrupoles when interfaced to corona discharge atmospheric
pressure ion sources.
French describes operating all mass filter analytical quadrupoles in
conventional manner with
low vacuum background pressures. In some embodiments of the present invention,
at least a
portion of the length of quadrupole ion guides operating in mass to charge
selection mode are
configured in a higher background pressure vacuum region where collisions
between ions and
neutrals can occur. This configuration of the invention allows increased
performance
capabilities and reduced instrument cost as is described in the following
sections.

The collision cell multipole ion guide configured in triple quadrupole mass
analyzers is
typically surrounded by an enclosure to maintain locally higher pressure in
the collision cell
multipole ion guide. The enclosure surrounding the collision cell multipole
ion guide is
generally located in a lower pressure vacuum region, is configured to minimize
the transfer of
higher pressure collision cell background gas into 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
triple quadrupole
centerline. One aspect of some embodiments of the present invention is the
configuration of multiple quadrupole ion guides positioned in a common region
of
higher vacuum pressure configured so that individual quadrupoles can be
operated in
ion mass to charge selection and/of CID fragmentation modes. A further aspect
of
some embodiments of the invention is the configuration of multiple quadrupole
ion
guides in a vacuum region of elevated background vacuum pressure wherein

3


CA 02626383 2011-01-04
60412-4222D

each quadrupole can be operated in mass to charge selection and/or ion
fragmentation modes
to achieve MS/MS'l mass analysis functions.

Conventional triple quadrupole mass analyzers interfaced to API sources are
configured with
sufficient vacuum pumping speed in the mass analyzer vacuum region to maintain
a vacuum
level that prevents or minimizes ion collisions with the background gas. The
low pressure
vacuum is maintained even with limited gas leaks into the chamber from a
collision cell and
an ion source. Vacuum pressure in a triple quadrupole collision cell enclosure
is generally
maintained at 0.5 to 8 millitorr and the surrounding analyzer vacuum chamber
pressure is
maintained in the low 10 5 to 10 6 ton range. A diagram of the multipole ion
guide
configuration of a conventional triple quadrupole mass analyzer 550 interfaced
to
Atmospheric Pressure Ion source 560 is shown in Figure 20. Individual
multipole ion guide
assemblies 558, 554, 555 and 556 are aligned along the same centerline axis in
a three stage
vacuum pumping system. Capillary 564 provides a leak from atmospheric pressure
Flectrospray ion source 560 into first vacuum pumping stage 551. Ions produced
in
Electrospray source 560 are transferred into vacuum through a supersonic free
jet expansion
formed on the vacuum side of capillary exit 561. A portion of the ions
introduced into
vacuum continue through the orifice in skimmer 559, multipole ion guide 558,
the orifice in
electrode 561, multipole ion guide 554, the orifice in electrode 566,
multipole ion guide 555,
the orifice in electrode 567, multipole ion guide 556, the orifice in
electrode 568 to detector
565. The pressures in vacuum stages 551, 552 and 553 are typically maintained
at .5 to 4 torn,
1 to 8 millitorr and <1 x 10-5 torr respectively while the pressure inside
collision cell 557 is
maintained at 0.5 to 8 millitorr. Triple quadrupoles are configured to perform
MS or a single
MS/MS sequence mass analysis functions. In an MS/MS experiment, ions produced
at or
near atmospheric pressure, are transported through multiple vacuum stages to
the low
pressure vacuum region 553 where mass to charge selection occurs in quadrupole
554 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 555. The
resulting fragment
ion population are directed into quadrupole 556 residing in low pressure
vacuum region 553.
Mass to charge selection is conducted on the ion population traversing
quadrupole 556 with
few or no ion to neutral collisions prior to detection of stable trajectory
ions exiting
quadrupole 556 by ion detector 565. Quadrupole 554 is configured with RF only
sections 562
and 568 at its entrance and exit ends respectively. Quadrupole 556 is also
shown with RF
only sections at its entrance and exit end. In commercially available hybrid
quadrupole TOF
mass analyzers quadrupole 556 is replaced by a TOF mass analyzer residing in a
fourth
vacuum pumping stage. Such conventional triple quadrupoles and hybrid
quadrupole TOF
mass analyzers can conduct only MS and MS/MS mass analysis functions with
axial DC
acceleration CID ion fragmentation. Mass to charge selection is conducted in
the quadrupoles
by operating the near the tip of the first stability region by applying the
appropriate RF and
DC potentials to the quadrupole rods. The embodiments described below allow
the
ability to conduct MS, MS/MS and MS/MS mass analysis functions with single or
multiple
axial DC acceleration CID ion fragmentation or resonant frequency excitation
CID ion
fragmentation. Single or multiple value quadrupole mass to charge selection in
some
embodiments of the present invention can be achieved using resonant frequency
ion
ejection applied to the quadrupole rods, by applying RF and DC potentials to
the
quadrupole rods or combinations of both.

4


CA 02626383 2011-01-04
60412-4222D

As diagrammed in Figure 20, a collision cell of a conventional triple
quadrupole is configured
inside vacuum chamber 553. The placement of a multipole ion guide collision
cell inside a
vacuum chamber maintained a pressures less than 10-5 torr requires that the
pumping speed
evacuating vacuum chamber 553 be sufficient to remove the gas load leaking
from collision
cell 557. This added vacuum pumping burden increases the cost and complexity
of an API
MS/MS mass analyzer. One aspect of some embodiments of the invention is the
configuration of
multiple quadrupole ion guides in a higher pressure vacuum region 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 first
or 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 higher pressure region of the
first or second
vacuum stage of API quadrupole and hybrid mass analyzers reduces the system
vacuum pumping
speed requirements and its associated costs. Another aspect of some
embodiments of the invention
is the configuration of multiple quadrupole ion guides that have pole
dimensions considerably
reduced in size from quadrupole assemblies typically found in commercially
available triple
quadrupoles or hybrid quadrupole TOF mass analyzers. The reduced quadrupole
rod or pole
diameters, cross center rod spacing (rp) and 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 and
power to operate, decreasing system size and cost without decreasing
performance. Another aspect of
some embodiments of the invention is the configuration of a multipole ion
guide that extends
continously into multiple vacuum stages into the multiple quadrupole assembly
positioned over at least a
portion of its length in the higher pressure region of an API MS instrument.
Multiple vacuum
pumping stage ion guides are described by Whitehouse et. al. 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 in a linear assembly allows
enables the
performing of a wide range of mass analysis functions with a single mass
analyzer instrument.
Quadrupole ion guides as described by Brubaker in U.S. Patent 3,410,997,
Thomson et. al. in
U.S. Patent 5,847,386 and Ijames, Proceedings of the 44th ASMS Conference on
Mass
Spectrometry and Allied Topics, 1996, p 795, have been configured with
segments or sections
where RF voltage generated from a single RF supply is applied to all segments
of the ion guide
assembly or rod set. Ijames describes operating the quadrupole assembly in RF
only ion transport
and trapping mode. Typically, as described by Brubaker, an AC or RF only
entrance and exit
segment will be configured in a quadrupole rod set to minimize fringing field
effects for ions
entering or leaving the quadrupole. The RF voltage is typically applied to the
entrance and exit
quadrupole sections through capacitive coupling with we primary to supplied to
the central
rod section or segment. Offset potentials, that is the common DC voltage
applied to all four
poles of a given quadrupole segment, can be set independently for each segment
to accelerate
ions from one ion guide segment to the next within the quadrupole ion guide
assembly. The
offset potential applied to segments of an ion guide can be set to trap ions
within an ion guide
section or segment as well. In the following discussions, a quadrupole or
multipole ion guide
assembly may include segments or sections but all RF voltage applied to each
rod of each segment
originates from a common RF supply. In one aspect of some embodiments of the
invention different
RF supplies connected to individual quadrupole assemblies may be synchronized
with respect to



CA 02626383 2011-01-04
60412-4222D

frequency and phase to maximize the ion transfer efficiency through the
multiple quadrupole
assembly.
Electrostatic tenses or electrodes may be positioned between individual
multipole ion guides
when multiple ion guide assemblies are configured in a mass analyzer.
Alternatively, multipole
ion guides may be aligned end to end with no electrostatic lens positioned
between ion guide
assemblies. Referring to Figure 20, electrostatic lenses 561, 566 and 567
serve the dual
purpose of minimizing gas conductance between quadrupole assemblies and
decoupling RF or
AC voltages applied to adjacent multipole ion guides. Electrodes positioned
between adjacent
multipole ion guide assemblies can be configured to minimize the fringing
field effects as ions
pass from one ion guide assembly to the next and to minimize any capacitive
coupling between different
ion guide sets avoiding beat frequency distortions of the RF fields. It is one
aspect of some embodiments
of the present invention that both sides of a junction between two independent
axially aligned
adjacent quadrupole assemblies reside in vacuum pressure maintained
sufficiently high to
insure ion to neutral collisions. In one embodiment of the invention, the
electrostatic lens
separating two adjacent multipole ion guide assemblies is replaced by an
independent RF only
quadrupole with an individual RF supply. As will be described below both the
higher vacuum
pressure interquadrupole junction and the positioning of a quadrupole lens
element between
two adjacent quadrupole assemblies allows increased flexibility in;conducting
mass analysis
functions at lower instrument costs when compared to conventional multiple
quadrupole
configurations. In one embodiment of the invention, individual quadrupole ion
guide
assemblies require separate RF, +/- DC and supplemental resonant or secular
frequency
voltage supplies to achieve ion mass to charge selection CII) ion
fragmentation and ion trapping
mass analysis functions. One aspect of some embodiments 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, CID fragmentation and trapping of ions. One or more multiple vacuum
stage
quadrupole assemblies can be configured, according to the invention in a
multiple quadrupole
assembly. Multiple vacuum stage multipole ion guides have been in described by
Whitehouse
and Dresch et. al. in U.S. Patents 5,652,427, 5,89, 111 and 6,011,259.

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 bi-directional transport of ions
along the axis of a
multiple quadrupole assembly allows a wide range analytical functions to be
run on a single
instrument. As mentioned above, one aspect of some embodiments of the
invention includes RF
quadrupoles configured between each analytical quadrupole assembly to minimize
any fringing fields
or capacitive coupling due to interquadrupole differences in RF amplitude, +/-
DC voltage and
resonant frequency voltages. In another aspect of some embodiments of the
invention, the RF only
quadrupoles may be configured as RF only segments of each quadrupole assembly
capacitively
coupled to the adjacent quadrupole ion guide RF supply. In yet another aspect
of some embodiments
of the invention, the junctions between individual quadrupole assemblies are
located in the higher
pressure vacuum region where little or no axial pressure gradient exists at
the junction between
quadrupole assemblies. Ion collisions with the background gas serve to damp
stable ion trajectories to
6


CA 02626383 2008-04-24

the quadrupole centerline where fringing field effects between quadrupoles are
minimized.
This collisional damping of ions trajectories by the background gas aids in
maximizing ion
transmission in the forward and backward direction between individual
quadrupole ion guide
assemblies even when different applied RF, DC and secular frequency AC fields
are present
between adjacent quadrupoles.

Triple quadrupoles, three dimensional ion traps, hybrid quadrupole-TOFs,
hybrid magnetic
sector and Fourier Transform (FTMS) mass analyzers have been configured to
perform
MS/MS analysis. Ion traps and FTMS mass analyzers can perform MS/MS" analysis,
however, ion CID fragmentation is performed with relatively low energy
resonant frequency
excitation. CID fragmentation in triple quadrupoles and hybrid quadrupole-TOF
mass
analyzers is achieved by acceleration of ions along the quadrupole axis into a
collision cell
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 collision cells with hundreds or even thousands of
electron volts.
In conventional triple quadrupoles as shown in Figure 20 and in hybrid
quadrupole TOF mass
analyzers, where the third quadrupole in a triple quadrupole has been replaced
by a TOF mass
analyzer, a single mass to charge range is selected in the first analytical
quadrupole by
applying appropriate RF and +/-DC potentials to the quadrupole rods. The mass
to charge
selection resolution in quadrupole ion guides operated in low vacuum pressures
is limited in
part by the rapid ion transit time through the quadrupole length. The single
mass to charge
range selected from a continuous ion beam with the first quadrupole
(quadrupole 554 in
Figure 20) is accelerated into the multipole ion guide collision cell
(multipole ion guide 555
in Figure 20) with sufficient energy to cause CID fragmentation. Fragment ions
exiting the
collision cell are mass analyzed by a second analytical quadrupole (quadrupole
556 in Figure
20) or a TOF mass analyzer, in hybrid TOF mass spectrometers. The MS/MS
analysis
functions performed using conventional triple quadrupoles and hybrid TOF
instruments are
limited to a single mass to charge range selection step, DC acceleration CID
fragmentation
with continuous ion beam operation.

Three dimensional ion traps can be operated with single or multiple mass to
charge range
selection followed by ion fragmentation analytical steps in the same ion
trapping volume.
Single or multiple MS/MS analysis steps can be achieved in three dimensional
quadrupole
ion traps by applying the appropriate RF, DC and resonant frequency ejection
and excitation
secular AC potentials in a step wise sequence. The space charge of trapped
ions in a three
dimensional ion trap imposes performance restrictions not encountered in non
trapping triple
quadrupole operation. Both quadrupole ion guides operated as mass filters in
triple
quadrupoles and three dimensional ion traps are scanning mass analyzers which
imposes
limitations with respect to mass spectral acquisition rates when compared to
non scanning
Time-Of-Flight mass analyzers. Triple quadrupoles operate with a continuous
ion beam
delivered from an ion source. The three dimensional ion trap performs analysis
in a batch-
wise manner imposing duty cycle limitations when ions are delivered from a
continuous beam
ion source. Three dimensional ion traps typically operated in RF mode using
added resonant
frequency AC waveforms with ion trapping to conduct mass to charge selection
and CID ion
fragmentation. Mass to charge selection is conducted in triple quadrupoles by
applying RF
plus +/- DC to the quadrupole rods in non trapping mode. CID ion fragmentation
in triple
quadrupoles is performed with DC acceleration fragmentation. Mass to charge
selection is

7


CA 02626383 2011-01-04
60412-4222D

performed in the presence of collision gas in three dimensional ion traps
whereas quadrupoles
conducting mass to charge selection in triple quadrupoles operate in a vacuum
region with
pressure maintained sufficiently low to minimize or eliminate ion to neutral
collisions.
Multiple multipole ion guides are configured in the invention in a region of
higher
background vacuum pressure. Each multipole ion guide can be operated in
trapping mode,
mass to charge selection mode and CID ion fragmentation mode using RE, +/- DC
and
applied resonant AC waveforms. To detect an ion trapped in a three dimensional
ion trap, the
ion must enter an unstable trajectory and be ejected through an endcap of the
ion trap. In
contrast, ions released axially from the end of multipole ion guide operated
in ion trapping
mode are in a stable trajectory. Consequently, a portion of the ions trapped
in a multipole ion
guide can be released while ions continue to enter the same ion guide. Ions
trapped in a
multipole ion guide are free to move along the ion guide axis so the term two
dimensional
trapping is used when referring to trapping in multipole ion guides. As will
become apparent in the
description of some embodiments of the invention given below, two dimensional
ion trapping in
multipole ion guides allows increased analytical flexibility when compared
with three dimensional ion
trap operation. MS/MS analysis functions can be performed using resonant
frequency excitation or
DC acceleration CID fragmentation or combinations of both. Some embodiments of
the invention
allow the full range of analytical three dimensional ion trap and triple
quadrupole functions in one
instrument and allows the performing of additional mass analysis functions not
available with
current mass analyzers.

In another embodiment of the invention the analytical functionality of triple
quadrupoles,
three dimensional ion traps and hybrid quadrupole TOF mass analyzers are
configured into a
single instrment. Some embodiments include but are not limited to resonant
frequency CID ion
fragmentation, DC acceleration CID fragmentation even for energies over one
hundred eV,
RF and +/- DC mass to charge selection, single or multiple mass range RF
amplitude and
resonant frequency ion ejection mass to charge selection, ion trapping in
quadrupole ion
guides and TOF mass analysis. Using the mass analysis capabilities described,
the hybrid quadrupole
TOF according to some embodiments of the invention can be operated with
several combinations of
MS/MS" analysis methods. For example, MS/MS" where n > 1 can be performed
using DC
acceleration fragmentation for each CID step or combinations of resonant
frequency
excitation and DC acceleration CID ion fragmentation. Ion trapping with mass
to charge
selection or CD ion fragmentation can be performed in each individual
quadrupole assembly without
stopping a continuous ion beam. These techniques, according to some
embodiments of the invention,
as described below increase the duty cycle and sensitivity of a hybrid
quadrupole-TOF during
MS/MS experiments. Alternatively, MS/MS analysis c be performed with or
without
trapping of a continuous ion beam during mass selection and ion fragmentation
steps. The
hybrid quadrupole-TOF configured according to some embodiments is a lower cost
bench-top
instrument that includes the performance capabilities described in U.S. Patent
Numbers
5,652,427 and 5,689,111 and U.S. Patent Nos. 6,011,259 and 6,621,073.
Emulation and
improved performance of prior art API triple quadrupole, three dimensional ion
trap, TOF and
hybrid quadrupole TOP mass analyzer functions can be. achieved with the hybrid
quadrupole
TOF mass analyzer configured according to some embodiments. The assemblies of
multiple
quadrupole ion guides configured according to some embodiments can be
interfaced to all mass
analyzer types, tandem and hybrid instruments and most ion source types that
produce ions
from gas, liquid or solid phases.

8


CA 02626383 2011-01-04
60412-4222D

Summary of the Invention

According to one aspect of the present invention, there is provided
an apparatus for analyzing chemical species, comprising: (a) an ion source for
producing ions from a sample substance; (b) at least two vacuum pumping
stages;
(c) a detector located in one of said at least two vacuum pumping stages; (d)
at
least one multipole ion guide each comprising at least two multipole ion guide
segments for transporting said ions, each said multipole ion guide being
located in
a plurality of vacuum stages such that each said multipole ion guide begins in
one
vacuum pumping stage and extends into at least a second vacuum stage of said
at least two vacuum stages; (e) a region comprising neutral gas molecules
wherein at least a portion of at least one of said at least two multipole ion
guide
segments is positioned, and wherein the neutral gas pressure is high enough
that
collisions occur between said ions traversing said ion guide and said neutral
gas
molecules; and (f) RF and DC voltage sources that supply DC voltages and RF
voltages with substantially the same RF frequency and phase to any one of said
at
least one multipole ion guide, and (g) means to control the amplitudes of said
RF
voltages and said DC voltages supplied to one of said at least two multipole
ion
guide segments independently of said RF voltages and said DC voltages supplied
to others of said at least two multipole ion guide segments.

According to another aspect of the present invention, there is
provided a method for analyzing chemical species, utilizing: an apparatus
comprising an ion source; at least two vacuum stages; a multipole ion guide
comprising at least two multipole ion guide segments for transporting said
ions,
said multipole ion guide being located in a plurality of vacuum stages,
wherein at
least a portion of said multipole ion guide is positioned in a region wherein
the
neutral gas pressure is high enough that collisions occur between said ions
traversing said ion guide and said neutral gas molecules; RF and DC voltage
sources that supply DC voltages and RF voltages with substantially the same RF
frequency and phase to said multipole ion guide, said method comprising:
(a) producing ions from said chemical species in said ion source; (b)
directing said
ions from said ion source into said multipole ion guide; (c) controlling the
amplitudes of said RF voltages and said DC voltages supplied to one of said at

9


CA 02626383 2011-01-04
60412-4222D

least two multipole ion guide segments to be independent of said RF voltages
and
said DC voltages supplied to others of said at least two multipole ion guide
segments, (d) directing said ions to collide with said neutral gas molecules
in said
region, whereby the kinetic energy of said ions is reduced due to collisional
cooling; and, (e) detecting at least a portion of said ions with said
detector.
Atmospheric Pressure Ion Sources including Electrospray (ES) and
Atmospheric Pressure Chemical Ionization (APCI) sources have been interfaced
to
single and triple quadrupole ion guide, three dimensional ion trap, Magnetic
Sector,
Fourier Transform, Time-Of-Flight and recently hybrid quadrupole-TOF mass
analyzers. It is one aspect of the invention that embodiments of the invention
can
be interfaced to atmospheric pressure ion sources. In another aspect of the
invention, embodiments of the invention can be configured in single or triple
quadrupole mass analyzers or configured in hybrid three dimensional ion trap,
Magnetic Sector, Fourier Transform and Time-Of-Flight mass analyzers
interfaced
to atmospheric pressure ion sources or ion sources that produce ions in
vacuum.
A number of embodiments of the invention are described below.
Each embodiment contains at least one multipole ion guide located in and
operated in a higher background pressure vacuum region 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. In 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. Each analytical 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 and/or
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 quadrupole
volume
defined by the inner rod radius (ro) and rod length. Unwanted ion ejection is

9a


CA 02626383 2011-01-04
60412-4222D

achieved by applying resonant or secular frequency waveforms to the ion
quadrupole rods
over selected time periods with or without ramping 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 potentials
are applied to
the quadrupole rods or poles while ramping or stepping the RF amplitude and
applying
resonant frequency excitation waveforms to eject unwanted ion mass to charge
values. In
another embodiment of the invention, at least one quadrupole ion guide
positioned in a higher
pressure region and operated in mass to charge selection and/or ion CID
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 least 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 CID 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.

