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Patent 2487135 Summary

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(12) Patent: (11) CA 2487135
(54) English Title: FRAGMENTATION METHODS FOR MASS SPECTROMETRY
(54) French Title: PROCEDES DE FRAGMENTATION POUR SPECTROMETRIE DE MASSE
Status: Expired
Bibliographic Data
(51) International Patent Classification (IPC):
  • H01J 37/12 (2006.01)
  • G01N 1/00 (2006.01)
  • H01J 49/42 (2006.01)
(72) Inventors :
  • WHITEHOUSE, CRAIG M. (United States of America)
  • WELKIE, DAVID G. (United States of America)
  • GHOLAMREZA, JAVAHERY (United States of America)
  • COUSINS, LISA (United States of America)
  • RAKOV, SERGEY (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 LP
(74) Associate agent:
(45) Issued: 2009-01-27
(86) PCT Filing Date: 2003-05-30
(87) Open to Public Inspection: 2003-12-11
Examination requested: 2004-11-24
Availability of licence: N/A
(25) Language of filing: English

Patent Cooperation Treaty (PCT): Yes
(86) PCT Filing Number: PCT/US2003/017436
(87) International Publication Number: WO2003/102545
(85) National Entry: 2004-11-24

(30) Application Priority Data:
Application No. Country/Territory Date
60/385,113 United States of America 2002-05-31

Abstracts

English Abstract




A method and apparatus for ion fragmentation comprising an RF multipole
collision cell (3) where precursor ions are extracted from and transported
through RF multipole ion guide (24), said ions being formed by electron
capture reaction with low energy electrons generated in low energy electron
source (5).


French Abstract