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
9b


CA 02626383 2011-01-04
60412-4222D

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 ion 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 CID ion fragmentation mode. Mass to charge selection
conducted 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 or ramping 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 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 applied to 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 background vacuum pressure 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 from 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 when
compared
with triple quadrupoles, three dimensional ion traps and hybrid quadrupole TOF
mass
analyzers as described in 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 efficiency between multipole
ion guides is
maximized by minimizing the fringing fields effects at the junction between
two multipole
ion guides. An electrostatic lens may or may not be positioned between two
adjacent
quadrupole assemblies.
In another embodiment 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 asemblies, configured according to some embodiments have
the same radial
cross section pole dimensions and pole elements are axially aligned at the
junction between



CA 02626383 2011-01-04
60412-4222D

the two quadrupole ion guides. Each quadrupole assembly has an independent set
of RE
resonant frequency, +/- DC and DC offset voltage supplies. In another
embodiment of the
invention, common RF frequency and phase and common DC polarity 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 he independently
adju. ted for each
quadrupole ion guide assembly. Adjustment of relative DC offset potentials
allo(vs ions with
stable trajectories to move in the forward or reverse direction between two
adjacent
quadrupoles with high transmission efficiency due to minimum fringing field
effects. In
another embodiment of the invention, at least one segmented quadrupole ion
guide assembly is
configured in axial alignment with another quadrupole ion guide assembly 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. Alternatively, the junction
between two
adjacent quadrupole assemblies is configured with an axially aligned
quadrupole assembly
operated in RF only mode. RF and DC potentials are supplied to this junction
quadrupole
from power supplies independent from those supplying the two adjacent
quadrupole
assemblies. In another embodiment 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 embodiment 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 amplitude differential applied between
quadrupole assemblies
can be used to fragment ions through DC acceleration Collisional Induced
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 ion
transmission
mode, single or multiple mass to charge selection mode and resonant frequency
CID ion
fragmentation modes. MS1MSn 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 configured in the axially aligned
set of
quadrupoles. 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/NTS" analytical functions. In one embodiment 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 ion guide assembly
can be
configured according to some embodiments encompassing the entire triple
quadrupole mass

ll .


CA 02626383 2011-01-04
60412-4222D

analyzer MS and MS/MS functionality operated with continuous ion beams
delivered from an
Atmospheric Pressure Ion source.

In another embodiment of the invention, a multiple quadrupole ion guide
axially aligned
assembly wherein 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
quadrupole
ion guide in the multiple quadrupole assembly is configured to be operated in
mass to charge
selection and/or CID ion fragmentation mode. In one embodiment of the
invention, the TOF mass
analyzer is configured and operated to conduct mass analysis of product ions
formed in any
step of a MS/MS" analytical sequence. Single step MS/MS analysis can be
achieved by first
conducting a mass to 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
MS/MS 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/MS"
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
some embodiments of
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
or any interim mass 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/MS"
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
embodiment 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 emulate the MS and MS/MS mass analysis functions of a triple quadrupole
mass
analyzer. Alternatively, the same multiple quadrupole TOF hybrid mass analyzer
can be
operated whereby ion trapping, with single or multiple steps of ion mass to
charge selection
and ion fragmentation can be conducted in a manner that can emulate the MS and
MS/MSn
mass analysis functions of three dimensional ion traps mass. analyzers. In
addition, the same
multiple quadrupole TOF mass analyzer configured according to some embodiments
can be
operated with MS and MS/MS" mass analysis functions that can not be conducted
triple
quadrupoles, three dimensional ion traps or by other mass spectrometers
described in the
prior art.

12


CA 02626383 2011-01-04
60412-4222D

In another embodiment of the invention, multiple quadrupole ion guide
assemblies configured
and operated according to the invention, are included in hybrid Fourier
Transform, three
dimensional ion trap or magnetic sector mass spectrometers. In one embodiment
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 some embodiments. In one
embodiment of
the invention, the individual RF voltage supplies supplying potentials to each
individual
quadrupole assembly of the multiple quadrupole set have variable amplitudes
but the same
primary RF frequency and phase output. Consequently, ions whose mass to charge
(m/z)
values have stable trajectories traversing each quadrupole ion guide assembly
can remain in a
stable trajectory through the entire multiple quadrupole ion guide assembly
length. Ions with
low axial translational or kinetic energies can be efficiently transported
through 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 to an adjacent
quadrupole
or to the TOF mass analyzer 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 ion trapping mode is that ions
can be released
from one end of an ion guide or segment simultaneously while ions continue to
enter 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

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
positioned in series 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 supply units
and control
modules for the three multipole ion guide assembly and surrounding electrodes
diagrammed'
in Figure 1.

Figure 3 is a diagram of the potentials applied to the quadrupole elements
diagramed in
Figure 1 during a MS/MS analysis.

13


CA 02626383 2008-04-24

Figure 4 is a diagram of an alternative embodiment of an Atmospheric Pressure
Ion Source
hybrid TOF mass analyzer configured with orthogonal pulsing in the TOF mass
analyzer and
configured with three quadrupole ion guide assemblies, two of which are
configured as
segmented quadrupole ion guides.

Figure 5 is a diagram of an alternative embodiment of an Atmospheric Pressure
Ion Source
hybrid TOF mass analyzer configured with electrostatic lenses positioned in
the junctions
between adjacent multipole ion guides.

Figure 6 is a diagram of an Electrospray ion source, orthogonal pulsing Time-
Of-Flight mass
analyzer with an ion reflector flight tube geometry, configured with a three
quadruopole ion
guide assembly wherein one qudrupole ion guide extends continuously into two
vacuum
pumping stages.

Figure 7 is a diagram of an Electrospray ion source, orthogonal pulsing Time-
Of Flight mass
analyzer with a linear flight tube geometry configured with a three segment
multipole ion
guide wherein one segment extends continuously into 2 vacuum pumping stages.

Figure 8 is a diagram of an Electrospray ion source, orthogonal pulsing Time-
Of-Flight mass
analyzer configured with a three quadrupole ion guide assembly wherein said
multiple
quadrupole assembly extends into 3 vacuum pumping stages.

Figure 9 is a diagram of an API TOF mass analyzer with orthogonal pulsing
configured with
three quadrupole ion guide assemblies, the second of which extends from vacuum
stage two
into vacuum stage three and the third of which is positioned in the orthogonal
pulsing region
of the TOF mass analyzer.

Figure 10 is a diagram of an alternative embodiment of an API source TOF mass
analyzer
with orthogonal pulsing configured with a two multipole ion guide assembly,
the first of
which is configured as a three segment multipole ion guide that extends into
the second and
third vacuum pumping stages and a second of which configured as an ion
collision cell in the
third vacuum stage.

Figure 11 is a diagram of an API TOF mass analyzer with orthogonal pulsing
configured with
a three segment quadrupole ion guide assembly positioned in vacuum stage two
and a second
and third multipole ion guide assembly positioned in vacuum stage three.

Figure 12 is it diagram of a portion of the stability diagram for a quadrupole
ion guide.
Figure 13 is a diagram of the cross section of a quadrupole ion guide
configured with round
rods.

Figure 14 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 15 is a diagram of an Electrospray source quadrupole mass analyzer
configured with
three quadrupole ion guides. The third quadrupole ion guide is positioned in
lower pressure
14


CA 02626383 2011-01-04
60412-4222D

vacuum stage three with an electrostatic lens configured in the junction
between adjacent
quadrupole assemblies two and three.
Figure 16 is a diagram of an Electrospray source quadrupole mass analyzer
configured with a
two quadrupole 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. I
Figure 17 is a diagram of an Electrospray source multiple quadrupole mass
analyzer
configured with a dual quadrupole assembly with the second quadrupole of said
assembly
segment extending continuously from the second into the third vacuum pumping
stage and
configured with a second and third multipole ion guide and detector located in
vacuum stage
three.

Figure 18 is a diagram of an Atmospheric Pressure Chemical Ionization source
single
quadrupole mass analyzer configured with a quadrupole ion guide that extends
continuously
from the second into the third vacuum pumping stage.

Figure 19 is a diagram of a glow discharge ion source three quadrupole mass
analyzer
configured with the third quadrupole ion guide extending continuously from the
second into
the third vacuum pumping stage.

Figure 20 is a diagram of an Electrospray ion source interfaced to a
conventional triple
quadrupole mass analyzer.

Figure 21 is a diagram of a triple quadrupole mass analyzer wherein all three
quadrupole ion
guide assemblies are configured in higher background pressure vacuum stage two
with the
detector configured in lower background pressure vacuum stage three.

Figure 22 is a diagram of an Electrospray Ionization source interfaced to a
single quadrupole
ion guide mass analyzer wherein said quadrupole ion guide and the ion detector
are
configured in a higher background pressure vacuum stage.

Figure 23 is a diagram of an Electrospray Ionization source interfaced to a
triple quadrupole
ion guide mass analyzer wherein said triple quadrupole ion guide mass analyzer
and the ion
detector are configured in a higher background pressure vacuum stage.

Detailed Description

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/MS
analytical capability has been described in U.S. Patent No. 6,011,259. The
embodiments described in the following sections include new embodiments of


CA 02626383 2011-01-04
60412-4222D

multipole ion guides, new configurations of multiple multipole ion guide
assemblies and
their incorporation into mass analyzers with new methods of operating said
multipole ion
guides and mass analyzers. The embodiments 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 conventional mass analyzer
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 multipole ion guide comprises 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 potentials can be set to
cause an
unstable ion trajectory for ion mass to charge values that fall outside the
operating stability
window. An ion with an unstable trajectory will be radially ejected from the
ion guide
volume by colliding with a rod or pole 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 have
been configured
as multipole ion guides in mass spectrometer instruments. Where ion mass to
charge
selection is required, higher mass to charge selection resolution can be
achieved with
quadrupoles when compared to mass to charge selection performance of hexapoles
or
octapoles. Quadrupole ion guides operated as mass analyzers or mass filters
have been
configured with round rods or with the more ideal hyperbolic rod shape. For a
given internal
rod to rod spacing (ro), 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 with a higher numbers of poles, operated in 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 to 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 guides axially aligned and positioned in
a common
vacuum pumping stage. RF and DC potentials applied to individual multipole ion
guide
assembly in a triple quadrupole are supplied from separate RF and DC supplies.
The
collision cell in "triple quadrupoles" may be configured as a quadrupole,
hexapole or octapole
ion guide and is typically operated in RF only mode.

The multipole ion guides described in embodiments of the invention can be
configured with any
number of poles. Where an assembly of individual multipole ion guides are
configured, a mixture of
quadrupole and hexapole or octapoles may be preferred for optimal performance.
Multipolc
ion guide rod assemblies have been described by Thomson et. al. in U.S. Patent
Number
5,847,386 that are configured with segmented, non parallel or conical rods
operated in RF
only mode. Such rod configurations in operated in RF only mode with single
polarity DC
applied to all rods of an assembly can produce an asymmetric electric field in
the z or axial
direction during operation. This axial electric field can aid in pushing the
ions through the

16


CA 02626383 2008-04-24

length of the ion guide more rapidly than can be achieved with a parallel set
of non segmented
rods for a given application. The presence of an axial field is useful in
moving ions through a
multipole ion guide with higher background pressure present in the multipole
ion guide
volume. 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. Conical or
assymetric rod assemblies can be used in some embodiments of the invention
Where RF only
operation is used for a given multipole ion guide assembly. In an effort to
limit the number of
embodiments presented, the invention will be described for multipole ion
guides configured
with parallel rod or electrode ion guide assemblies. Axial fields within a
given multipole ion
guide assembly are applied as described in some embodiments using RF only
entrance ~.nd
exit pole sections or segments.

Single section or segmented multipole ion guid.. assemblies can be configured
such that at
least one segment extends from one vacuum pumping stage continuously into at
least one
adjacent vacuum pumping stage. In one aspect of the invention, individual
multipole ion
guides having the same cross sectional geometries are configured as axially
aligned
assemblies with at least one junction between multipole ion guide assemblies
located in a
higher pressure vacuum pumping region where multiple ion to neutral gas
collisions occur.
Operation of multiple multipole ion guides in a 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 operating in ion trapping mode 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 while operating
in trapping
mode can selectively release all or 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 entering a multipole ion guide from a
continuous ion beam
are not lost in between discontinuous or batch-wise :Hass analysis steps. One
preferred
embodiment of the invention is the configuration of a hybrid API source
quadrupole TOF
mass analyzer comprising an API source, an assembly of three quadrupole ion
guides with at
least two quadrupole mass analyzers operated in mass to charge selection and
ion
fragmentation modes and a Time-Of-flight mass analyzer. A multiple quadrupole
ion guide
assembly configured according to the invention in such a hybrid API source
quadrupole TOF
mass analyzer allows the conducting of a wide range of MS and MS/MS"
analytical functions
with high sensitivity, high mass to charge resolution and high mass
measurement accuracy.

17


CA 02626383 2008-04-24

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 Tirne-Of-Flight hybrid mass
spectrometer
apparatus. Although the hybrid instrument as described includes a TOF mass
analyzer, an
FTMS, magnetic sector, three dimensional ion trap or quadrupole mass analyzer
can be
substituted for the Time-Of-Flight mass analyzer. 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 similar to conventional low vacuum pressure 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 perform the API
MS mass
analysis functions similar to conventional single quadrupole mass analyzers
operated in low
vacuum pressure. The smaller size higher pressure quadrupole ion guides
configured
according to the invention can reduce instrument cost and size while improving
instrument
performance and analytical capability.

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 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
or mass filters. Hexapoles and octapoles which have a broader rnlz stability
window and a
larger effective entrance acceptance area, when compared to quadrupoles, are
often used as
collision cells or ion transport multipole ion guides operated in RF only mode
with and
without ion trapping in low and higher pressure vacuum regions. The multipole
ion guides
diagrammed in the preferred embodiments presented will be described as
quadrupoles.
However, for some embodiments configured and operated according to the
invention,
multipole ion guides configured with more than four poles can be readily
substituted for the
quadrupole ion guides configured in the embodiments described.

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 I has a tapered entrance end contoured to match the angle of skimmer
26. Power
supply module 63 applies RF, AC and DC potentials to the poles of both
segments of
segmented quadrupole 60. Quadrupole assembly 60, 61 and 62 are configured
along common
axis 5 when the junctions 7 and 10 between each independent quadrupole
assemblies are
positioned i(, higher pressure vacuum stage 72. Vacuum stages 71, 72, 73 and
74 are
typically maintained at pressures 0.5 to 3 torr, 0.1 to 10 millitorr, 1 to 8 x
105 ton and I to 5
x 10-7 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. In the embodiment shown in Figure 1, no electrostatic lenses are
configured in junctions

18


CA 02626383 2008-04-24

7 and 10 between independent quadrupole assemblies 60, 61 and 62. To avoid
fringing field
effects and to maximize ion transmission between quadrupole assemblies,
quadrupole ion
guide assemblies 60, 61 and 62 are configured with the same radial cross
section geometries
with each adjacent pole axially aligned. In addition, independent RF
generators configured in
power supply modules 63, 64 and 65 are configured and tuned to apply the same
RF
frequency and phase to axially aligned adjacent quadrupole electrode. The
phase shift
between adjacent quadrupole rods should less than 0.05 cycles to avoid
fringing geld effects.
In the embodiment shown in Figure 2, the primary RF frequency is established
by a resonant
frequency operating point for quadrupole 60 and the RF power supply in power
supply
module 63. The primary RF frequency is fed back into controller 80 and
distributed as the
reference oscillator frequency to power supply modules 64 and 65 that apply
potentials to;,
quadrupole assemblies 61 and 62 respectively. Adjustable RF phase shifters 89
and 90 adjust
the phase of the RF output from power supply modules 64 and 65 respectively so
that axially
aligned ion guide poles have the same RF frequency and phase applied. To
reduce the RF
power required to drive quadrupole assemblies 61 and 62, variable capacitance
loads 92 and
93 can be adjusted to match the desired RF frequency with a resonant inductive
and
capacitance load for quadrupole assemblies 61 and 62 respectively. The same
polarity DC is
applied to axially aligned rods by power supply modules 63, 64 and 65 to
minimize fringing
field effects. Power supply modules 63 and 65 supply resonant waveforms or
secular
frequency AC indicated as "SF" in Figure 2 to quadrupole assemblies 60 and 62
respectively.
Power supply modules 63, 64 and 65 also supply a common offset DC to the rods
of
quadrupoles 60, 61 and 62 respectively. +/-DC, SF and offset DC potentials may
be rapidly
applied to quadrupole rods through switching circuits from multiple supplies
or voltages may
be changed through Digital to Analog (DAC) input controls. The offset DC
supplied by
power supply module 60 will need to change rapidly for some analytical
functions. This is
accomplished by switching between multiple preset +/- DC power supplies to
avoid the
settling time of a DAC input change to a DC power supply. When operating with
+/- DC
applied, the DC offset potential is achieved by applying asymmetric + and - DC
amplitudes.
The outputs of multiple DC power supplies are rapidly switched to lenses 83,
26, 33, 34, 41
and 42 through +/- DC power supply modules 66 and 67 respectively to achieve
the analytical
functions 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/MS" functions
with Time-
Of-Flight mass analysis. Segmented ion guide 60 is configured such that the
same RF voltage
supply 63 applies RF voltage to segments 1 and 2 through connections 68 and 69
respectively. Junction 6 between segments 1 and 2 is configured to allow some
degree of
capacitive coupling between adjacent axially aligned poles. The RF potential
to segment I
can be supplied through this capacitive coupling or supplied directly from
power supply
module 63. Different DC offset potentials to be applied to sections 1 and 2 of
segmented ion
guide 60 to direct ion movement through segmented multipole ion guide 60 or to
trap ions
within section 1 or 2 or both. Segment or section 1 of quadrupole assembly 60
is typically
operated in RF only mode to minimize fringing field effects for ions entering
section 2 when
section 2 of quadrupole 60 is operated in mass to charge selection or ion
fragmentation
mode. Junctions 7 and 10 between quadrupole assemblies 60 and 61 and 61 and 62
respectively are configured according to the invention to minimize capacitive
coupling or the
resonant frequency waveforms applied to independently operating quadrupole
assemblies 60
and 61. Constructive or destructive interference to applied resonant waveforms
are avioded
19


CA 02626383 2008-04-24

byrninimizing the capacitive coupling between quadrupole assemblies 60 and 62
during ion
mass to charge selection and fragmentation operation. 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, as shown in Figure 5, quadrupole 61
can be
configured as a single flat electrode comprising an aperture centered on
centerline 5 with DC
applied to electrically isolate quadrupole assemblies 60 and 62. A preferred
embodiment as
shown in Figure 1 comprises 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 13. The same RF, SF 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 RF potential, single or multiple resonant frequency AC waveforms
voltage can be
applied to the quadrupole rods to achieve ion mass to charge 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 +/- DC, common DC and resonant frequency AC
potentials can be
applied simultaneously or individually to the poles of a segmented quadrupole
ion guide to
achieve a range of analytical functions. In a segmented ion guide assembly
each section of
each rod or pole are electrically insulated allowing different amplitude RF,
SF and +/- DC
applied to each section of a segmented ion guide assembly. Junctions 6, 7 and
10 in Figure 1
are configured to provide electrical insulation while minimizing any space
charge effects that
can distort the electric fields within the region bounded by the rods.
Junctions 6, 7 and 10
between quadrupole assemblies 60 and 61 and.61 and 62 respectively are also
configured to
minimize RF field distortion to maximize stable ion transmission efficiency
between
individual quadrupole ion guides 60, 61 and 62 in 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 10-4 tort. At background pressures greater than 1 x 10-4
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 rn/z values, ramping the RF frequency or
amplitude with or
without +/- DC ramping or combinations of these techniques. Those portions of
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 any combination of
these
individual 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 mass to charge filter or mass to
charge selection



CA 02626383 2008-04-24

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 collision free 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 mass analyzer instruments with reduced vacuum pumping
speed
requirements. A smaller multipole ion guide configuration reduces the cost of
RF power
supply electronics and the higher pressure operation reduces the vacuum system
costs. An
instrument configured with a segmented multipole ion guide, allows the
conducting of ion
mass to charge selection and ion fragmentation functions in higher background
pressures
while delivering the resulting ion populations into a low vacuum pressure
region with high
ion transmission efficiency.
Electrospray probe 15, diagrammed in Figure 1, can be configured to
accommodate solution
flow rates to probe tip 16 ranging from below 25 nl/min to above I ml/min.
Alternatively, the
API MS embodiment diagrammed in Figure 1 can be configured with all
Atmospheric
Pressure Chemical Ionization (APCI) source, an Inductively Coupled Plasma
(ICP) source, a
Glow Discharge (GD) source, an atmospheric pressure MALDI source or other
atmospheric
pressure ion source types. API sources may be configured with multiple probes
or
combinations of different probes in one source as is known. Ion sources that
operate in
vacuum or partial vacuum including but not limited to chemical Ionization
(CI), Electron
Ionization (EI), Fast Atom Bombardment (FAB), Flow FAB, Laser Desorption (LD),
Matrix
Assisted Laser Desorption Ionization (MALDI), Thermospray (TS) and Particle
Beam (PB)
can also be configured with the hybrid mass analyzer apparatus diagrammed in
Figure 1.
Sample bearing solutions 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 with-
out auto injectors, separation systems such as liquid chromatography or
capillary electro-
phoresis, 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 unto the ES source chamber through endplate nosepiece 24 opening
22. Bore or
channel 57 through dielectric capillary tube 23 comprises entrance orifice 13
and exit.orifice
14. The potential of an ion being swept through dielectric capillary tube 23
into vacuum may
change there potential energy relative to ground as described in US patent
number 4,542,293,
Ions enter and exit the dielectric capillary tube with potential energy
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 15 remains at ground potential during operation. To produce negative
ions, the polarity
of electrodes 17, 18 and 19 are reversed with ES probe 15 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 15 with lower potentials
applied to cylindrical

21


CA 02626383 2008-04-24

electrode 17, endplate electrode 18 and electrode 19 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.
Capillary exit heater 25 is configured with dielectric capillary 23 to
independently heat the
exit end of capillary 23.

With the appropriate potentials applied to elements in ES source 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 potentials
applied to ES
probe 15 and ES chamber electrodes 17, 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 bore 57.
Vacuum partition 53 includes a vacuum seal with dielectric capillary 23. 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
capillary bore 57 as
charged droplets traverse the length of capillary 23 towards first vacuum
pumping stage 71.
The neutral background gas forms a supersonic jet as it expands into vacuum
from capillary
exit orifice 14 and sweeps the entrained ions along through multiple
collisions during the
expansion. A portion of the ions entering first stage vacuum 71 are directed
through the
skimmer orifice 27 and into second vacuum stage 72.

The hybrid quadrupole TOF 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
APVMS 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 vacuum pumping stages are employed in API/MS
instruments.
With the development of 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. 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 respectively. 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 3
torr. 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 10-4 to 2
x 10-t 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
quadrupole ion guide assembly 60 where they are trapped radially by the
electric fields
applied to the quaadrupole rods. The locally higher pressure in the entrance
region 9 of
section 1 of segmented quadrupole assembly 60 damps the ion trajectories as
they pass
through the quadrupole RF fringing fields. The collisional damping of ion
trajectories in this

22


CA 02626383 2008-04-24

locally higher pressure region 9 results in a high capture efficiency for ions
entering
quadrupole assembly 60. Ion m/z values that fall within the operating
stability window will
remain radially confined within the internal volume described by the rods of
quadrupole
assembly 60. The trajectories of ions that fall within the stability window
defined by the
potentials applied to the rodes of quadrupole segment 1 will damp towards
centerline 5 while
traversing the length of segment 1. Ion trajectories that have been damped to
the/ centerline in
segment 1 are efficiently transferred into segment 2 of quadrupole 60 when the
appropriate
relative bias voltages are. applied between segments 1 and 2. For many
applications segment 1
of quadrupole assembly 60 will be operated in RF only mode. Similarly, when
the
appropriate relative bias or offset potentials are applied between to the rods
of segment 2 of
quadrupole 60 and the rods 3 and 4 of quadrupoles 61 and 62 respectively, ions
traversing
segment 2 of quadrupole 60 can pass through quadrupole 61 and into quadrupole
assembly
62. Ions pass into third vacuum pumping stage 73 while traversing the length
of quadrupole
assembly 62. Each rod 4 of quadrupole assembly 62 passes through but is
electrically
insulated from vacuum partition 32. Third vacuum stage 73 is evacuated through
vacuum
pumping port 30. Ions exit multiple qudrupole assembly 8 at exit end 11 and
pass through
electrostatic lenses 33, 34, and 35 into orthogonal pulsing region 37 of Time-
Of-Flight mass
analyzer 40. Lens 33 is configured as part of vacuum partition 36 between
third and fourth
vacuum pumping 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 to low 10-7 torr vacuum pressure region. TOF pulsing region
37 is
bounded by electrostatic lenses 41 and 42. Ions which exit from multiple
quadrupole
assembly 8 move into TOF pulsing region 37. Ions traversing pulsing region 37
are either
pulsed into TOF flight drift region 58 or continue through pulsing region 37
passing through
orifice 55 in lens 54. By applying appropriate voltages to lens 54, electron
multiplier 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 on Faraday cup 56. Secondary
electrons
or photons released from conversion dynode 39 after an ion impact are detected
by electron
multiplier 38. In the hybrid mass analyzer embodiment diagrammed in Figure 1,
ions
entering TOF pulsing region 37 can be either TOF mass analyzed, detected by
electron
multiplier 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
during TOF 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
pulsing region 37. Positive ions are accelerated or pulsed into TOF drift
region 58 by raising
the potential of pulsing lens to 41 some positive voltage, raising 42 to
approximately half that
positive voltage and applying ground potential to lens 43. The positive ions
are accelerated
out of pulsing region 37 and into entrance region 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. Ions traversing TOF
drift region in
the reverse direction 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

23


CA 02626383 2008-04-24

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. Individual
mass spectrum generated per TOF pulse can be added to produce summed mass
spectra that
can be saved to disk in a computer, TOF mass analyzers have been developed
that can save
over 100 summed spectra per second to disk. Signals generated by detector 47
can be
recorded with data acquisition systems using Analog to Digital (A/D)
converters or Time to
Digital converters (TDC). Time-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 an orthogonal pulsing of ions into drift region 58, is
decoupled from any
trapping, non-trapping, mass selection or ion fragmentation steps which occur
in multiple
quadrupole assembly 8 prior to the resulting ion population entering pulsing
region 37. TOF
mass analyzer 40 can acquire full mass spectra at maximum resolution and
sensitivity with
rapid spectra acquisition rates independent of the ion mass to charge
selection or ion
fragmentation steps conducted in multiple quadrupole assembly 8.

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 ion
mass to charge selection and ion fragmentation 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
individual
techniques can be used to perform collisionally induced dissociation ion
fragmentation.
These include:
1. DC ion acceleration through higher pressure gas. in the capillary to
skimmer region;
2. single or multiple ion resonant frequency excitation fragmentation in
quadrupole
ion guides 60, or 62 with or without ion trapping;
3. DC ion acceleration axially from one quadrupole to another or from one
quadrupole segment to another in multiple quadrupole assembly 8 with or
without
ion trapping;
4. higher energy reverse DC ion acceleration into multiple quadrupole assembly
8 by
switching potentials applied to exit lenses 33 and 34; or
5. overfilling of quadrupoles 60 or 62 during ion trapping until CID
fragmentation
occurs.
Each of these ion CID fragmentation techniques can be used individually or in
combination in
multiple quadrupole assembly 8.

At least four individual single or multiple ion mass to charge value selection
techniques can
be used with multiple quadrupole assembly 8 including:
1. resonant frequency rejection of unwanted ion mass to charge values with or
vyithout trapping in a given quadrupole asserribly or segment of a segmented
quadrupole assembly;
2. applying AC and +/- DC potentials to the rods of a quadrupole assembly or
segment of a segmented quadrupole assembly to achieve ion mass to charge
selection with or without trapping;

24


CA 02626383 2008-04-24

3. scanning RF amplitude or frequency to remove unwanted ion mass to charge
values from a quadrupole assembly or a segment of a segmented quadrupole
assembly with or without trapping; or
4. Controlling the release of trapped ions into TOF pulsing region 37 as
described in
U.S. patent 5,689,111.

Each mass to charge selection technique listed.above can be applied
individually or in
combination in the hybrid quadrupole TOF diagrammed in Figure 1. Combinations
of m/z
selection and fragmentation techniques can be run to optimize performance for
a given
analytical application, Some examples of combining techniques to achieve
optimal MS or
MS/MS" performance are given below.
Mass to charge selection or ion fragmentation can be performed in a quadrupole
ion guide
with ion trapping. Mass to charge selection with ion trapping can be conducted
with or
without preventing the ions in the primary ion beam from entering the
quadrupole where ion
mass to charge selection or ion CD fragmentation is being conducted.
Electrospray ion source
12 delivers a continuous ion beam into vacuum. By trapping and release of ions
in multiple
quadrupole assembly 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. Multiple quadrupole assembly 8 can be operated in non
trapping or
trapping mode where individual quadrupoles or segments of segmented
quadrupoles are
selectably operated in trapping or non trapping modes. Specific examples of
segmented ion
guide operating modes will be described below as a means to achieve MS, MS/MS
and
MS/MS" analytical functions with and without ion trapping. In the simplest
case multiple
quadrupole assembly 8 can be operated effectively as a segmented ion guide by
applying the
same AC and DC potentials to all segments of quadrupole assemblies 60, 61 and
62. Single
quadrupole MS and MS/MS" TOF operating sequences are described in U.S. Patent
No.
6,011,259. Analytical sequences employing multiple quadrupoles operating in
ion mass to
charge selection an ion fragmentation modes are described below.
An MS experiment with and without ion fragmentation can be run with a number
analytical
variations. If a specific range of ion mass to charge is of interest, one or
more quadrupole ion
guide in multiple quadrupole ion guide assembly 8 can be operated in rin/z
selection mode.
Mass to charge selection operation using quadrupole assembly 60 or 62 can be
conducted in
ion trapping or in single pass non trapping mode. Narrowing the m/z charge
range of ions
entering TOF pulsing region 37 can improve the duty cycle and TOF system
performance.
Pulsed a reduced range of mass to charge value ions 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 nn/7- 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 signal noise in the mass spectrum
acquired.
Restricting the range of m/z ions entering TOF drift region 58 allows the
setting of a
maximum TOP pulse rate while eliminating chemical noise contributions from
adjacent
pulses. Preventing unwanted ion rn/z 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 (MCP) detector, that channel requires a
certain recovery time
to replace its charge depletion. This charge depletion recovery time can be as
long as one



CA 02626383 2008-04-24

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 signal having a low m/z value may be of no interest in a
particular analytical
experiment but may 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. Radially
ejecting undesired m/z value ions from the multipole ion guide prior to TOF
pulsing to limit
the ion population pulsed into flight tube drift region 56 to only those rn/z
values of analytical
interest for a given application, helps to improve the TOF sensitivity,
consistency in detector
response and improves detector life.

Non trapping or trapping mass to charge selection can be conducted in
quadrupole assembly
60 and 62. 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. Segmented quadrupole assembly 60 is operated in non trapping RF only mode.
Section or segment 2 of quadrupole assembly 60 is operated with a low mass
cutoff of
300 m/z by applying the appropriate RF and +/- DC to the poles of segment 2.
Quadrupole assembly 61 is operated in non trapping RF only mode and quadrupole
assembly 62 is operated in trapping mode with a high mass cutoff of 500 m/z.
The
high mass to charge cutoff operation in quadrupole assembly 62 is achieved by
applying with multiple resonant frequency ion ejection to quadrupole rods 4
while
retaining an m/z stability window for m/z values below 500 m/z by applying the
appropriate RF and +/- DC amplitudes. Ions are trapped quadrupole assembly 62
and
released into TOF pulsing region 37 by gating ions out of exit end 11. The
potential
applied to lens 33 is switched a potential to trap ions in quadrupole assembly
62 and
switched to a low potential to release ions. Alternatively, a combination
switching
individual high and low potentials to both lenses 33 and 34 or by switching
values of
the quadrupole 62 offset voltage can be used to trap and release ions from
quadrupole
62 respectively. Such ion trapping and release techniques are described in
U.S. Patent
Number 5,689,111. Ions trapped in quadrupole assembly 62 are prevented from
moving back into quadrupole assembly 60 by applying the appropriate relative
offset
potentials to poles 3 of quadrupole assembly 61 and the poles of segment 2 of
quadrupole assembly 60. In this manner, ions moving through multiple
gaudrupole
ion guide assembly 8 which have mass to charge values above 500 and below 300
will
be rejected before entering TOF pulsing region 37.
2. Segment 1 of segmented quadrupole assembly 60 is operated in non trapping
RF only
mode to maximize ion transmission into segment 2. RF and +/- DC amplitude
values
are applied to the poles of segment 2 to pass an ions with mass to charge
values in
range between 300 to 500. Quadrupole ion guide assembly 62 is operated in RF
only
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
10,0?0 I-Iz. The individual DC offset potentials applied on the rods of
segments 1 and
2 of quadrupole assembly 60, rods 3 of quadrupole assembly 61 and rods 4 of
quadrupole assembly 62 are set to allow the transmission of ions from multiple
quadrupole assembly 8 entranc region 9 into quadrupole assembly 62. The DC
offset
potential differences across each segment and quadrupole junction are set
sufficiently
low to avoid DC acceleration CID fragmentation as ions are accelerated from
one
segment or quadrupole into the subsequent segment or quadrupole assembly.

26


CA 02626383 2008-04-24

3. Segment 1 of segmented quadrupole assembly 60 is operated in non trapping
RF bnly
mode to maximize ion transmission into segment 2. A range of resonant
excitation
frequencies is added to the RF potential applied to the rods of segment 2 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 I -1z. DC offset potential differences across
each
segment or quadrupole junction are set to move ions in a forward direction
through
multiple quadrupole assembly 8 without causing DC acceleration CID f
/agmentation
of ions.

Other combinations of multiple quadrupole 8 operation can be performed to
achieve selected
mass to charge values delivered 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 with respect to ion transmission
efficiency. The
application of RF and +/- DC to achieve mass selection in quadrupoles may
decrease the
effective entrance ion acceptance aperture potentially reducing ion
transmission efficiency for
the ion mass to charge values of interest. If mass to charge selection can be
achieved with
resonant frequency excitation ejection of unwanted ions, the quadrupole is
operating
essentially in RF only mode so that the effective entrance ion acceptance area
or aperture is
not reduced. Mass to charge selection with resonant frequency excitation
ejection of
unwanted ions also allows the selection of separate multiple ion m/z values
where ion m/z
values falling between selected ion mlz values are ejected. If a narrow ion
mlz selection was
desired say 1 mass to charge 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 excitation ejection 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 individual quadrupole assemblies 60, 61
and 62 or
single or multiple segments of quadrupole assembly 60. Ion trapping during ion
mass to
charge selection allows the ion population in a given segment or quadrupole to
be exposed to
more RF cycles before being released to an adjacent segment, effectively
increasing mass to
charge selection resolution. Ion collisions with the background neutral gas
pressure in second
vacuum stage 72 aid in maintaining stable ion trajectories in multiple
quadrupole assembly 8
for those ions which fall in the ion guide stability window. Trapping ions in
a given segment
or quadrupole assembly allows time for ions which fall outside the stability
window,
established by the voltages applied to the poles or each segment or quadrupole
assembly to be
ejected from the quadrupole volume in the presence of ion to neutral gas
collisions. The exit
end of quadrupole assembly 62 resides in a low pressure region where ion to
neutral collsions
are minimized or eliminated. Due to the lack of collisional damping effects in
this low
pressure portion of quadrupole assembly 62, ion m/z values not falling in the
stability region
as established by the potentials applied to rods 4, can be more rapidly
ejected from the ion
guide volume.

Although different RF frequencies can be applied to the rods of each segment
or quadrupole
assembly of multiple quadrupole ion guide 8, applying the same RF frequency
and phase to
quadrupole assemblies 60, 61 and through 62 minimizes the fringing field
effects
experienced by ions traversing between segment or quadrupole assemblies and
maximizes the
efficiency of ion transfer from one segment or quadrupole to the next. Ion m/z
values falling
within the stability region can move freely in either forward or backward
directions from
one quadrupole assembly or segment to an adjacent quadrupole or segment when
the same RF
frequency and phase is applied. The RF amplitude, however, may be set to
different values

27


CA 02626383 2008-04-24

for each segment or quadruole assembly to conduct different analytical
functions from one
quadrupole assembly to the next. At least a portion of each quadrupole
assembly 60, 61 and
62 is located in a region of higher background pressure so each quadrupole
assembly can
individually or jointly conduct mass to charge and/or CID ion fragmentation.
Reduction in
cost of electronics can be achieved if the RF potential applied to each
quadrupole assembly in
multiple quadrupole assembly 8 is supplied from a single RF supply. A single
RF supply,
however, would reduce the range of analytical capability for the hybrid TOF
diagrammed in
Figure 1. Tradeoffs between system cost and instrument performance can be
decided based
on specific analytical applications requirements. In an instrument with the
most analytical
capability, the set of poles of each quadrupole assembly 60, 61 and 62 of
multiple quadruple
assembly 8 are connected to individual and independently controlled, -r-/- DC,
RF and secular
or resonant frequency supplies as diagrammed in Figure 2. A. range of
analytical functions
can be achieved by independently controlling the RF frequency, amplitude,
offset DC
amplitude, +/- DC amplitude and the resonant frequency amplitude and frequency
spectrum.
The amplitude and frequency components of a resonant waveform delivered from
independent waveform generators in power supply units 63 64 and 65 of Figure 2
can be used
to apply simple or complex AC wave forms to the poles of quadnupoles 60, 61
and 62. The
applied set of secular frequency waveforms can be applied to achieve a range
of simultaneous
or sequential mass to charge selection and/or CID fragmentation analytical
functions.
Minimally, each segment of each quadrupole ion guide assembly has an
independent DC
offset supply or supplies where the DC offset value for a given segment of
each quadrupole
assembly 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. Segment 2 of
quadrupole
assembly 60 or quadrupole assembly 62 multiple quadrupole ion guide 8 can be
operated in
non trapping mass to charge selection scan mode with ions detected by detector
38.
Alternatively ions can be fragmented with resonant frequency excitation in
quadrupole
assembly 60 while mass to charge scanning quadrupole 62. Multiple quadrupole
assembly 8
can be operated in triple quadrupole mode by selecting mass to charge value
ions in
quadrupole assembly 60, DC accelerated the mass to charge selected ions into
quadrupole 61,
operating in RF only mode, with sufficient energy to cause CID fragmentation
and mass to
charge scanning quadrupole 62 and detecting the fragment ion peaks with
detector 38. 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 to generate full mass spectrum from ions exiting
quadrupole
assembly 62 will yield higher analytical duty cycle and hence sensitivity when
compared with
analytical techniques utilizing mass to charge scanning of quadrupole 62 of
multiple
quadrupole ion guide assembly 8.

Quadrupole assemblies 60, 61 and 62 configured in multiple quadrupole assembly
8 are
operated individually and jointly in both trapping and non trapping modes with
DC
acceleration/fragmentation and resonant frequency excitation CID fragmentation
and mass to
charge selection with RF and +/- DC and resonant frequency ejection of
unwanted ions.
Optimal quadrupole geometries, segmentation, gas pressure and composition, RF
and +/- DC
amplitudes and secular frequencies applied and the timing of applying RF, +/-
DC and SF
potentials may not be the same for each analytical function mentioned above
and will vary

28


CA 02626383 2008-04-24

with the mass to charge of an ion of interest. Specific variables and
operating conditions that
require optimization include but are not limited to the following:
1. quadrupole geometries;
A smaller rod to rod spacing (ro) provides a shorter distance for an ion to
travel
before being ejected from the quadrupole ion volume in resonant frequency
excitation mass to charge selection. Smaller ro also allows less neutrrll gas
conductance through multiple vacuum stage ion guides. Conversely,/smaller rod
to
rod spacing reduces the quadrupole trapping volume potentially causing space
charge effects to increase more rapidly in trapping mode. Non hyperbolic
quadrupole rods create non quadrupole fields or higher order (hexapole,
octapole
etc. field components) in the quadrupole ion guide volume when sinusoidal
potentials are applied. The addition of higher multipole fields to .improve
performance has been practiced extensively in three dimensional ion trap
construction and operation. The length of each quadrupole segment or assembly
will effect the number of RF cycles to which an ion in single pass mode will
be
exposed.
2. neutral gas composition
In DC acceleration CID ion fragmentation, a heavier neutral gas is favored to
improve ion fragmentation efficiency for a given ion acceleration energy. In
resonant frequency excitation CID ion fragmentation, a lighter gas may be
favored
to reduce the center of mass collisional energy and the potential losses from
fragment ion scattering. The invention includes the addition of a supplement
gas in
the second vacuum stage as diagrammed in Figure 4 to allow a partial change
ion
collision 'gas and to introduce reactive gas if desired in analytical
applications that
may require it.
3. neutral gas pressure
A longer mean free path between collisions or lower pressure is favorable for
ejecting unwanted m/z value ions without premature fragmentation. A shorter
mean free path may be favored in DC acceleration fragmentation.
4. Variable frequency and amplitude secular frequency waveforms
Optimization of the frequency and amplitude composition of secular waveforms
and the timing sequence of applying said waveforms to maximize performance for
ion mass to charge isolation and resonant frequency excitation CID ion
fragmentation is highly dependent on the analytical application.
5. RF and +/-DC amplitudes
The amplitudes of the RF and +/- DC potentials applied to the rods of a given
quadrupole may be varied to effectively shift the resonant frequency of a
given
mass to charge value ion during ion mass to charge ion isolation or resonant
frequency CID ion fragmentation.
6. DC offset differential between quadrupole assemblies
A longer DC acceleration of ions through the background gas may result in less
scattering losses when compared with a single rapid acceleration in some
applications. Multiple segments allow the gradual acceleration of ions in the
presence of an RF field.
Alternative embodiments of the invention as described herein provide different
tradeoffs to
optimize the variables listed above for different analytical applications.

29


CA 02626383 2008-04-24

Higher resolution mass to charge selection is generally required when
conducting MS/MS"
functions than is needed in MS analysis as described above. Resolution is a
function of the
ion mass to charge values that can, in a stable trajectory, pass through or
are trapped in a
quadrupole ion guide compared with those ion mass to charge values that are
ejected from the
quadrupole ion guide. Typically, quadrupoles 60, 61 and 62 of multiple
quadrupole assembly
8 are operated to pass or trap ions with mass to charge values that are stable
in the first
stability region 102 as shown in Figure 12.. Solving the equations of ion
motion in a
quadrupole ion guide as described by Dawson, Chapter 11 of "Quadrupole Mass
Spectrometry
and Its Applications", Elsevier Scientific Publishing Company, New York, 1976,
the first
stability region can be determined by the solution of the Mathieu parameters
qõ and aõ where:

au = ac = -ay = 4zU/ m0)2ru2 (1)
rlu=qr=-qy=2zV/mwr02 (2)
U is the +/- DC amplitude, m is the ion mass, z is the ion charge, V is the RF
amplitude, r0 is
the distance from the centerline to the quadrupole rod inside surface and co
(= 270 is the
angular frequency of the applied RF field. Solutions for the equations of
motion plotted
along iso-a lines as a function of qõ and aõ are given in Figure 12. Only
those ions having
mass to charge values that fall within operating stability region 102 as shown
in Figure 12
have stable trajectories in the x and y (radial) directions during ion
trapping or ion
transmission operating mode in a quadrupole ion guide. In low vacuum pressure
quadrupole
ion guide operation, mass to charge selection is typically conducted by
operating near apex
100 of stability region 102 where au = 0.23699 and qu = 0.70600. As noted by
Dawson, ions
with mass to charge values that fall close to the stability diagram boundary
increase their
magnitude of radial oscillation causing loss of ions due to collisions with
the rods. Operating
a quadrupole ion guide close to apex 100 of stability diagram 102 increases
resolution in +/-
DC and RF mass to charge selection but causes loss of ions of the selected
mass to charge
value. The precise position of the stability boundary for a specific ion mass
to charge can be
modified by physical, electrical and ion space charge factors. Imperfections
in the electric
fields within the quadrupole ion guide volume due to non ideal rod dimensions
or shape or
electronic control tolerances, ion location in the quadrupole field and space
charge in the
quadrupole ion guide can contribute to inaccuracies in the precise position of
the stability
region boundaries for a given ion species. For example, round shaped rods
cause higher order
fields to occur within the quadrupole volume leading to distortion of the
boundaries of
stability region 102. In the invention disclosed herein, mass to charge
selection is conducted
in the presence of background gas that can cause CID fragmentation of ions
with mass to
charge values experiencing increased secular frequency amplitude oscillations
when operating
near the stability region boundary. As is known in mass to charge selection or
isolation in
three dimensional ion traps, unwanted ion CID fragmentation can also occur in
resonant
frequency io 1 ejection. Several operating techniques have been developed in
three
dimensional ion trap RF only operation to achieve higher resolution mass to
charge selection
with minimal loss of the selected ion species. The resonant or secular
frequency, s0, of ion
motion in the radial direction while traversing or trapped in a quadrupole ion
guide is
approximated by the relation:



CA 02626383 2008-04-24

so = quuk)/V8 (3)
for /3 < 0.6. The precise secular frequency for a given ion mass to charge
value can be
effected by the same physical, electrical and ion space charge factors that
effect the
boundaries of the stability diagram.

During quadrupole ion guide mass to charge selection operation in the presence
of
background gas,
it is desirable to maintain the radial trapping energy well sufficiently deep
to efficiently trap
ions while minimizing the selected ion species secular frequency oscillation
amplitude. More
than one operating technique can be employed to achieve these ends and the
preferred method
may depend on the specific mass analysis conducted. When it is desirable to
simultaneously
select multiple mass to charge ion species, it may be preferred to operate
along the a,, = 0 or
RF only line applying a multiple notch resonant frequency waveform to the
quadrupole rods
to cause secular or resonant frequency excitation ejection of non selected ion
m/z values.
When selecting or isolating only one mass to charge value ion species it may
be desirable to
apply a small amplitude -t-/-DC to the quadrupole rods in addition to applying
a single notch
resonant frequency waveform to cause secular frequency excitation ion ejection
of non
selected ion m/z values. Increasing the A-/- DC amplitude reduces the radial
trapping energy
well depth for the desired ion species but may provide a more efficient means
to eliminate
non selected lower and higher mass to charge value ions by reducing while
reducing the range
of secular frequencies required. One example of operating the hybrid TOF as
diagrammed in
Figure 1 in MS/MS mode with a single mass to charge value ion selection using
a method
according the invention is given below.

Multiple quadrupole assembly 8 configured in a hybrid TOF as diagrammed in
Figure 1 is
operated in MS/MS mode with a continuous ion beam delivered into segment 1 of
quadrupole
assembly 60. Ion mass to charge selection is conducted in segment 2 of
quadrupole assembly
60 by varying the amplitude of the RF potential while applying, /- DC and a
single notch
resonant frequency waveform during repetitive ion trapping and release
operation. DC
acceleration CID fragmentation of the selected ion species by accelerating
ions from segment
2 of quadrupole assembly 60 through quadrupole assembly 61 and into quadrupole
assembly
62. Quadrupole assembly 62 is operated in ion trap and release mode as
described in U.S.
Patent Number 5,689,111 and mass to charge analysis of the fragment ions is
conducted in
TOF mass analyzer 40. A diagram of some of the potentials applied to multiple
quadrupole
assembly 8 and TOF pulsing region 37 during MS/MS analysis is given in Figure
3. Segment
1 of quadrupole assembly 60 is operated in RF only mode. Referring to Figure
3, the
different DC potentials applied to capillary exit electrode 112 and skimmer 26
and the
different DC offset potentials applied to the poles of segments 1 and 2 of
quadrupole
assembly 60 and poles 4 of quadrupole assembly 62 remain fixed during MS/MS
operation.
The capillary to skimmer potentials are set to maximize the target ion
transmission efficiency
without causing DC acceleration CID fragmentation in the capillary to skimmer
region. The
potential difference between the skimmer and the DC offset potential of
segment I of
quadrupole assembly 60 is set to maximize ion transmission efficiency into
segment 1. The
DC offset potential applied to the poles of segments I and 2 of quadrupole
assembly 60 are
set to transfer ions efficiently from segment 1 into segment 2 without CID
fragmentation.
Due to the collisional damping of ion kinetic energy in segments 1 and 2, the
ion energy of
the parent ion beam is determined by the DC offset potential of segment 2. The
frequency
31


CA 02626383 2008-04-24

and amplitude of the RF potential applied to segments I and 2 of quadrupole
assembly 60 is
set to maintain radial ion trapping operation for the selected ion mass to
charge value well
within stability diagram 102 and away from the stability region boundaries of
/3y = 0 and /3X =
1. DC potential composite curve 143 shows the DC offset potentials applied to
quadrupole
assemblies 61 and 62 during ion transmission mode. The different value DC
offset potentials
146, 147 and 148 applied to the poles of segment 2 of quadrupole assembly 1,
quadrupole 61
and quadrupole 62 respectively create DC acceleration electric fields in
regions 107 and 110
sufficient to cause DC acceleration CID fragmentation of ions accelerated into
quadrupole
assembly 62. The selected ion DC acceleration collisional energy is set by the
relative DC
offset potentials applied to the poles of segment 2 of quadrupole assembly 60,
quadrupole 61
and quadrupole 62. The selected ion internal energy can be elevated prior to
acceleration into
quadrupole assembly 62 by increasing the DC electric field between points 114
and 127 in the
capillary to skimmer region, between points 127 and 109 or at point 109
between segments 1
and 2 of quadrupole assembly 60. The internal energy of the selected ion
species can also
increase due to some degree of resonant frequency excitation in quadrupole 60
segment 2
during ion mass to charge selection. Increasing the internal energy of a mass
to charge
selected ion prior to acceleration into quadrupole assembly 62, reduces the
amount of DC
acceleration energy required to fragment the ion.

Quadrupole assembly 62 is operated in RF only mode with the RF amplitude set
to maximize
ion trapping and transmission efficiency for the fragment ion mass to charge
values of
interest. For example if the ion species selected in quadrupole assembly 60 is
multiply
charged, some fragment ions would occur higher in mass to charge than the
selected parent.
For a singly charged ion selected in quadrupole assembly 60 all fragment ions
would be lower
in mass to charge than the parent. When fragmenting a multiply charged ion,
the amplitude
of the RF potential applied to poles 4 of quadrupole assembly 62 may be set at
a higher value
than when fragmenting a singly charge ion of similar mass to charge value. The
RF potential
applied to the rods of quadrupole 62 allows the lower m/z ions to remain in a
stable trajectory
unlike the higher rn/z cutoff for low rn/z value ions inherent in resonant
frequency excitation
CID fragmentation as practiced in three dimensional ion traps. The amplitude
of the RF
amplitude applied to poles 3 of quadrupole assembly 61 operated in RF only
mode can be set
to fall between the RF amplitude values set on quadrupole assemblies 60 and 62
to minimize
fringing field effects in interquadrupole junctions 7 and 10. The RF potential
applied aligned
poles of quadrupole assemblies 60, 61 and 62 have the same frequency and phase
to minimize
fringing field effects at junctions 6, 7 and 10. DC waveform 143 shows the DC
potentials
applied to lenses 33, 34, 35, 41 and 42 are set to allow ion transmission from
quadrupole
assembly 62 into TOF pulsing region 37. In particular potential 151 applied to
lens 41 is set
near ground potential. The electric fields between points 11, 13, 134, 135 and
141 are set to
optunize beam ion energy and shape in TOF pulsing region 37. DC curve 143
corresponds to
point 153 drawn through timing diagram 156 shown in Figure 3.

The background pressure in the entrance end 71 of quadrupole assembly 62
serves initially as
collision gas in DC acceleration CID ion fragmentation and then as the ion
kinetic energy
damping gab for the resulting parent and fragment ion population traversing
the length of
quadrupole assembly 62. DC electrical potentials applied to exit lens 33 serve
to trap and
release ions from exit end 11 of quadrupole assembly 62. Trapped ions that are
released or
gated from exit end 11 of quadrupole assembly 62 pass into TOF pulsing region
37 where
they are pulsed into TOF drift region 58 and mass to charge analyzed. Ion
trapping in
quadrupole assembly 62 causes ions to take multiple passes back and forth
through the length

32


CA 02626383 2008-04-24

of quadrupole assembly 62 before being gated out. As trapped ions move back
toward
entrance end 71 of quadrupole assembly 62, they pass through the higher
pressure background
gas present in entrance end 71 where collisional damping of ion kinetic energy
occurs. Even
for high energy ion acceleration into quadrupole assembly 62 sufficient to
cause CID
fragmentation, the resulting fragment ion kinetic energy spread can be damped
to create it
monoenergetic ion population in quadrupole ion guide assembly 62 having close
to thermal
energy spread. The average potential energy of ions traversing quadrupole
assembly 62 is
determined by the DC offset potential applied to poles 4 of quadrupole
assembly 62. The
background pressure in third vacuum stage 73 is maintained in the 10-5 torr
range or lower so
that ions exiting quadrupole assembly 62 exit end 11 experience no further
collisions with
background gas as they move into TOP pulsing region 37. Ion molecule
collisions in th'i's
region would cause scattering and defocusing of the ion beam being transferred
into TOF
pulsing region 37 reducing TOF performance.

To achieve ion mass to charge selection in segment 2 of quadrupole assembly
60, low
amplitude /- DC potentials, RF and a mixture of resonant or secular frequency
waveforms
arc applied to the rods of quadrupole assembly 60, segment 2. The +/- DC, RF
and secular
frequency waveforms applied over time are shown in potential curves 137, 138
and 136
respectively in timing diagram 156. The amplitudes, phase and frequency
components of
each secular frequency in resonant waveform 136 waveform and the +/-.DC
potentials remain
constant during ion mass to charge selection in quadrupole assembly 60 segment
2. The
frequency and amplitude composition of applied secular frequency waveform 136
comprises
a number of subranges as described by Wells et. al. in U.S. Patent Number
5,521,380 for
mass to charge selection in three dimensional quadrupole ion traps. Creating a
multiple
subrange set of secular frequencies combined with modulating the RF amplitude
minimizes
the number secular frequency components required to eject non selected ion m/z
values and
minimizes selected ion losses from off resonant frequency excitation during
single or multiple
ion mass to charge selection. The spacing of the frequency resonant frequency
components
remains within a subrange. A frequency notch in maintained around the selected
ion mass to
charge value and the amplitudes of the frequency components on either side of
the frequency
notch or gap taper.in amplitude as the frequencies approach the selected mass
to charge notch.
The RF amplitude is ramped as ions traversing segment 2 of quadrupole assembly
60,
effectively changing the resonant frequency for a given ion mass to charge
value. The RF
amplitude ramp waveform as shown in curve 138 is asymmetric to account for the
asymmetry
of energy accumulation from off resonant frequencies when approaching the
resonant
frequency of the selected ion species from a lower or higher of resonant
frequency. This
asymmetry is due to the effect of higher order pole electric field components
present in the
segment 2 of quadrupole 60 during ion mass to charge selection or isolation
operation.
Ramping of the RF amplitude allows control of how much time the selected ion
species
spends exposed to a near resonant frequency while resident in segment 2 of
quadrupole
assembly 60. Higher resolution mass to charge selection with minimum loss to
the desired
ion species can be achieved with a careful selection of the frequency, phase
and amplitude
components of the resonant or secular composite waveform coupled with optimal
RF
amplitude ramping functions.

I-Iigher resolution ion mass to charge selection can be achieved with the
appropriate electric
fields as described above applied to the rods of segment 2 of quadrupole
assembly 60 if the
ion population of interest spends more time resident in segment 2. Increasing
the exposure of

33


CA 02626383 2008-04-24

non selected mass to charge value ions to more RF and resonant frequency
cycles improves
the efficiency of non selected ion ejection from segment 2 of quadrupole 60 in
the presence of
background gas. The same background gas effectively damps the radial
oscillations of
selected non excited ion species to the quadrupole 60 centerline 5. DC
acceleration of ions
damped to centerline 5 into quadrupole 62 minimizes scattering losses of
parent and fragment
ions. To increase the selected ion resident time in segment 2 of quadrupole
assembly 60 ions
can be trapped in and released from segment 2 in a repetitive manner by
changing or
switching the offset potential applied to the rods of quadrupole assembly 61.
Any effect on the
resonant frequencies of selected ion species due to space charging can be
minimized or
eliminated by choosing the appropriate fill and empty cycle time periods.
Curves 139, 140
and 142 show an example of the ion trapping and release timing of ions in
quadrupoles 60
and 62 synchronized with the TOF pulsing voltage applied to lens 41, Curve 139
diagrams
the offset potentials applied to rods 3 of quadrupole assembly 61 during MS/MS
operation.
Ions are trapped in segment 2 of quadrupole assembly 60 when offset potential
148 is applied.
Ions are released from segment 2 and accelerated through quadrupole 61 and
into quadrupole
62 with sufficient energy to cause ion CID fragmentation when DC offset
potential 147 is
applied rods 3 of quadrupole 61. When increasing the DC offset trapping
potential applied to
quadrupole 61, an interim voltage 149 is applied briefly to clear ions from
the volume of
quadruple 61 without significantly increasing the kinetic energy of said ions
accelerated into
quadrupole 62 above the offset potential applied to the rods of segment 2. DC
offset potential
149 can be set to a value just above the offset potential of segment 2 to
prevent ions from
entering quadrupole 61 while allowing ions in quadrupole 61 to be accelerated
into quadrupole
62. Some ions in the volume of quadrupole 61 will also return to segment 2
unfragmented
when DC offset voltage 158 is applied. If desired, the offset potential
applied to the rods of
quadrupole 61 can be used to increase the potential energy of ions accelerated
forward into
quadrupole assembly 62 or backward into quadrupole assembly 60 by applying the
appropriate timing and voltage amplitude to the trapping and release DC offset
potentials.
This pulsed ion kinetic energy increase is analogous to the backward DC
acceleration CID ion
fragmentation using switch potentials applied to lenses 33 and 34 as described
in U.S. Patent
No. 6,011,259.

The switching of quadrupole 61 DC offset voltages is synchronized with the TOF
ion pulsing
and ion flight time in TOF drift region 58 so that no voltage switching occurs
during ion
flight time in TOF drift region 58. This avoids electrical noise spikes from
occurring in the
acquired mass spectrum. DC potential curve 144 occurs at timeline 154 drawn
through
timing diagram 156. DC voltage curve 144 shows DC trapping potentials 148 and
150
applied to the rods of quadrupole 61 and lens 33 respectively while DC
potential 152 applied
to TOF pulsing lens 41 is raised to accelerate ions into TOF drift tube 58.
TOF mass analysis
is conducted on ions pulsed into TOF drift region 58. The repetitive trapping
and release of
ions from quadrupole ion guide assembly 62 followed by TOF mass analysis is
described in
U.S. Patent Number 5,689,111. MS/MS analysis can be conducted using the
application of
RF, SF and DC potentials and switching sequences as described above with high
efficiency
ion mass to charge selection and DC acceleration CID fragmentation. The MS/MS
sequence
is conducted using a small compact multiple quadrupole assembly configured
with a TOF
mass analyzer. Alternative methods can be used to achieve efficient MS/MS
analysis from
the specific technique described. For example, the resonant frequency
waveform, 136, can be
turned off and a higher +/- DC amplitude applied to the rods of segment 2. The
amplitude of
the repetitive ramping of the RF is set to move the selected ion m/7- value
back and forth
across stability diagram 102 minimizing the time the m/z value spends near
stability region

34


CA 02626383 2008-04-24

boundaries of jay = 0 and J3x = 1. With this technique, ion mass to charge
value ions falling
above and below the selected m/z value ion species would be ejected from the
quadrupole
while imparting minimum excitation energy to the selected ion species.
Alternatively, an
excitation resonant frequency can be applied to the rods of quadrupole
assembly 62 that
matches the selected parent ion m/z value to aid in selectively fragmenting
the parent ion.
Quadrupole assemblies 60 and 62 may also be operated in ion single pass non
trapping mode.
Additional techniques for performing MS/MS" analysis functions are described
below.
Optimization of the RF, SF and DC potentials and electrical potential
switching and ramping
sequences applied to the poles of multiple quadrupole assembly 8 is to
effected by the
background pressure maintained in second vacuum pumping stage 72 as diagrammed
ii;`
Figure 1. Ion collisions with the background gas can cause desired
fragmentation and
undesired fragmentation, can increase the time of unstable trajectory ion
ejection, can damp
stable ion trajectories to the quadrupole centerline, can reduce the ion
transfer time through a
quadruole length and provide a reaction media for ion to neutral gas phase
reaction studies.
The higher the background pressure, the larger the number of ion to neutral
gas collisions
occur per time period. By configuring the appropriate skimmer orifice 27 size
and the
appropriate vacuum pumping speed through vacuum port 29, the background
pressure in
second vacuum stage 72 can be varied between 1 x 10-4 torn to over 500
millitorr. For many
of the operational sequences described below, a background pressure should be
maintained in
vacuum stage 72 where multiple collisions between ions and background gas
occurs as ions
traverse each quadrupole length. The mean free path should be maintained at a
balance where
efficient stable ion trajectory damping occurs, efficient DC acceleration and
resonant
frequency excitation CID ion fragmentation occurs yet trajectory damping does
not prevent
the ejection of ions in unstable trajectories within experimentally useful
time frames.
Typically, a background pressure between 4 and 8 millitorr is maintained in
vacuum stage 72
during operation. The gas composition may be nitrogen is the only supply of
background gas
provided from the atmospheric pressure ion source. The background gas
composition in can
be modified by adding additional gas such as helium or argon into vacuum stage
72 as
diagrammed in the embodiment of the invention shown ill Figure 4. Reactive gas
may also be
added to vacuum stage 72 to study ion and neutral gas reactions. In one
embodiment of the
invention multipole quadrupole assembly 8 was configured with an ro of 1.25 mm
and operate
with an RF frequency of approximately 5 MHz.

The optimal background vacuum pressure and gas composition will be a function
of the
multipole ion guide geometry including pole to pole spacing, individual
segment or
quadrupole assembly 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 to ten millitorr.
One to ten
rillitorr 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
into the collision
cell of a triple quadrupole is typically argon. The gas load in second vacuum
stage 72 will be
primarily composed of countercurrent drying gas 21 from ES source 12.
Countercurrent
drying gas 21 is typically nitrogen but, depending on the analytical
application may also
contain carbon dioxide, sulfur hexaflouride, oxygen and residual solvent
evaporated from the
sample solution. The pressure and composition of the background gas in second
vacuum



CA 02626383 2008-04-24

stage 2 can be controlled and maintained constant during MS operation allowing
the
optimization of applied potentials. The pressure in ES source 12 atmospheric
chamber is
maintained close to atmospheric pressure and the temperature in capillary bore
57 is steady
state during 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 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
and by directly measuring the background vacuum pressure in vacuum stage 72
the
background pressure can be maintained constant over extended time periods.
With a
consistent composition and pressure for the neutral background gas in second
vacuum stage
72, 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 CID 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 quadrupolcs, all MS and MS/MSn
functional sequences of three dimensional ion traps and can perform several MS
and
MS/MS" functions that are not possible with either triple quadrupoles or three
dimensional
quadrupole ion traps. Examples of some MS/MSn functions that can be performed
with the
hybrid TOF embodiment diagrammed in Figure 1 will be described below.

Four non trapping single pass primary MS/MS operating modes are used in triple
quadrupoles
that employ DC ion acceleration into an RF only collision cell to achieve CID
fragmentation.
These four operating modes include:
1. transmitting a single selected m/z range in quadrupole 1, fragmented the
selected
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 with fragmentation of parent ions in the RF only collision
cell;
3. scanning quadrupole I while setting quadrupole 3 to pass a selected m/z
range with
fragmentation of parent ions in the RF only collision cell; and,
4. setting both quadrupoles 1 and 3 to pass different m/z values without
scanning with
fragmentation of parent ions in the RF only collision cell to monitor selected
fragmentation events.
In the embodiment of the hybrid TOF shown in Figure 1, full fragment ion
spectra are
recorded in the TOF analyzer without scanning resulting in higher sensitivity
and resolution
performance than can be achieved in triple quadrupole operation. The hybrid
TOF MS as
diagrammed in Figure 1 can be operated to emulate triple quadrupole
performance with full
TOF mass 14)ectra acquired replacing the third quadrupole single mass
selection and mass
scan analytical functions. MS/MS analysis requires the steps of mass to charge
selection,
fragmentation of the selected mass to charge parent ions and mass analysis of
the first
generation fragment or product ions. The final mass to charge selection step
in any given
MS/MS sequence is performed with TOF mass analyzer 40. The mass to charge
selection and
ion fragmentation steps are performed in multiple quadrupole assembly ion
guide 8 with

36


CA 02626383 2008-04-24

additional ion fragmentation, when required, performed in the capillary to
skdInrner region.
An MS/MS experimental sequence such was described in the previous section can
he
conducted which results in fragment ions similar to those produced in a triple
quadrupole
MS/MS operating mode 1 listed above. Alternatively, using a different
experimental,
sequence, fragment ion populations can result which are similar to those
produced in an ion
trap MS/MS experiment.

The hybrid multiple quadrupole TOP as configured in Figure I can operated to
simulate triple
quadrupole neutral loss MS/MS operating mode 2 as listed above in which
quadrupoles 1 and
3 of a triple quadruple are scanned during data acquisition. TOF operation
replacing scanning
quadrupole 3 produces, full TOF spectra of fragment ions. A Reconstructed Ion
Chromatographs (RIC) can be generated from acquired TOF full spectra to match
triple
quadrupole like neutral loss MS/MS data. To achieve this subset of neutral
loss data, the
hybrid multiple quadrupole TOF embodiment shown in Figure 1 can be operated in
as
follows:
1. segment 1 of quadrupole assembly 60 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 of quadrupole assembly 60 is operated in non trapping ion m/z
selection
mode with the application of modululated RF, /- DC and an appropriate
composite resonant frequency waveform as described in the previous section. 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 to
charge of any given first generation fragment ion spectrum is known.
3. segment 3 is operated in trapping RF only mode. The different DC offset
potentials applied to the poles of segment 2 of quadrupole 60, quadrupole 61
and
62 are set to accelerate ions from segment 2 into quadrupole 62 with
sufficient
energy to cause the desired amount of CID ion fragmentation of the selected
parent
ions. Ions released or gated from the exit end of quadrupole 62 and
transferred 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 selected by segment 2 of quadrupole assembly
60, 100 steps
would be required to cover the rn/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 TOP 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
listed operating sequence contains complete fragment ion information unlike
the more limited
information recorded from a triple quadrupole neutral loss scan or the case
where the first
quadrupole is scanned with the third quadrupole n/z range selection fixed.
Consequently,
either triple quadrupole experiment can be simulated with the above listed
segmented ion
guide TOP operating sequence. Variations in the above sequence can be used to
achieve the
same ends. For example, rn/z range selection can be conducted in segment 1 or
segment I
and 2 of quadrupole assembly 60 in trapping or non trapping mode. Quadrupole
ion guide

37


CA 02626383 2008-04-24

assembly 62 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 of
quadrupole 60 is switched. Trapped ions fragments formed from the previous
parent mn/z
value are then allowed to exit the trap formed by quadrupole 62. A small delay
time may be
added after a nh/z range selection step to allow the segment 4 trap to fill
prior to resuming
TOF pulsing. Alternatively, parent ions may be trapped in segment 2 of ion
guide 60 while
fragment ions from the previous parent mass to charge value are being gated
into TOF
pulsing region 37 from quadrupole 62. M/z selected parent ions trapped in
segment 2 are
then accelerated into quadrupole 62 after the fragment ions from the previous
parent ion set
have been gated into TOF pulsing region 37. A new mass to charge value set of
parent ions
are then isolated in quadrupole 60 segment 2. The transfer of all ions trapped
within segment
2 at a time when the DC offset potential applied to the rods of quadrupole 61
differs from the
pa tial ion population release as described in the previous section. However,
a continuous ion
beam can be accepted into segment 1 of quadrupole assembly 60 in either
operating mode,
maximizing overall duty cycle.

In the above simulated triple quadrupole neutral loss scan operating mode, DC
ion
acceleration is employed to achieve CID first generation ion fragmentation.
Alternatively,
resonant frequency excitation CID fragmentation can be employed in quadrupole
assemblies
61 and 62 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 selected nl/z values, particularly fragment product ions. Due to
the multiple
collisions experienced by all ion species produced in DC ion acceleration CID,
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 is increased. To radially trap
the ions being
excited, theRF amplitude must be increased proportionally resulting in an
increased the low
rn/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/MS" performance without ejecting the lower portion of the mass to
charge
scale. The hybrid segmented ion guide TOF embodiment diagrammed in Figure 1
can be
configured to achieve all triple quadrupole as listed above and ion trap
MS/MS" functions
with combinations of DC acceleration and resonant frequency excitation CID ion
fragmentation operation not conducted in either triple quadrupoles or an ion
traps.

A Wide range of MS/MS analysis functions can be conducted using the hybrid TOF
embodiment shown in Figure 1. To simplify the description of the operational
sequences
required to conduct specific MS/MS" functions, the techniques used can be
divided into two
groups. Th9j first group includes those 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/MS" techniques which accept a continuous ion beam
from
electrospray ion source 12 will be describe below.

38


CA 02626383 2008-04-24

Consider running an MS/MS2 experiment with the embodiment shown in Figure 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 of quadurole
assembly 60
after non trapping mass to ion mass to charge selection is conducted in
segment 1.
Specifically the hybrid multiple quadrupole TOF is operated with the following
sequence to
achieve MS/MS` mass analysis.
1. Segment I of quadrupole assembly 60 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 of quadrupole 60 is operated trapping or non trapping mass to
charge
selection mode where one or more first generation product ions is selected.
The
m/z selected first generation product ions are then accelerated through
quadrupole
61 and into quadrupole 62 applying the appropriate relative DC offset
potentials to
the poles of segment 2 and quadnipoles 61 adn 62 to cause CID fragmentation of
the selected first generation fragment ions.
3. Quadrupole 62 is operated in RF only trapping mode from which second
generation fragment ions are gated into TOF pulsing region 37. The second
generation fragments ions are subsequently pulsed into TOF drift region 58 and
mass to charge analyzed.

Ion mass to charge selection operation in segments 1 and 2 of quadrupole
assembly 60 may
employ fixed of modulated RF and +/- DC mass filtering or composite resonant
frequency
waveform ejection of unwanted m/z ions or a combination of both as has been
described
above. Different +/- DC and composite resonant frequency waveform AC
potentials and
common RF potentials are simultaneously applied to the poles of segments 1 and
2. Ion
fragmentation may be achieved using resonant frequency excitation instead of
or in
conjunction with DC ion acceleration fragmentation in segments 2 of quadrupole
60 and
quadrupoles 61 and 62. Resonant frequency excitation can occur simultaneously
with ion
m/z selection in segment 2 of quadrupole assembly 60 by including the
appropriate frequency
notches and variation in amplitudes in the composite resonant frequency
waveform applied to
the poles of segment 2. Segment. 2 can be operated in trapping mode by
applying the
appropriate relative DC offset potentials to the poles of quadrupole assembly
61 to trap ions
in segment 2 of quadrupole assembly 60 or release ions from segment 2 into
quadrupole
assembly 62. In all MS/MSn experiments, the relative capillary to skimmer
potential can be
raised to increase the internal energies of ions in the primary ion beam to
facilitate ion
fragmentation in multiple quadrupole ion guide assembly 8.

MS/MS2 can alternatively be achieved by mixing DC ion acceleration and
resonant frequency
excitation ion fragmentation techniques by operating multiple quadrupole ion
guide assembly
8 in the following mode.
1. Segment I of quadrupole assembly 60 is operated in RF only ion pass mode.
Ions
are transferred from segment 1 into segment 2 with low energy and with no ion
fragmentation.
2. Segment 2 of quadrupole assembly 60 is operated trapping mode with ion mass
to
charge selection. Ions, when released from segment 2, are accelerated from
segment 2 through quadrupole 61 and into quadrupole 62 with sufficient energy
to
cause CID fragmentation of the m/z selected ions.

39


CA 02626383 2008-04-24

3. Quadrupole assembly 62 is operated in ion trapping mode with two step m/z
selection and resonant frequency excitation fragmentation of the selected
first
generation ion. Second generation fragment or product ions are gated into TOP
pulsing region 37 and subsequently TOF mass analyzed. The m/z selection and
ion
CID fragmentation steps are conducted in series prior to initiating TOF mass
analysis. Parent ions are trapped and accumulated in segment 2 during the
first
generation fragment ion m/z isolation and fragmentation steps conducted in
quadrupole assembly 62. Amer the second generation fragment ion population has
been released from quadrupole 62 and TOF mass to charge analyzed, a new set of
selected mass to charge value ions are accelerated into quadrupole 62, The new
first generation fragment ion population is trapped in quadrupole 62 and
undergoes
sequential mass to charge isolation, ion fragmentation and TOP mass analysis
steps.

Quasi MS/MS" experiments can be achieved with a continuous primary ion beam
using
techniques described in U.S. Patent No. 6,011,259. In the techniques
described, true m/z
selection does not take place prior a ion fragmentation. Instead two spectra
are acquired
sequentially, the first with 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 containing peaks of just the MS/MS" fragment ions.
This method
requires multiple component resonant frequency excitation waveforms for
conducting CID
excitation ion fragmentation. Using this technique, an MS/MS4 experiment can
be conducted
with the hybrid quadrupole TOF diagrammed in Figure 1 as described below.
Mass spectrum 1 is acquired with the following operating sequences conducted
with multiple
quadrupole ion guide assembly 8.
1. Segment 1 of quadrupole assembly 60 is operated in mass to charge selection
mode.
The resulting ion population is accelerated into segment 2 with sufficient
energy to
cause CID fragmentation.
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 quadrupole assembly 61 into quadrupole
assembly
62 without further fragmentation.
3. Quadrupole assembly 62 is operated in trapping or non-trapping RF only mode
with
ions transferred 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
excitation applied to segment 2 or a single resonant excitation frequency
applied to poles 4 of
quadrupole assembly 62 to fragment the selected third generation product ion
having the
matching resonant excitation 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/MS" analysis technique can be used which may use either a
continuous or
non continuous primary ion beam depending on the specific analytical
application. With this
technique, ions are moved from one segment or quadrupole assembly to an
adjacent segment


CA 02626383 2008-04-24

or quadruole assembly in blocks. All ions trapped in one segment or quadrupole
are
transferred to the next sequential segment or quadrupole ion guide assembly
before accepting
a new population of ions from the previous segment or quadrupole assembly.
Each segment
or quadrupole assembly can independently perform single or multiple m/z
selection and /or
resonant frequency excitation CID ion fragmentation functions or ions are
fragmented using
DC acceleration CID as ions are transferred between segments or quadrupole
assemblies.
The steps of an MS/MS3 analysis using this technique are listed below.
1. Segment 1 of quadrupole assembly 60 is operated in RF only mode with ion
m/z
selection or isolation using multiple frequency composite waveform resonant
frequency ejection of unwanted ions. The relative DC offset potentials applied
to
the poles of segments I and 2 of quadrupole assembly 60 are set to accelerafÃ
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.
2. The relative DC offset potentials applied to the rods of segment 2 of
quadrupole
assembly 60 and quadrupole assembly 61 are set to trap ions in segment 2 for a
given time period. Segment 2 is operated in m/z selection mode and the
selected
m/z value first generation fragment ions are trapped in segment 2 for the
given time
period.
3. The DC offset potential applied to rods 3 of quadrupole assembly 61 is then
switched low to pass ions from segment 2 of quadrupole assembly 60 through
quadrupole 61 and into quadrupole 62 for a time period of a duration
sufficient to
substantially empty segment 2 of trapped ions to the level of the continuous
primary ion beam operating in single pass mode. Ions are accelerated from
segment 2 of quadrupole assembly 60 through quadrupole 61 and into quadrupole
62 with sufficient kinetic energy to cause DC acceleration CID ion
fragmentation.
After the ion transfer period, the DC offset potential applied to poles 3 of
quadrupole 61 is switched high trapping ions in segment 2 and preventing
trapped
ions quadrupole assembly 62 from re-entering segment 2 of quadrupole assembly
60 in the reverse direction.
4. Quadrupole assembly 62 is initially operated in m/z selection mode while
ions are
being transferred into quadrupole 62 from segment 2 through quadrupole 61. The
potential applied to lens 33 is initially set to trap and hold ions in
quadrupole
assembly 62. After the DC offset potential applied to poles 3 of quadrupole
assembly 61 is raised to stop ion flow from segment 2 of quadrupole assembly
60,
the potentials applied to poles 4 of quadrupole 62 are switched such that
quadrupole 62 is operated in RF only mode with resonant frequency excitation
CID
fragmentation of the selected m/z value second generation fragment ions
trapped in
quadrupole 62. If an MS/MS3 experiment is desired, the resulting third
generation
product or fragment ions trapped in quadrupole 62 are released, by switching
the
voltage applied to lens 33, in gated ion packets into TOF pulsing region 37
and
subsequently TOF mass analyzed. If higher order MS/MSI' steps are required,
additional sequential m/z selection and CID fragmentation steps can be
continued
with the ions trapped in quadrupole assembly 62, prior to releasing ions into
TOF
pulsing region 37. TOF spectra of a portion of the products ions can be
acquired at
each MS/MS step or at the end of the MS/MS" sequence. While MS/MS steps are
being conducted with ions trapped in quadrupole assembly 62, selected first

41


CA 02626383 2008-04-24

generation product ions continue to accumulate in segment 2 of quadrupole
assembly 60.
5. When all n generation product ions trapped in quadrupole assembly 62 have
been
gated into TOF pulsing region 37 and subsequently TOF mass analyzed, the DC
offset potential applied to poles 3 of quadrupole assembly 61 is lowered and
steps
3 and 4 above are repeated.
MS/MS" analytical functions can he run using the hybrid TOF diagrammed in
Figure 1
operating with a non continuous primary ion beam. Several functional sequences
are possible
with multiple quadrupole assembly 8 and TOF mass analyzer 40 to conduct MS/MS"
analysis
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 m/z ion selection and resonant
frequency
excitation CID ion fragmentation steps prior to TOF mass analysis. The
addition of multiple
segments and additional quadrupole assemblies configured in a higher
background pressure
region allows operational and analytical variations not possible when
conducting MS/MS"
mass analysis sequences with a single segment two dimensional trap TOF with a
non-
continuous primary ion beam. Unlike three dimensional ion traps or F'TMS mass
analyzers,
the hybrid multiple quadrupole assembly TOF configuration can configured and
operated to
achieve MS/MS" functionality with higher energy DC acceleration ion
fragmentation at each
ion m/z selection and fragmentation step. Alternatively, multiple quadrupole
ion guide
assembly 8 can be configured to conduct resonant frequency excitation
fragmentation or
combinations of both CID fragmentation techniques during an MS/MS" experiment
to
optimize performance for a given mass analysis. One example of a MS/MS"
experiment
conducted with DC acceleration CID ion fragmentation using the multiple
quadrupole ion
guide TOF hybrid diagrammed in Figure 1 is described below.
1. Segment 1 of quadrupole assembly 60 is operated in RF only non mass
selection
mode with ions being transferred into segment 2 with no fragmentation.
2. Segment 2 of quadrupole assembly 60 is operated in trapping or non trapping
mass
to charge selection mode and the resulting ion population is accelerated
through
quadrupole 61 and into quadrupole assembly 62 with sufficient kinetic energy
to
cause CID fragmentation.
3. Quadrupole ion guide 62 is operated in trapping mass to charge selection
mode and
a selected m/z range of first generation fragment ions is collected in
quadrupole 62
with little or no ion 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 ion population in quadrupole 62 to avoid saturation, the
primary
ion beam is prevented from entering segment 1 quadrupole assembly 60 by
decreasing the potential on capillary exit lens 112 relative to the potential
applied to
skinnmer 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 quadrupole ion guide 62 are then DC accelerated in the
reverse
direction through quadrupole ion guide 61 and into segment 2 of quadrupole
assembly 60 by applying the appropriate relative DC offset potentials to the
rods of
segment 2, quadrupole 61 and quadrupole 62 to cause CID fragmentation of ions
accelerated into segment 2. Ions accelerated in the reverse direction into
segment 2
42


CA 02626383 2008-04-24

are prevented from entering segment I by increasing the relative DC bias
potentials
of segments 1 and 2. If a short MS/MS" 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 I volume. Ions are
prevented from exiting segment I in the reverse direction through ei/trance
end 9
by applying a DC retarding field between skimmer 26 and the poles of segment
1.
Collisions with the neutral gas molecules from the free jet expansion
continuing to
enter second vacuum stage 72 through skimmer aperture 27, serve to damp the
reverse direction axial trajectories of ions and prevents trapped ions from
being lost
through entrance end 9 of quadrupole assembly 60. The potentials applied to
the
rods of segment 2 and segment 1 just prior to receiving the ion population
from
quadrupole 62 are switched such that segments I and 2 are operated in ion m/z
selection mode.
5. A selected m/z range of second generation fragment ions is collected in
segment 2
of quadrupole assembly 60. The resulting population of second generation
fragment ions is re-accelerated through quadrupole ion guide 61 and into
quadrupole ion guide 62 with sufficient kinetic energy to cause CID
fragmentation
of the selected second generation ions.
6. Quadrupole ion guide 62 is again operated in ion trapping mode. If the
experiment
is to end at third generation ions, the resulting ion population in quadrupole
62 is
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/MS" 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/MSnth
step until the entire ion population is emptied from quadrupole 62 of multiple
quadrupole ion guide assembly 8.
7. The voltage applied to capillary exit lens 112 14 is raised to allow ions
in the
primary ion beam to again pass through skimmer aperture 27 and into segmented
1
of quadrupole ion guide assembly 60 entrance end 9.
8. Sequence steps I through 7 are 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 I of quadrupole assembly 60 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 quadrupole ion guide 61and into quadrupole
ion
guide 62 with no DC acceleration fragmentation.
3. Quadrupole assembly 62 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 first generation fragment m/z value
ions.
The internal energy of the m/z selected first generation fragment ions does
increase
43


CA 02626383 2011-01-04
60412-4222D

in quadrupole ion guide 62 during parent ion CID fragmentation. First
generation
ni/z selected fragment ions are accumulated in quadrupole 62 for a set time
period
or until a desired ion population density is reached, checked by short
duration TOF
mass analysis.
4. When quadrupole ion guide 62 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 capillary exit electrode 112.
5. The selected first generation fragmentation ions are accelerated in the
reverse
direction from quadrupole ion guide 62 through quadrupole ion guide 61 and
into
segment 2 of quadrupole ion guide assembly 60 with sufficient kinetic energy
to
cause CID fragmentation.
6. Prior to receiving the first generation ions and second generation fragment
ions, the
potentials applied to the poles of segment 2 are switched to operate in mass
to
charge selection mode for nr/z selection of second generation fragment ions.
7. If further MS/MS analytical sequences are desired, steps 2 through 6 can be
repeated. If no additional MS/MS steps are desired TOF mass analysis can be
performed on the entire ion population trapped in segment 2 of quadruole
assembly
60 by transferring the ions without further fragmentation through quadrupole
assemblies 61 and 62.
8. When TOF mass analysis is completed and multiple quadrupole ion guide
assembly 8 has been emptied, the primary ion beam is again allowed to pass
through skimmer aperture 27 and into segment 1 of quadrupole assembly 60.
Steps
1 through 7 can be repeated to continue data acquisition with MS/MSn analysis.

As is described in U.S. Patent No. 6,011,259, higher energy CID fragmentation
can
be achieved by accelerating ions back into quadrupole ion guide 62 from exit
end 11
configured 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 the
voltage applied
to lenses 33 and 34. The potential applied to lens 33 is then decreased to
accelerate ions back
into multiple quadrupole ion guide assembly 8. The reverse direction DC
accelerated ions
impact the background gas in multiple quadrupole ion guide assembly 8 as they
traverse the
length of multiple quadrupole assembly 8 or individual quadrupole assemblies
62, 61 and 60.
In a similar manner, quadrupole ion guide 61or a combination quadrupole ion
guides 61 and
62 can be used to reverse accelerate ions into segment 2 of quadrupole
assembly 60 in a
repetitive manner to rapidly increase the internal energy of an ion
population. Ion
acceleration from quadrupole ion guide assembly 61, however, occurs in the
presence of
background collision gas so the ion terminal velocities achieved may be lower
than the
velocities attained by reverse accelerating ions from the collision free
region at ion guide exit
end,rl 1. Unlike a three dimensional ion trap or FTMS mass analyzers that can
be operated
MS/MSn mass analysis mode, the multiple quadrupole ion guide TOF hybrid shown
in Figure
1 can deliver a broader range of collisional energies to achieve ion
fragmentation at each
MS/MS step. The control of MS/MSn function sequences is simplified by
preprogrammed
software fun&ions that calculate the resonant frequency waveforms and control
the RF, DC
potentials applied to each segment and quadrupole assembly. Software directed
controller 80
as diagrammed in Figure 2 sends waveform, amplitude, switch timing and other
control
information through control connections 81,77, 78, 79, and 82 to DC, RF, SF
and +/-DC
power supplies and switching units 66, 63, 64, 65 and 67 respectively. Outputs
connections
85, 86, 68, 69, 70, 87, 75, 76, 88 and 84 apply the appropriate potentials to
the capillary exit

44


CA 02626383 2008-04-24

lens 112, skimmer 26, the rods of multiple quadrupole assembly 8, exit lenses
33, 34 and 35,
and TOF pulsing lenses 41 and 42 respectively.

Rapid switching of DC offset potentials can be achieved by switching between
two individual
DC power supplies set at the appropriate potentials. The poles of each segment
or quadrupole
assembly can be connected to a set of +/- DC power supplies and waveform
generators
through switches. The primary RF applied to the poles of each quadrupole
assembly through
capacitive coupling directly from individual RF supplies configured in power
supply units 63,
64 and 65. The -+-/- DC potentials can be added after the RF coupling
capacitor and the
resonant frequency AC waveform can be inductively coupled into the RF
connections to
appropriate poles of each segment of each quadrupole assembly. Alternatively,
the resonant
frequency AC waveform can be capacitively added to at least two poles of each
segment of
each quadrupole assembly. The state of each switch can be controlled by
controller 80 from a
computer program that can synchronously change the status all switches
required to achieve a
change of instrument state. RF, SF and DC power supply amplitudes can be set
through
interfaces such as Digital to Analog converters using the same computer
control program.
With such a computer controlled system, MS/MS11 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 preset values or based on the data
received.
Data dependent software control decisions may be used for example to select
and fragment
the ion species comprising the largest peak in a parent mass spectrum. The
ions species that
have resulted in the largest amplitude parent peak being detected for a given
mass spectrum
are then m/z selected and subsequently fragmented in a preprogrammed data
dependent
automated software control sequence.

Quadrupole ion guide assembly 61 of multiple quadruple assembly 8 serves to
decouple
quadrupole ion guides 60 and 62 both electrically and functionally. Ions can
be trapped in
segment 2 of quadrupole assembly 60 and released when the DC offset potentials
applied to
poles 3 of quadrupole ion guide 61 are increased to trap ions and lowered to
pass ions from
segment 2 into quadrupole ion guide 61. Multiple quadrupole assembly 8 can be
constructed
with an increased number of segments per quadrupole assembly or with an
increased number
of quadrupole assemblies to achieve greater instrument flexibility resulting
in a greater range
of analytical capability. Instrument flexibility and to some extent complexity
can be
increased to achieve additional functional capability by increasing the number
of quadrupole
assemblies and segments per quadrupole multiple quadrupole ion guide assembly
160
configured in hybrid quadrupole TOF 170 as daigramrned in Figure 4. Multiple
quadrupole
ion guide assembly 160 comprises four quadrupole assemblies 161 through 164.
Two
segment quadrupole assembly 161 includes analytical segment 165 and exit
segment 166.
Two segment quadrupole assembly 162 comprises analytical segment 167 and exit
segment
168. Single segment quadrupole assembly 163 comprises segment 169 and four
segment
quadrupole assembly 164 comprises segments 170 through 173. The rods of each
of the four
quadrupole assemblies are connected to four independent RF supplies whose
output RF
waveforms have common frequency and phase. The rods of each of the four
quadrupole
assemblies are connected to independent resonant or secular frequency
composite waveform
supplies. The rods of each segment of each quadrupole assembly are connected
to
independent DC offset or +/- DC voltage supplies. Alternatively, to achieve a
reduction in
system cost and complexity with some reduction in analytical capability, a
common RF



CA 02626383 2008-04-24

supply can be connected to all segments of all quadrupole assemblies of
multiple quadrupole
assembly 160. Care must be taken to decouple the electrical reactance when
changing DC
and SF potential to individual quadrupole segments during operation when a
common RI'
supply is used. The inadvertent coupling of a rapidly switched DC potential
into the RF
potential can result in rapid and unwanted ion ejection from the effected
quadrupole volume.
Auxiliary background gas is added through channel 178 into second vacuum
pumping stage
198 to modify the background gas composition in multiple quadrupole assembly
160. Valve
199 controls the auxiliary gas flow rate through channel 178 into vacuum stage
198. Helium
can be added to reduce the mass of the collision gas, argon can be added to
increase the mass
of the collision gas or a reactant gas can be added to study ion to neutral
gas phase reactions.
Each adjacent segment of each quadrupole assembly and each adjacent quadrupole
assembly
is electrically insulated to isolate different electrical potentials applied
to the rods or poles of
each adjacent segment. Quadrupole assemblies 161, 162, 163 and 164 are
sequentially
configured along a common centerline. Multiple quadrupole assembly 160 is
diagrammed in
a linear configuration. Alternatively, multiple quadrupole assembly 160 can be
configured
with quadrupole assemblies comprising curved rods or poles.

Effectively multiple a third independent quadrupole assembly 161 has been
added to multiple
quadrupole assembly 160 when compared to the configuration of multiple
quadrupole
assembly 8 diagrammed in Figure 1. The additional quadrupole assembly 161
configured in
the higher background pressure region of vacuum pumping stage 198 enables the
conducting
of an independent mass selection and/or fragmentation step with trapping of
ions. Ions can be
independently trapped in and released from quadrupole assemblies 161, 162 163
and 164 in
multiple quadrupole assembly 160. The individual DC offset potential applied
to the poles of
segment 166 of quadrupole assembly 161 can be set to trap ions in segment 165
or release
ions from segment 165 into segment 167 of quadrupole assembly 162. Mass to
charge
selection and DC acceleration and resonant frequency excitation CID ion
fragmentation can
be conducted in quadruole assemblies 161, 162. and 164. Ions can be
transferred between
quadrupole ion guide assemblies in the forward and reverse directions by
applying the
appropriate DC offset potentials to specific segments of each quadrupole ion
guide assembly.
Exit segment 168 and two entrance segments 170 and 171 have been added to
quadrupole
assemblies 162 and 164 respectively. These added segments in conjunction with
quadrupole
assembly 163 provide a five step ion acceleration junction between quadrupole
assemblies
162 and 164. Higher energy DC acceleration CID ion fragmentation can be
achieved,
particularly in higher background pressures, using a longer acceleration path
provided by the
added quadrupole segments. Multiple passes can also be made through the five
step junction
to increase ion internal energy leading to fragmentation.

The addition of a third quadrupole assembly 161 to multiple quadrupole
assembly 160 in
hybrid TOP 170 increases the range of analytical functions that can be.
conducted when
compared to the hybrid TOF mass analyzer as diagrammed in Figure 1. Hybrid TOP
170 can
be used to conduct MS/MS" analysis functions that are not possible using the
hybrid TOF
mass analyz r as diagrammed in Figure 1, triple quadrupoles or three
dimensional ion trap
mass arralycr-s. An example of a new MS/MS2 functional sequence with a
continuous ion
beam and DC acceleration CID fragmentation for each MS/MS step is given below
using
Hybrid TOF 170.
1. Quadrupole assembly 161 is operated in mass to charge selection mode with
or
without repetitive ion trapping and release.

46


CA 02626383 2008-04-24

2. Parent ions mass to charge selected in quadrupole assembly 161 are
accelerated
into quadrupole assembly 162 with sufficient kinetic energy to cause DC
acceleration CID ion fragmentation.
3. Quadrupole assembly 162 is operated in mass to charge selection mode,
selecting
at least one first generation fragment ion species with or without repetitive
ion
trapping and release.
4. First generation fragment ions mass to charge selected in quadrupole
assembly 162
are accelerated through quadrupole assembly 163 and into quadrupole assembly
164 with sufficient kinetic energy to cause DC acceleration CID ion
fragmentation.
Quadrupole assembly 164 is operated in RF only ion trap and release mode
trapping second generation fragment ions.
5. Second generation fragment ions are transferred from quadrupole ion guide
164
into pulsing region 175 where they are pulsed into TOF drift region 176 and
mass
to charge analyzed.

Segment 173 has been added at exit end 174 of quadrupole ion guide assembly
164 to serve
as an alternative means to trap ions in quadrupole ion guide 164 and gate ions
from
quadrupole 164 into TOF pulsing region 175. Ions are trapped trap in
quadrupole assembly
164 by raising the DC offset potential applied to the rods of segment 173.
Trapping with DC
offset potentials applied to the poles of segment 173 compared with using a DC
retarding
potential applied to lens 179 reduces any defocusing effects which may occur
due to fringing
field effects occurring at exit end 174. Segment 173 can be operated primarily
in RF only ion
transfer mode to reduce or minimize asymmetric DC fringing field effects that
may exist at
exit end 174 of quadrup~,1e ion guide 164. Segment 173 can be configured to
work in
conjunction with exit lens 179 or in place of exit lens 179 for ion trapping
or reverse ion
acceleration functions. As is apparent to one skilled in the art, several
unique analytical
functional sequences are possible in addition to the example given above with
four
quadrupole ion guide assembly hybrid TOF 170 as diagrammed in Figure 4.
Quadrupole
assemblies 161, 162 and 164 configured in higher background pressure region
171 can be
operated independently in mass to charge selection mode and/or resonant
frequency excitation
CID ion fragmentation modes. Quadrupole assemblies 161, 162, 163 and 164 can
be
operated in conjunction with one another to achieve DC acceleration CID ion
fragmentation.
A wide range of functions can be conducted to achieve MS/MSn mass analysis
using hybrid
quadrupole TOF 170 fora given analytical application.

An alternative embodiment to API source hybrid quadrupole TOF 170 is
diagrammed in
Figure 5. Referring to Figure 5, multiple quadrupole assembly 180 configured
in hybrid
quadrupole TOF 194 comprises individual quadrupole assemblies 181, 182 and 183
separated
with electrostatic lenses 192 and 193. Electrostatic lens 192 is configured in
the junction
between quadrupole assemblies 181 and 182 and
Electrostatic lens 19 is configured in the junction between quadrupole
assemblies 182 and
183. Electrostatic lens 192 replaces quadrupole assembly 163 in multiple
quadrupole
assembly 1 30 as diagrammed in Figure 4. Electrostatic lenses 192 and 193,
connected to DC
power supplies, allow trapping and release of ions from adjacent quadrupole
assemblies. Ions
can still be moved in the forward and reverse directions between quadrupole
assemblies in
multiple quadrupole assembly 180, however, the presence of DC lenses in the
interquadrupole junctions causes some distortion of the applied RF radial
trapping field and
the resonant AC field at ends of adjacent quadrupoles. This RF and AC field
distortion plus
47


CA 02626383 2008-04-24

the reduced transmission areas of orifices 195 and 196 in lenses 192 and 193
respectively can
result in ion transmission losses between quadrupole assemblies reducing
sensitivity. The
tradeoff in performance is balanced against a potential reduction in cost from
the elimination
RF power supplies while retaining the ability to trap and release ions
independently in
quadrupole ion guide assemblies 181, 182 and 183. Alternatively, electrostatic
lenses 192
and/or 193 can be configured as multiple lens sets to allow electrostatic
focusin or
acceleration of ions as they traverse the junctions between quadruole ion
guide assemblies.
Three individual sets of RF, A-/- DC and resonant frequencies waveform power
supplies apply
electrical potentials independently to the rods of quadrupole assemblies 181,
182 and 183.
Separate DC offset potentials can be applied independently to each segment
184, 185, 186,
187, 188, 189, 190 and 191 of multiple quadrupole assembly 180. Quadrupole
assemblies
181 and 182 and a portion of quadrupole assembly 183 are configured in higher
background
pressure vacuum stage 197. Independent mass to charge selection and resonant
frequency
excitation CID ion fragmentation can be conducted in quadrupole assemblies
181, 182 and
183. DC acceleration CID ion fragmentation can be achieved by ion acceleration
between
segments within quadrupole assemblies or by accelerating ions between
quadrupole
assemblies 181 and 182 182 and 183 in the forward or reverse directions.
Alternatively, ions
can be accelerated in reverse direction from the exit end of quadrupole 183
into quadrupole
183 to achieve DC acceleration CID ion fragmentation. As is apparent from the
description
given above for the hybrid quadrupole TOP embodiments as diagrammed in Figures
1 and 4,
API source hybrid quadrupole TOF 194 can be operated to conduct a range of
MS/MSn mass
analysis functions with the option of using different methods to achieve mass
to charge
selection and ion fragmentation in each MS/MS step. Hybrid quadrupole TOP 194
can be
used to perform triple quadrupole and three dimensional quadrupole ion trap
mass analysis
and is capable of performing mass analysis functions not possible using either
triple
quadrupoles or three dimensional ion traps.

Less complex single or multiple quadrupole assemblies can be configured in
hybrid
quadrupole TOF apparatus to lower instrument cost and reduce
operating.complexity.
Flexibility in operation and analytical capability may be reduced, depending
on the
application desired, as the multiple quadrupole configuration is simplified.
Quadrupole ion
guide assembly 61 of multiple quadruple assembly 8 serves to decouple
quadrupole ion
guides 60 and 62 both electrically and functionally. Ions can be trapped in
segment 2 of
quadrupole assembly 60 and released when the DC offset potentials applied to
poles 3 of
quadrupole ion guide 61 are increased to trap ions and lowered to pass ions
from segment 2
into quadrupole ion guide 61. Figure 6 shows an alternative embodiment of a
hybrid multiple
quadrupole ion guide TOP instrument 215 comprising electrospray ion source
212, four
vacuum pumping stages 208, 209, 210 and 211, multiple quadrupole assembly 204
and TOF
mass analyzer 216. Multipole ion guide 204 comprises individual quadrupole
assemblies
201, 202 and 203 positioned along common centerline 205 having individual RF, -
+-/-DC and
resonant waveform supplies allowing the performing of independent mass
selection and ion
fragmentation functions with each quadrupole assembly. In one aspect of the
invention, all
three RF power supplies are operated with a common frequency and phase output.
Common
frequency and phase are applied to axially aligned rods of each quadrupole
assembly 201, 202
and 203 in multiple quadrupole assembly 204 to maximize ion transfer
efficiency between
quadrupole assemblies. Quadrupole assembly 203 extends continuously from
higher
background pressure vacuum pumping stage 209 into lower background pressure
vacuum
stage 210. Examples of combinations mass to charge selection and in
fragmentation steps

48


CA 02626383 2008-04-24

conducted multiple quadrupole ion guides with TOF mass analysis given above
can be
applied to multiple quadrupole assembly 204 configured in hybrid TOF 215.
Alternatively, individual quadrupole assemblies 201 and 202 can be configured
as two
segments of a quadupole assembly where the RF potentials applied to the rods
of both
segments originates from a common RF power supply. In this alternative
embodiment,
multiple quadrupole assembly 204 comprises two quadrupole assemblies, the
first quadrupole
assembly comprising segments 201 and 202 and the second quadrupole 203
assembly
comprises a single segment. Independent +/-DC (including offset DC) and
resonant
frequency waveforms are applied to the rods of quadrupole sections and
assemblies 201, 202
and 203 allowing the performing of independent mass to charge selection and
ion
fragmentation functions in each quadrupole section or assembly. Comparing this
alternative
embodiment with multiple quadrupole assembly 8 as diagrammed Figure 1,
quadrupole
assembly 61 has been removed in dual quadrupole assembly 204. The removal of
quadrupole assembly 62 segmented ion guide 8 simplifies operational sequences
and reduces
cost of electronic components. Many MS/MS" sequences described using the
embodiment
shown in Figure I can be run with the dual quadrupole assembly 202 as
diagrammed in
Figure 2. . By setting the appropriate relative DC offset potentials between
quadrupole
segments and/or assemblies 201, 202 and 203, DC acceleration CID ion
fragmentation can
occur by accelerating ions in the forward or reverse directions between
quadrupole segments
or individual quadrupole assemblies through junctions 206 and/or 207 or in the
reverse
direction from the exit end of quadrupole 203. The background pressure in
vacuum second
stage 209 is maintained above 0.1 millitorr to allow collisional damping of
stable trajectory
ion energies and to enable CID fragmentation of ions in each multipole ion
guide section or
assembly. The local pressure at entrance end 213 of segment or quadrupole 201
is higher due
to the free jet expansion and aids in increasing the ion guide capture
efficiency at entrance
213 of multiple quadrupole assembly 204. Elimination of and independent
quadrupole
assembly 61 or segment in the junction between segments 202 and quadrupole 203
results in
reduced flexibility in simultaneously trapping different ion populations ions
in both segment
202 and quadrupole 203. This reduced functionality simplifies instrument
operation and cost
by reducing variables and components. Combining aspects of the invention shown
Figures 1
through 5, alternative embodiments of the invention can be configured into
hybrid TOF 215.
For example, electrostatic lenses can be included in junctions 206 and 207 to
allow trapping
of ions in segments or quadrupoles or the transfer of ions across junctions
206 and 207.
Electrostatic also serve to isolate capacitive coupling of electric fields
between quadrupole
assemblies. Multiple quadrupole assembly 204 can also operated as a three
segment ion
guide with RF applied to the poles of all three segments originating from one
power supply.
Several MS/MS" mass analysis functions can be conducted in this single RF
supply
embodiment with a reduced electrical component complexity and cost.

Tile configuration of the guide assembly configured in a hybrid quadrupole TOT
can be
further siml) lified while retaining the ability of performing MS/MS" analysis
functions. An
alternative Embodiment of the invention is diagrammed in Figure 7 in which
three segment
quadrupole ion guide 408 is configured in a hybrid API TOF mass analyzer. In
the simplest
embgdiment, RF potential is applied to the rods of the three segments 401, 402
and 403 from
a common RF power supply, with separate DC offset applied to each segment.
Individual +/-
DC and resonant waveforms can be applied to the rods of segments 401 and 402
to conduct
mass.to charge selection and resonant frequency excitation CID fragmentation
of selected

49


CA 02626383 2008-04-24

ions. Three segment multipole ion guide 408 extends continuously from higher
backgr6und
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 pulsing region 415
or as a two
dimensional trap configured with full MS/MS" function capability when coupled
with TOF
mass analysis as is described in U.S. Patent No. 6,011,259. The embodiment in
Figure
4. includes two additional segments configured in quadrupole assembly 408 not
described in
U.S. Patent No. 6,011,259. Segments 401 and 403 can be operated in modes that
serve to
decouple or minimize the fringing field effects of potentials applied to
segment 408 during
mass to charge selection and ion fragmentation operating modes. Minimizing the
fringing field
effects allow optimization of the trajectories of ions entering or exiting
quadrupole ion guide
408 at entrance and exit ends 416 and 417 respectively. For example segment
401 can be
operated in RF only mode to efficiently transfer ions from 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 enter segment 408 closer to centerline 418 where the defocusing
effects of DC
fringing fields will have minimum 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 region 415. Ions traversing pulsing region
415 are pulsed
into TOF drift region 414 and mass analyzed. A linear TOFYlight tube geometry
is shown in
Figure 7 as an alternative embodiment to a TOF flight tube geometry which
includes an ion
reflector geometry.

Segment 403 operating in RF only mode provides consistent ion trajectories for
ions
traversing from multipole ion guide exit region 417 into TOF pulsing region
415 by shielding
non uniform 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 m/z
selection and/or
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 CID
functions described in previous embodiments and in U.S. Patent No. 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 segment 403 and lens 419 in a
synchronous manner to
initially raise the ion energy of the ions in exit region 417 and then
accelerate the ions in
reverse direction along quadrupole centerline 418 into segment 402. Some DC
field
penetration into segment 403 from lens 419 and the poles of segment 402 will
occur with DC
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 MS/MS"
functionality in a cost effective configuration with some tradeoffs in
functional flexibility due
to the reduced number of multipole ion guide segments or individual quadrupole
assemblies
operated in a higher pressure vacuum region.

An alternative embodiment of a three segment multipole ion guide diagrammed in
Figure 8 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 first
multipole ion guide segment 441 where they are radially confined by the RF
fields applied to


CA 02626383 2008-04-24

the poles on segment 441. Ions with m/z values which fall within the stability
window
determined by the electric fields applied to the poles of segment 441 move
through segment
441 and are transferred into segment 442. MS/MS" functions with TOF mass to
charge
analysis can be achieved using techniques similar to those described for the
three segment ion
guide shown in Figure 7. 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
some analysis
applications. Additional configurations of the multiple quadrupole or multiple
segment
quadruole assembly configured in a hybrid quadrupole TOF mass analyzer are
diagrammed
in Figures 9 through 11.

Independent quadrupole or segmented multipole ion guide assembly 502
diagrammed in
Figure 9 extends into TOF pulsing region 507. Ions traversing the length of
multipole ion
guide 508 pass through independent quadrupole assemblies or segments 501, 502
and 503
and are transferred into quadrupole or segment 507. The relative DC voltages
applied to the
poles of segments 503 and 504 and lens 506 trap ions in quadrupole assembly
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 as described by
Franzen in U.S.
Patent Number 5,763,878. In the alternative configuration, Ijames, C.F.
Proceedings of the 44th
ASMS Conference on Mass Spectrometry and Ion Physics, Page 795, 1996,
describes replacing
trapping lens 506 with a quadrupole ion guide with lateral ion extraction of
trapped ions from
quadrupole 504 into the TOF drift region.

Full MS/MSn functions with TOF mass to charge analysis can be achieved using
the hybrid
TOF embodiment shown in Figure 9. Individual quadrupole assemblies or segments
501, 502
and 503 can be operated individually or in complementary fashion to achieve
ion mass to
charge selection and/or ion CID fragmentation of ions prior to TOF mass to
charge analysis.
Similar to embodiments described above, multiple quadrupole assembly 508 is
configured
with four independent sets of RF, +/DC and resonant frequency waveform power
supplies
applying different potentials to the rods of individual quadrupole assemblies
501, 502, 503
and 504 with common RF frequency and phase. Each quadrupole assembly 501, 502
and 503
located in higher pressure vacuum stage 512 can be independently cooperatively
operated in
mass to charge selection and/or ion fragmentation modes to conduct MS/MS steps
of
MS/MS1' mass analysis functions with TOF mass to charge analysis. Quadrupole
507 is
configured in a low pressure vacuum region where little or no ion collisions
occur with the
neutral background gas. Consequently, no collisional damping can occur for
ions trapped in
quadrupole assembly 504 prior to pulsing laterally into TOF drift region 510.

The ions tramped in quadrupole assembly 504 prior to pulsing into TOF drift
region 510 may
be traveling in either direction axially along the length of quadrupole 504.
The axial
trajectory of ions moving in opposite directions in quadrupole 504 cannot be
simultaneously
directed by steering lenses 511 to impact on the TOF detector. To increase the
number of
ions which have the required trajectory to impact the detector in the TOF
tube, ions must be
accelerated laterally from quadrupole assembly 504 during the initial first
pass of ions that

51


CA 02626383 2008-04-24

enter quadrupole ion guide 504 or ions must be transferred into quadrupole 504
with cry low
axial kinetic energy. The latter has the disadvantage that the pulsing region
fill time may be
quite long resulting in the reduction of the TOF pulse rate. Undamped radial
ion motion in
quadrupole assembly 504 due to the RF field contributes to the spatial and
energy spread of
ions accelerated laterally into TOF drift region 510. An additional constraint
that must be
considered when operating with a two dimensional trap configured in the TOF
pulsing region
is that a multichannel plate detector commonly used in TOF analyzers has a
limited
instantaneous charge depletion linear dynamic range response, 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 quadrupole 504 prior to pulsing the trapped ions into
TOF driff
region 510 can help to avoid detector saturation. The potentials applied to
steering lens set
511 can be optimized maximize the number of ions pulsed from quadrupole 504
that impact
on the TOF detector.
An alternative embodiment of a hybrid API source multipole ion guide TOP is
diagrammed in
Figure 10. Referring to Figure 10, an additional multipole ion guide 610 has
been configured
between segmented quadrupole ion guide assembly 608 and TOF pulsing region
611.
Multipole ion guide 610 can be operated as a collision cell when gas is added
to collision cell
assembly 612 surrounded by partition 614 or, configured as a quadrupole ion
guide, can also
be operated in mass to charge selection mode. Segments 601, 602 and 603
comprising
quadrupole ion guide 608 can be operated individually or collectively in mass
to charge
selection and/or CID ion fragmentation modes to achieve MS/MS" 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 mass to charge selected with DC
acceleration or
resonant frequency excitation CID ion fragmentation in multipole ion guide
610. Multipole
ion guide 608 extends continuously from higher background pressure vacuum
stage 613 into
lower pressure vacuum stage 615 where ions. exiting from segment 603 are not
subjected to
collisional scattering from collisions with neutral background gas molecules.
Ion transfer
efficiency into multipole ion guide 610 is aided by the collsional damping of
ions as they
traverse segment 601 and the portion of segment 602 positioned in vacuum
pumping stage
613. The configuration of separate collision cell assembly 612 comprising
multipole ion
guide 610 allows the introduction of a collision or reactive background gas
that has the same
or different composition from the background gas present in second vacuum
stage 613. The
hybrid TOF embodiment shown in Figure 10 allows studies of gas phase ion
neutral reactions
or the use of different gases for CID fragmentation of ions with full MS/MS".
mass analysis
capability. Multipole ion guide 610 can be operated in single pass or ion trap
and release mode
with the gating of ions into TOF pulsing region 611. An additional RF
multipole ion guide may
be configured in vacuum stage 615 between multipole ion guide 610 configured
in a collision
cell and TOF pulsing region 611 to reduce the background pressure between CID
region 612
and fourth vacuum stage 618 which is maintained at low background pressure.
Multipole ion
guide 608 may also be configured to extend into poles of ion guide 610 to
improve ion
transmission efficiency as is described in U.S. Patent Nos. 6,121,607 and
6,403,952. The dual
multipole ion guide embodiment shown in Figure 10 allows specialized operating
modes such
as employing two separate collision gases in an MS/MS or MS/MS" mass analysis
sequence.
The hybrid TOP embodiment as diagrammed in Figure 10 also allows the
conducting of ion
mass to mass to charge selection and/or CID ion fragmentation functions in
either quadrupole
ion guide ---------------------------------------------------------------------
-----------------------------
52


CA 02626383 2008-04-24

assemblies 608 or 610 that may be configured with different cross sections and
have different
+/- DC and RF frequency, phase and amplitude potentials applied to rods of
each quadruole
assembly. Ions can be accelerated in the forward and reverse directions
between quadrupole
assemblies 608 and 610 to cause DC acceleration CID ion fragmentation.

Figure 1.1 shows an alternative embodiment for a multipole ion guide hybrid
TOF mass
analyzer that can be operated in MS/MSr' analysis mode. Segmented quadrupole
ion guide
assembly 708, configured with segments 701, 702 and 703, is positioned in
higher
background pressure vacuum second vacuum stage 710. A second quadrupole ion
guide
assembly 704 located in lower background pressure 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 above the backgound pressure in vacuum stage 711
when it is
desirable to operate ion guide 704 as a collision cell. A third multipole ion
guide 714 is
positioned in vacuum stage 711 to efficiently transfer ions from multipole ion
guide 704 into
pulsing region 712 allowing sufficient vacuum pumping between higher pressure
collision
region 713 and lower pressure TOF pulsing region 712. Quadrupole ion guide 704
may be
operated in single pass or ion trapping mode with gating of ions into TOF
pulsing region 712.
Positioning quadrupole ion guide assemblies 708 and 704 in separate vacuum
stages allows
increased flexibility in configuring multipole ion guide geometries
particularly for quadrupole
assembly 708. Multipole ion guides which extend into more than one vacuum
stage are
configured with relatively small inner diameters (small ro) to minimize the
neutral gas
conductance from one vacuum stage to the next. Minimizing gas conductance
reduces
vacuum pumping costs for a given background target pressure. The poles of
multipole ion
guide assemblies 708, 704 and 714 begin and end vacuum stages 710 and 711
respectively so
there are no vacuum pumping constraints imposed on any multipole ion guide
geometry. The
inner radius (r0) of ion guide 708, 704 or 714 are not constrained due to
vacuum pumping
requirements. in the embodiment shown in Figure 7.

Analogous to previously described embodiments, the background pressure in
vacuum stage
710 is maintained sufficiently high to insure that collisions between
background gas and ions
occur as ions traverse the length of quadrupole assembly 708. The background
pressure in
vacuum stage 710 allows CID 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 CID ion fragmentation operating modes.
Voltages applied
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 708.
Each segment
in niultipole 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 ion m/z selection mode with low or
higher
background pressure or in resonant frequency excitation CID ion fragmentation
mode when
collision ga, is present in region 713. Ions can also be DC accelerated into
multipole ion
guide 704 7ith sufficient kinetic energy to cause CID fragmentation. Ions can
be accelerated
the forward or reverse directions between quadrupole or multipole ion guide
assemblies 708
and 704 with sufficient energy to cause DC acceleration CID ion fragmentation.
Combinations of ion m/z selection and CID ion fragmentation functions can
conducted with
quadrupole ion guide assemblies 708 and 704 to achieve a variety of MS/MSn
analytical

53


CA 02626383 2008-04-24

functions with TOF mass analysis. As with the collision cell embodiment 612
diagrammed in
Figure 10, collision gas or reactant gas can be introduced into region 713
with a composition
that s different than the composition of the background gas in vacuum stage
710. Selected
ion-molecule reactions can be studied by added the appropriate reactant gas
into collision cell
region 713. Reactant product ions can be mass to charge selected or fragmented
in one or
more steps in either quadrupole ion guide 704 or 708. The resulting ion
population ultimately
flowing through or trapped in multipole ion guide 704 is subsequently TOF mass
analyzed.
The embodiments of the invention diagrammed in Figures 1. through 11 are some
examples of
configurations and operation of hybrid multiple quadrupole ion guide TOF mass
analyzers
where ion mass to charge selection and ion fragmentation is conducted using at
least one
quadrupole ion guide positioned in a higher pressure vacuum region. Multiple
collisions
between ions and neutral background gas molecules occur in the quadrupole ion
guides
configured in the higher pressure vacuum region. The invention is not limited
to the specific
embodiments shown and techniques described. For example, where segmented
quadrupole
ion guides are described , individual quadrupole ion guides may be positioned
in the higher
background pressure region and used to conduct independent or coordinated m/z
and ion
fragmentation steps in an MS/MS" analysis. A preferred embodiment is to apply
the same RF
frequency and phase from different synchronized RF power supplies to
individual quadrupole
ion guides in an assembly. RF amplitude, +/- DC (including DC offset) and
resonant
frequency waveforms can be independently varied for each quadrupole ion guide
in such an
assembly. Alternatively, RF with different frequency and phase can be
independently
applied to individual quadrupole ion guides comprising an assembly. One
preferred
embodiment with non synchronized RF frequency and phase between quadrupole ion
guides,
is the configuration of an electrostatic lens in the junction between two
adjacent quadrupole
ion guides to minimize fringing field effects for ions traversing between ion
guides.

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 at
least one multipole ion guides located in a higher background pressure vacuum
region.
Different ion sources can be configured with the hybrid multiple quadrupole
ion guide TOF
hybrid instrument. Even ion sources which operate in vacuum or partial 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 line pulsing
region, a multiple
stage or curved field ion reflector or a discrete dynode multiplier. In
alternative
embodiments, the portions of segmented multipole ion guides or individual
multipole ion
guides located in a higher pressure vacuum regions can also be configured to
operate in ion
transfer, ion trapping and any of the CID ion fragmentation modes described
above as well as
in rn/z scanning or in/z selection mode or combinations of these individual
operating modes.
The CID ion fragmentation, ion mass to charge selection, and MS/MS" methods
described in
the embodiments of the invention can be extended to alternative embodiments of
the
invention. In one such alternative embodiment of the invention, the last mass
analysis step
of any MS or MS/MS" sequence is performed by a quadrupole ion guide.

54


CA 02626383 2008-04-24

Detector 38 as diagrammed in Figure I is used to detect ions prior to TOF mass
analysis.
One aspect of the invention is the configuration and operation of at least one
or a portion of
one quadrupole ion guide configured and operated in a higher pressure vacuum.
region where
multiple collisions between ions and neutral gas molecules occur. AS was
described above,
an important feature of multipole ion guides is that ions in stable
trajectories can be released
from one end of an ion guide or ion guide segment operating in single pass or
ion trapping
mode simultaneously while ions are entering the opposite end of the multipole
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 another
multipole ion guide or other mass analyzer which performs mass analysis on the
released
ions. In this mariner ions delivered in it continuous ion beam are not lost in
between discrete
mass analysis steps. Another aspect of the invention is the configuration of
an API source
with a segmented multipole ion guide positioned in a higher pressure vacuum
region where
the multipole ion guide may or may not be configured with additional
quadrupole mass
analyzers or multipole ion guide collision cells. The segmented quadrupole ion
guide can be
configured as an MS or MS/MS" mass analyzer with a portion of the segmented
ion guide
length operated in background vacuum pressures above 10-4 tort. The electron
multiplier ion
detector configured with quadrupole mass analyzers configured according to the
invention
may be located and operated in a lower or higher background pressure vacuum
region. Single
or multiple vacuum stage segmented multipole ion guides configured as mass
analyzers or as
a portion of a multiple quadruole mass analyzer operated in a higher pressure
vacuum region
be used to perform it wider range of MS or MS/MSn analytical functions for
lower cost and
instrument complexity than can be achieved conventional quadrupole mass
analyzer
configurations. Operating an API source quadrupole mass analyzer at higher
vacuum
background pressures can reduce instrument size and cost by reducing the
vacuum pumping
speed requirements.

Figure 14 shows an embodiment of the invention where multiple quadrupole
assembly 1010
comprises four independent quadrupole ion guide assemblies configured in an
API
quadrupole mass analyzer. Quadrupole ion guide 1008 is configured with
segments 1001
and 1002. Individual quadrupole assemblies 1003, 1004 and 1005 are configured
with one
segment each. Segments 1001 and 1002 and quadrupole assemblies 1008, 1003,
1004 and
1005 are configured along common centerline 1011 with electrically insulated
junctions 1018,
1019, 1020 and 1021 separating each segment or quadrupole assembly
respectively. Up to
junction 1021 in third vacuum stage 1017, Electrospray source 1012, segmented
quadrupole
ion guide 1008, quadrupole assemblies 1003 and 1004 and vacuum pumping stages
1015,
1016 and 1017 are configured and can be operated similar to those common
elements of the
hybrid quadrupole TOF embodiment as diagrammed in Figure 1'. TOF mass analyzer
40 of
Figure 1 has been replaced by quadrupole assembly 1005 in the embodiment of
the invention
diagrammed in Figure 14.
As diagrammed in Figure 2, individual power supply units each supplying RF, +/-
DC
(including 9C offset) and resonant frequency waveforms potentials to the rods
of quadrupole
assemblies 1008, 1003, 1004. An independent RF and +/-DC power supply unit
also supplies
potential to the rods of quadrupole assembly 1005. In it preferred embodiment
of the
invention, the same RF frequency and phase is applied to all aligned rods in
multiple
quadrupole assembly 1010 to provide maximum transfer efficiency of ions in
stable
trajectories between segments or quadrupole assemblies in the forward or
reverse direction.
Different RF amplitude, +/-DC (including DC offset) and resonant frequency
waveforms can



CA 02626383 2008-04-24

be applied to the rods of each individual quadrupole assembly. Different DC
offset and
resonant frequency waveforms can be applied to different segment 1001 and 1002
of ion
guide assembly 1008. Alternatively, RF potentials having different frequency
and phase can
be applied to individual quadrupole assemblies 1008, 1003, 1004 and 1005
during mass
analysis operation. It may be preferable with non synchronized RF applied to
different
quadrupoles to replace quadrupole assembly 1003 with an electrostatic lens and
include an
electrostatic lens in junction 1021 between quadrupole assemblies 1004 and
1005.
Alternatively, RF potential can be applied to the rods of segments 1001, 1002
and quadrupole
ion guides 1003 and 1004 from a common RF supply.

Second vacuum stage 1016 is operated with a background maintained above of .10-
4 tore
where multiple collisions occur between ions and neutral gas molecules as ions
traverse the
length of multiple quadrupole assembly 1010. Quadrupole ion guide assembly
1005 is
configured in third vacuum stage 1017 which is maintained at a background
pressure below
10-4 torr where few collisions occur between ions and background gas molecules
as ions
traverse the length of quadrupole assembly 1005. Quadrupole ion guide 1005
maybe
operated in mass to charge scanning or selected ion monitoring mode. The
embodiment
shown in Figure 10 can perform all MS and MS/MS analytical functions performed
by
conventional triple quadrupole configurations as diagrammed in Figure 20 as
well as.
additional MS/MS analytical functions. The four basic MS/MS triple quadrupole
operating
modes are listed in a previous section.

The previously listed MS/MS triple quadrupole mass analysis functions can be
performed
with the API multiple quadrupole embodiment shown in Figure 14 by using the
following
operating sequences.
1. Segment 1001 is operated in ion single pass (non trapping) RF only mode
with the
applied RF amplitude set to pass the desired range of m/z values. The relative
DC
offset potentials applied to the poles of segments 1001 and 1002 are set to
transfer
ions from segment 1001 into segment 1002 without DC acceleration ion
fragmentation.
2. Segment 1002 in operated in single pass (non trapping) ion mass to charge
selection mode. Ion mass to charge selection can be conducted using segment
1002 using the mass to charge selection techiques described for segment 2 of
quadrupole assembly 60 as diagrammed in Figure 1. The RF amplitude may be
modulated while applying the appropriate +/- DC potentials to the rods of
segment
1002. Alternatively, RF modulation can be used with +/- DC and a resonant
frequency waveform applied to the rods of segment 1002 to conduct single pass
ion
mass to charge selection. For MS/MS applications that require mass to charge
scanning of quadrupole 1008, the same mass to charge separation techniques can
be used stepping the appropriate RF and +/- DC amplitude potentials or
resonant
waveform m/z excitation frequency notch through the desired mass to charge
range
with or without RF modulation.
3. Quadrupole assemblies 1003 and 1004 are operated in RF only mode. The
relative
DC offset potentials applied to segment 1002 and quadrupole assemblies 1003,
1004 and 1005 are set to accelerate mass to charge selected ions from segment
1002 through quadrupole 1003 and 1004 and into quadrupole ion guide 1005 with
sufficient energy to cause CID fragmentation of accelerated ions in quadrupole
ion
guides 1003 and 1004. The background pressure in the entrance end of
quadrupole

56 0


CA 02626383 2008-04-24

1004 can be maintained sufficiently high to damp ion trajectories toward the
centerline after ion fragmentation has occurred to produce an ion beam with
low
kinetic energy spread transferred into quadrupole ion guide 1005. With
sufficient
post fragmentation ion kinetic energy collisional damping in quadruole 1004,
the
kinetic energy of ions entering quadrupole 1005 is determined by the relative
DC
offset potentials applied to the poles of quadrupole 1004 and 1005. Low
velocity
ions traversing quadruole 1005 are exposed to more RF cycles improving mass to
charge selection resolution.
4. Segment 1005 is operated in mass to charge selection mode. The ion mass to
charge value selection range may be fixed in some triple quadrupole MS/MS
operating modes or scanned as is required in other MS/MS operating modes. Ion
mass to charge selection in quadrupole assembly 1005 can be conducted using
the
more conventional ramping of RF and +/- DC amplitude applied to the rods of
quadrupole 1005. The m/z selection scanning ramps of segments 1002 and 1005
can be synchronized to perform neutral loss scans or monitoring of selected
fragmentation events.
5. Ions passing from quadrupole ion guide 1005 through lens 1006 are
accelerated
into conversion dynode 1007. The resulting secondary electrons and photons are
detected with electron or photomultiplier 1024. Alternatively, ions can be
accelerated directly into electron multiplier 1024 and detected.

The embodiment of the invention as diagrammed in Figure 14 is capable of
conducting
additional analytical functions not possible with conventional triple
quadrupole
configurations as diagrammed in Figure 20 where the first and third analytical
quadrupoles,
554 and 556 respectively, are operated in a low pressure 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 DC
acceleration CID fragmentation in segment 2 of quadrupole assembly 1008.
Segment 1001
can be operated in static or scanning ion mass to charge selection mode.
Alternatively,
MS/MS2 analysis can be conducted with resonant frequency excitation CID ion
fragmentation
of the parent ion if it is desirable to not increase the internal energy of
the fragment ions. This
can be achieved in scanning or non scanning modes as follows;
1. Segment 1001 is operated in single pass (non trapping) RF only mode with
the
applied RF amplitude set to pass the desired range of ion m/z values.
2. Segment 1002 is operated in single pass (non trapping) m/z selection mode.
Ion
mass to charge selection can be conducted with static single range ion m/z
selection or with repetitive scanning over a range of ion mass to charge
values at
the desired scan speed.. With resonant frequency excitation ejection mass to
charge
selection operation, multiple parent ion m/z values can be selected
simultaneously.
3. The relative DC offset potentials applied to the rods of segment 1002 and
quadrupole ion guides 1003 and 1004 are set to accelerate mass to charge
selected
id's through quadruole 1003 and into quadrupole 1004 without causing DC
acceleration CID ion fragmentation. Quadrupole 1004 is operated in resonant
frequency excitation CID ion fragmentation mode to fragment the parent ion m/z
value ions selected in segment 1002. The first generation fragment ions
produced
in quadrupole 1,004 pass into quadrupole ion guide 1005 with the appropriate
relative DC offset potentials set to optimally pass ions through quadrupole
ion

57


CA 02626383 2008-04-24

guide 1005 with maximum m/z selcction resolution. The background pressure in
the entrance end of quadrupole assembly 1004 is maintained sufficiently high
to
damp ion trajectories after fragmentation to achieve an ion beam clamped
radially
to centerline 1011 with low energy spread. In this manner, the kinetic energy
of
ions entering segment 1005 is determined by the relative DC offset potentials
applied to the rods of quadrupole assemblies 1004 and 1005.
4. Quadrupole ion guide 1005 is operated in mass to charge selection mode. The
ion
mass to charge value selection range may be fixed in some triple quadrupole
MS/MS applications or scanned as is required in other applications. The ion
mass
to charge selection scanning ramps of segment 1002 quadrupole 1005 can be
synchronized to perform neutral loss scans or monitoring of selected
fragmentation
events.
5. Ions passing from quadrupole ion guide 1005 through lens 1006 are
accelerated
into conversion dynode 1007. The resulting secondary electrons and photons are
detected with electron or photomultiplier 1024. Alternatively, ions can be
accelerated directly into electron multiplier 1024 and detected.

In the preferred embodiment with common RF frequency and phase applied to all
four
quadrupole assemblies, ions can be transferred efficiently from quadrupole ion
guide 1004 to
quadrupole 1005 with low kinetic energy to achieve higher resolution mass to
charge
selection scanning in quadrupole 1005. Ions can be temporarily trapped in
quadrupole ion
guides 1008, 1003 and 1004 to increase the ion resident time. Increased ion
resident time
exposes ions to an increased number of RF cycles leading to improved ion mass
to charge
selection resolution or more efficient resonant frequency excitation CID ion
fragmentation.
Mass to charge selection scan speeds can be matched to the ion trapping and
release rates, for
example with discrete m/z value scan steps, to improve MS/MS" performance. An
electrostatic lens can be configured in junction 1021 between quadrupole
assemblies 1004
and 1005. Said electrostatic lens would serve to decouple any rapidly changing
RF and +/-
DC potentials applied to the rods of quadrupole 1005 during mass to charge
scanning from
effecting the potentials applied to the rods of quadrupole assembly 1004. An
added
electrostatic lens would also reduce any fringing field effects in junction
1021 allowing
different RF frequency, phase and amplitude potentials to be applied to the
rods of
quadrupoles 1004 and 1005. If a detector is used that can operate in a higher
background
pressure, the entire multiple quadrupole ion guide assembly 1008 can be
configured in a
single 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 vacuum pumping stage eliminates any size constraint on the internal
diameter to
minimize neutral gas conductance between multiple vacuum pumping stages.
Alternatively,
multiple quadruole ion guide assembly 1008 can also be configured to extend
into first
vacuum stage 1015 in a two or three vacuum stage system: Additional
alternative
embodiments for triple quadrupole like mass analyzers configured with a
multiple quadrupole
ion guide assemblies with at least one quadrupole ion guide operated in mass
to charge
selection mode in a higher pressure vacuum region are diagrammed in Figures 15
through 17.
Figure 15 is a diagram of an alternative embodiment of the invention in which
dual
quadrupole ion guide assembly 1110 is configured with an additional quadrupole
ion guide
assembly 1104 configured in a low background pressure vacuum stage 1117. The

58


CA 02626383 2008-04-24

configuration of quadrupole assembly 1104 in the triple quadrupole mass
analyzer
embodiment shown in Figure 15 is a variation of the embodiment shown in Figure
14. In the
embodiment of the invention diagrammed in Figure 15 quadrupole 1104 may be
configured
with rods having a different cross section than the cross section geometry and
dimensions of
the rod assembly of multiple quadrupole assembly 11 10. Multiple quadrupole
assembly 1110
comprises two segment quadrupole 1108 and quadupoie assembly 1103. Segments
1101 and
1102 can be operated in mass to charge selection mode with CID fragmentation
of ions in
quadrupole assembly 1003 operated in RF only mode. Segments 1 101 and 1102 and
the
entrance end of quadrupole ion guide 1.103 are configured in higher background
pressure
vacuum pumping stage 1116. Electrostatic lens 1105 is configured in junction
1118 between
quadrupole 1103 and quadrupole 1104. Lens 1103 minimizes the effects of
fringing fields in
junction 1118 created by different RF frequency, phase and amplitude and
different +/-DC
applied to the rods or adjacent quadrupole 1103 and 1104 during operation.
Electrostatic lens
also serves to minimize any capacitive coupling of RF or resonant waveform
potentials
between quadrupole assemblies 1103 and 1104. Alternatively, single
electrostatic lens 1105
can be configured as a plurality of electrostatic lenses to enable focusing or
multiple stepped
acceleration of ions transferred between quadrupole ion guides 1103 and 1104.
Whether or
not multipole ion guide 1104 has a different geometric cross section compared
to the cross
section dimensions of multiple quadruple assembly 1108, quadruole 1 104 can be
operated
with a different RF frequency than that applied to quadrupole ion guide 1103.
Full triple
quadrupole MS and MS/MS function analysis can be achieved with the embodiment
of the
invention diagrammed in Figure 15 using techniques and methods described
previously.

An alternative embodiment of the invention is diagrammed in Figure 16 in which
multiple
quadrupole ion guide 1208 is configured in higher vacuum pressure stage 1210
and extends
into the rod volume described by separate multipole ion guide 1204. Quadrupole
ion guide
assembly 1203 extends into exit lens 1205 through which ions can be
efficiently transferred,
even at low kinetic energies, into multipole ion guide 1204. Full triple
quadrupole MS and
MS/MS functions can be achieved by operating segments 1201, 1202, and
quadrupole 1203
and quadrupole 1204 in scanning and static ion m/z selection and ion CID
fragmentation
modes as described in the above sections.

An alternative embodiment of the invention is shown in Figure 17 in which an
additional
multipole ion guide collision cell 1312 has been added to a three vacuum
pumping stage
multiple quadrupole ion guide mass analyzer. Dual quadrupole or three segment
quadrupole
ion guide assembly 1308 is configured in higher vacuum pressure vacuum stage
1314
extending into lower pressure vacuum stage 1315. Mass to charge selected
and/or fragment
ions are transferred from quadrupole ion guide 1309 into multipole ion guide
1310 which is
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 diagrammed in the hybrid API
quadrupole
TOF hybrid embodiments shown in Figures 10 or 11, collision or reactive gas
can be
introduced ii to region 1312 that has a different composition than the
background gas
compositionin vacuum stage 1314. 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 17 operating with mass to ion charge selection in segment 1301,
quadrupole ion guide
1309 and and 1304 and DC acceleration or resonant frequency excitation CID ion

59


CA 02626383 2008-04-24

fragmentation in segment 1302 and multipole ion guide 1310. When MS only
functions are
required for a given mass analyzer operation, a simpler embodiment of the
invention can be
configured to reduce instrument cost, size and complexity.

In one aspect of the invention at least a portion of a segmented or non
segmented quadrupole
ion guide is configured in a higher pressure vacuum stage where multiple
collisions with ions
and background neutral gas molecules occur. Figure 1.8 shows a high pressure
non-
segmented quadrupole multipole ion guide or mass analyzer 1400 that extends
continuously
from second vacuum pumping stage 1401 where the background pressure is
maintained
greater than 1x10 4 ton into third vacuum stage 1402 where detector 1403 is
located. The
quadrupole ion guide assembly 1400 diagrammed in Figure 18 comprises four
parallel; p"bles
or rods equally spaced around common centerline 1404. In an ideal quadrupole
mass
analyzer each rod cross section would have a hyperbolic shape 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 13. The same RF and +/- DC potentials are
applied to
opposite rods 104, 106 and 105, 107 respectively for most quadrupole operating
modes.
Adjacent rods have the same RF and DC amplitude but opposite polarity. In
addition, a
common DC offset can be applied to all rods 104, 105, 106, and 107. Multiple
frequency
resonant waveforms may be applied as a dipole to opposite rods or a more
complex resonant
waveform may be inductively or capacitively added to all four rods.

In the embodiment of the invention diagrammed in Figure 18, non-segmented
quadrupole ion
guide 1400 analyzer begins in pumping stage two 1401 where the pressure is
maintained
sufficiently high where ions traversing the length of multipole ion guide 1400
will encounter
collisions with neutral background gas molecules. Quadrupole ion guide 1400
can be
operated to conduct ion mass to charge selection by applying RF, +/- DC or
resonant
frequency excitation ion ejection waveforms with or without RF amplitude
modulation as
describe above. Ion mass to charge selection scanning can be performed by
conventional RF
and +/- DC voltage amplitude scanning or by stepping RF, +/- DC and resonant
frequency
waveform notch frequencies over the appropriate ranges to mass analyzer a
desired mass to
charge range or by a combination of these methods. In m/z analysis or m/z
selection
operating mode, ion collisions with the background gas slow clown the selected
ion m/z
trajectories in the radial and axial directions as the ions traverse
quadrupole ion guide 1400
length in single pass or ion trapping and release mode. Ions spending
increased time in
quadrupole ion guide 1400 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 the API MS analyzer diagranuned in
Figure 18 allows
the configuration of smaller more compact mass analyzer instruments systems
with reduced
vacuum pumping speed requirements. A smaller quadrupole ion guide size 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 operating at
background pressure
maintained sufficiently to avoid or minimize ion collisions with neutral
background gas.
Atmospheric Pressure Chemical Ionization (APCI) source 1405 can be configured
and
operated with solvent delivered to APCI nebulizer 1417 tip 1406 at flow rates
ranging from



CA 02626383 2008-04-24

below 500 nl/min to above 2 ml/min. The API MS embodiment diagrammed in Figure
18 can
be reconfigured with any of the following alternative sources but is not
limited to
Electrospray, Inductively Coupled Plasma, Glow Discharge sources, multiple
probes
mounted one APl source, or combinations of different probes configured one API
source,
Sample bearing solution can be introduced into APCI source 1405 with pressure
or positive
displacement 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 diagrammed in Figure 18 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 remain at ground potential during operation. To produce
negative ions,
the polarity of the electrodes listed above 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 operated 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-
ion charge exchange reactions. Sample solution is introduced through
connecting tube 1420
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 1421 is configured with a droplet separator
ball. Separator
ball 1424- removes larger droplets from the sprays produced by the nebulizer
inlet probes to
prevent them from entering vaporizer 1418. Separator ball 1424 can be removea
when lower
solution flow rates are introduced to improve sensitivity. The liquid droplets
are evaporated
in vaporizer 1418 forming a vapor prior to entering 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 14-11, 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 n,pedle 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 141.6. 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 may be useful for additional drying or to
elevate ion internal

61


CA 02626383 2008-04-24

energy to aid in ion fragmentation. A portion of the ions entering 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 through vacuum partition 1428 carried along by the neutral background
grs. The
neutral background gas forms a supersonic jet as it expands into vacuum from
exit orifice
1429 and accelerates the entrained ions through multiple collisions during the
expansion. 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 10 l torr depending on the skimmer orifice 1432 size and the
pumping speed
employed in vacuum stage two 1401 through pump port 1433. 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 API/MS instrument can be reduced if
a minimum
number of 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. Ions are delivered to third
vacuum pumping
stage 1402 through quadrupole ion guide 1400 which pass through vacuum
partition 1434.
Vacuum stage 1402 evacuated through pumping port 1435. Ions exiting quadruole
ion guide
1400 pass through exit lens 1436 which focuses the ions into the region
between lens 1437
and detector 1403. Lens 1437 can be operated as a conversion dynode or a
repeller plate
either attracting ions or repelling them into detector 1403. Quadrupole ion
guide can be
operated in single pass or ion trap and release mode during ion mass to charge
scanning mode
or single or multiple selected ion monitoring operating modes. Selected mass
to charge value
ion fragmentation operation can be conducted using resonant frequency waveform
excitation
CID methods as described above.

An alternative embodiment of the invention is diagrammed in Figure 19.=
Segmented or
multiple quadrupole ion guide assembly 1500 is configured in a three stage
vacuum system
with vacuum stages 1514, 1501 and 1502. Three segment quadrupole ion guide
assembly
1500 extends continuously from higher background pressure second vacuum
pumping stage
1501 into lower background pressure vacuum stage 1502. With the appropriate
individual or
shared RF, +/-DC or resonant frequency excitation waveform power supplies
applying
potentials to the rods of segments or independent quadrupoles 1503, 1504 'and
1505, a range
of MS or MS/MS functions can be conducted using multiple quadrupole assembly
1500.
Continuous ion beam MS/MS experiments can be conducted using the following
operating
conditions;
1. Quadrupole 1503 is operated in single value or scanning ion mass to charge
selection mode, depending on the analytical application, using methods
described
above.
2. Quadrupole 1504 is operated in RF only mode. Mass to charge selected parent
ions are DC accelerated from quadrupole 1503 into quadrupole 1504. The
appropriate relative DC offset potentials are applied to the rods of
quadrupoles
1503 and 1504 so that ions are accelerated across junction 1507 with
sufficient
velocity to cause DC acceleration CID ion fragmention. Alternatively or in
combination, resonant excitation frequencies can be applied to the rods of

62


CA 02626383 2008-04-24

quadrupole 1504 to cause CID ion fragmentation of parent and/or fragment ions
in
quadrupole 1504.
3. Fragment ions are transferred across junction 1508 into quadrupole 1505
without
fragmentation.
4. Quadrupole 1505 is operated in single value mass to charge scanning mass to
charge selection mode, depending on the analytical application. The ion mass
to
charge selection scanning ramps of quadruoles 1503 and 1505 can be
synchronized
to perform neutral loss scans or monitoring of selected fragmentation events.
5. Ions passing from quadrupole ion guide 1505 through lens 1517 are
accelerated
into conversion dynode 1518. The resulting secondary electrons and photons are
detected with electron or photomultiplier 1.519. Alternatively, ions can be
accelerated directly into electron multiplier 1519 and detected.

Electrostatic lenses can be added in junction 1507 isolating quadrupole ion
guides s 1503 and
1504 and in junction 1508 isolating qudrupole ion guides 1504 and 1505. Said
electrostatic
lenses would serve to decouple any rapidly changing RF and +/- DC potentials
applied to the
rods of quadrupoles 1503 and 1505 during mass to charge scanning from
effecting the
potentials applied to the rods of quadrupole assembly 1504. The added
electrostatic
isolations lenses would also reduce any fringing field effects for ions
traversing junctions
1507 and/or 1508 allowing different RF frequency, phase and amplitude
potentials to be
applied to the rods of quadrupoles 1503, 1504 and 1505 of multiple quadrupole
assembly
1500. The triple quadrupole mass analyzer as diagrammed in Figure 19 is
configured with a
medium pressure glow discharge ion source comprising electrodes 1511 and 1512,
sample
gas inlet 1510 and pumping port 1514. A portion of the ions produced in the
glow discharge
source pass through skimmer 1513 and into multiple quadrupole mass analyzer
assembly
1500. Alternatively, triple quadrupole 1500 as diagrammed in Figure 19 can be
configured
with Electrospray and APCI atmospheric pressure ion sources with the glow
discharge source
vacuum stage serving as the first vacuum stage of a three vacuum stage
instrument.

Multiple quadrupole ion guide assembly 1500 is reconfigured in a single vacuum
pumping
stage in an alternative embodiment of the invention as diagrammed in Figure
21. Individual
quadrupole assemblies 1715, 1717 and 1719 are configured along a common
centerline in
higher background pressure vacuum pumping stage 1702. The triple quadrupole
mass
analyzer embodiment as diagrammed in Figure 21 is configured in a three vacuum
pumping
stage system with vacuum stages 1701, 1702 and 1703 evacuated through vacuum
pumping
ports 1711, 1712 and 1713 respectively. Exit lens 1704 configured as part of
but electrically
insulated from vacuum partition 1705, minimizes the neutral gas conductance
into third
vacuum stage 1703 wherein conversion dynode and electron multiplier detector
1706 are
configured. This allows the maintenance of lower background pressure vacuum in
vacuum
stage 1703 with smaller, reduced vacuum pumping speed and lower cost vacuum
pumps.
Ions entering triple quadrupole assembly 1700 through the orifice in skimmer
1709
electrically insulated from vacuum partition 1710 can undergo MS or MS/MS
analysis using
operating methods as described above for triple quadrupole assembly 1500
diagrammed in
Figure 19. Alternatively, as described above for multiple quadrupole assembly
1500,
electrostatic lenses can be configured in junctions 1716 and 1718 to isolate
quadrupoles 1715
and 1719 from quadrupole 1717. DC voltages can be switched to said added
electrostatic
lenses configured in junctions 1716 and 1718 to allow independent trapping and
release of
ions from quadrupoles 1715, 1717 and 1719 for specific analytical
applications. Multiple
resonant frequency ejection and excitation waveforms can be applied to the
rods of

63


CA 02626383 2008-04-24

quadrupoles 1715, 1717 and/or 1.719 to achieve quasi MS/MS" mass analysis, as
described in
an earlier section. For example, to conduct a quasi MS/MS'. mass analysis, a
first mass
spectrum is acquired using MS/MS operating mode with parent ion mass to charge
selection
conducted in quadrupole 1715. Parent ions are fragmented in quadrupole 1717
using single
mass range resonant frequency excitation CID ion fragmentation operation or DC
acceleration
CID ion fragmentation or a combination of both and mass to charge scanning i,t
conducted
with quadrupole 1719. A second mass spectrum is acquired with two mass range
resonant
frequency excitation CID ion fragmentation conducted in quadrupole 1717 where
second
generation ions are produced by simultaneously conducting parent and first
generation ion
CID fragmentation. Alternatively, single mass range resonant frequency
excitation CID
-Jon
fragmentation of first generation fragment ions combined with DC acceleration
CID
fragmentation of parent ions is conducted in quadrupole 1717 while acquiring
the second
mass spectrum by scanning quadrupole 1719. The first acquired mass spectrum is
then
subtracted from the second acquired mass spectrum to produce a quasi MS/MS3
mass
spectrum of second generation fragment ions.

API MS analyzer cost and complexity can be further reduced by configuring the
ion detectors
in higher pressure vacuum stages according to the invention. Multichannel
plate detectors are
available that can operate in pressures higher than 1x10-4 torr due to the
configuration of thin
plates comprising small diameter and short length channels. In said
multichannel plate
detectors, the cascading election path resulting from an ion impact in a
detector channel is
shorter than the background pressure mean free path, minimizing electron
scattering and loss
of signal. Single segment quadrupole ion guide 1800 is configured in a two
vacuum pumping
stage Electrospray mass analyzer configured according to the invention as
diagrammed in
Figure 22. First vacuum stage 1801 is evacuated through pumping port 1811
typically backed
by a rotary pump. Second vacuum stage 1802 is evacuated through pumping port
1812 and
can be backed by a small turbomolecular pump or even a rotary vacuum pump.
Quadrupole
ion guide 1800 is configured in higher pressure vacuum stage 1802 with-exit
lens 1804 and
multichannel plate detector 1806. Ions passing through the orifice in skimmer
1809 are mass
to charge analyzed in quadrupole 1800 using single value or selected ion
monitoring ion mass
to charge selection operation or or scanning mass to charge selection
operation as described
above. The embodiment of the invention as diagrammed in Figure 22 can be
configured as a
small, compact and low cost instrument while retaining full MS analysis
capability. MS/MS
and even quasi MS/MSn mass analysis functions can be performed using the
triple
quadrupole embodiment of the invention as diagrammed in Figure 23.

Individual quadrupole assemblies 1913, 1915 and 1917 are configured along a
comnnon
centerline in higher background pressure vacuum stage 1902. The Electrospray
MS analyzer
as diagrammed in Figure 23 is configured with two vacuum pumping stages 1901
and 1902
evacuated through vacuum ports 1911 and 1912 respectively. Triple quadrupole
ion guide
assembly 1900, exit lens 1904 and multichannel plate detector 1906 are
configured in second
vacuum pumping stage 1902. Using methods described for multiple quadruple ion
guides
configured as diagrammed in Figures 21 and 19, a range of MS/MS and quasi
MS/MSn mass
analysis functions can be conducted using the embodiment of the invention as
diagrammed in
Figure 23. Individual quadrupole assemblies 1913, 1915 and 1917 can be
operated in single
pass or ion trap and release mode by coordinating DC offset potentials applied
to adjacent
quadrupoles and skimmer 1909 and exit lens 1904. Alternatively electrostatic
lenses may be

64


CA 02626383 2008-04-24

configured in junctions 1914 and 1917 between quadrupoles 1913 and 1915 and
quadrupoles
1915 and 1917 respectively allowing independent ion trapping and release
operation
independently in individual quadrupoles 1913, 1915, and 1917. The
configuration of
electrostatic lenses in junctions 1914 and 191.6 also allows the operation of
all three
quadrupoles with different RF frequency, phase and amplitude applied to the
rods of each
quadrupole during MS and MS/MS analysis. The embodiment of the invention as
diagrammed in Figure 23 allows the configuration of a small, compact and low
cost API
source triple quadrupole mass analyzer. A range of MS, MS/MS and quasi MS/MS
mass
analysis operations can be conducted using said API source triple quadrupole
mass analyzer
configured according to the invention.

Although the invention has been described in terms of specific preferred
embodiments, it will
be obvious and understood to one of ordinary skill in the art that various
modifications and
substitutions are included within the scope of the inventions as defined in
the appended
claims. In particular other types of mass analyzers including but not limited
to conventional
quadrupole, magnetic sector, Fourier Transform three dimensional ion traps and
Time Of
Flight mass analyzers can be configured with embodiments of the invention as
described
herein. Any type of ion source including but not limited to the atmospheric
pressure ion
sources described herein and the ion sources that produce ions in vacuum
listed in the above
description can also be interfaced with embodiments of the invention described
herein, and
in addition, according to US Patent No. 5,652,427 and other documents
referenced herein.

Representative Drawing
A single figure which represents the drawing illustrating the invention.
Administrative Status

For a clearer understanding of the status of the application/patent presented on this page, the site Disclaimer , as well as the definitions for Patent , Administrative Status , Maintenance Fee  and Payment History  should be consulted.

Administrative Status

Title Date
Forecasted Issue Date 2011-07-19
(22) Filed 1999-05-29
(41) Open to Public Inspection 1999-12-02
Examination Requested 2008-04-24
(45) Issued 2011-07-19
Expired 2019-05-29

Abandonment History

There is no abandonment history.

Payment History

Fee Type Anniversary Year Due Date Amount Paid Paid Date
Request for Examination $800.00 2008-04-24
Registration of a document - section 124 $100.00 2008-04-24
Application Fee $400.00 2008-04-24
Maintenance Fee - Application - New Act 2 2001-05-29 $100.00 2008-04-24
Maintenance Fee - Application - New Act 3 2002-05-29 $100.00 2008-04-24
Maintenance Fee - Application - New Act 4 2003-05-29 $100.00 2008-04-24
Maintenance Fee - Application - New Act 5 2004-05-31 $200.00 2008-04-24
Maintenance Fee - Application - New Act 6 2005-05-30 $200.00 2008-04-24
Maintenance Fee - Application - New Act 7 2006-05-29 $200.00 2008-04-24
Maintenance Fee - Application - New Act 8 2007-05-29 $200.00 2008-04-24
Maintenance Fee - Application - New Act 9 2008-05-29 $200.00 2008-04-24
Maintenance Fee - Application - New Act 10 2009-05-29 $250.00 2009-05-13
Registration of a document - section 124 $100.00 2010-02-23
Maintenance Fee - Application - New Act 11 2010-05-31 $250.00 2010-05-18
Final Fee $300.00 2011-03-22
Maintenance Fee - Application - New Act 12 2011-05-30 $250.00 2011-05-03
Maintenance Fee - Patent - New Act 13 2012-05-29 $250.00 2012-04-30
Maintenance Fee - Patent - New Act 14 2013-05-29 $250.00 2013-04-30
Maintenance Fee - Patent - New Act 15 2014-05-29 $450.00 2014-05-27
Maintenance Fee - Patent - New Act 16 2015-05-29 $450.00 2015-05-26
Maintenance Fee - Patent - New Act 17 2016-05-30 $450.00 2016-05-23
Maintenance Fee - Patent - New Act 18 2017-05-29 $450.00 2017-05-22
Maintenance Fee - Patent - New Act 19 2018-05-29 $450.00 2018-05-29
Owners on Record

Note: Records showing the ownership history in alphabetical order.

Current Owners on Record
PERKINELMER HEALTH SCIENCES, INC.
Past Owners on Record
ANALYTICA OF BRANFORD, INC.
ANDRIEN, BRUCE A., JR.
GULCICEK, EROL E.
WHITEHOUSE, CRAIG M.
Past Owners that do not appear in the "Owners on Record" listing will appear in other documentation within the application.
Documents

To view selected files, please enter reCAPTCHA code :



To view images, click a link in the Document Description column. To download the documents, select one or more checkboxes in the first column and then click the "Download Selected in PDF format (Zip Archive)" or the "Download Selected as Single PDF" button.

List of published and non-published patent-specific documents on the CPD .

If you have any difficulty accessing content, you can call the Client Service Centre at 1-866-997-1936 or send them an e-mail at CIPO Client Service Centre.


Document
Description 
Date
(yyyy-mm-dd) 
Number of pages   Size of Image (KB) 
Claims 2008-04-25 6 238
Abstract 2008-04-24 1 27
Description 2008-04-24 65 5,635
Claims 2008-04-24 3 167
Drawings 2008-04-24 22 396
Representative Drawing 2008-08-14 1 14
Cover Page 2008-08-25 2 59
Description 2011-01-04 67 5,689
Cover Page 2011-06-21 1 54
Correspondence 2008-05-06 1 39
Assignment 2008-04-24 4 113
Assignment 2010-02-23 7 258
Prosecution-Amendment 2008-04-24 8 276
Correspondence 2008-08-19 1 15
Fees 2009-05-13 1 39
Correspondence 2010-01-22 4 102
Correspondence 2010-02-08 1 14
Correspondence 2010-02-09 1 28
Correspondence 2010-06-15 4 139
Correspondence 2010-06-21 1 27
Prosecution-Amendment 2010-07-02 2 36
Prosecution-Amendment 2011-01-04 19 1,360
Correspondence 2011-03-22 2 61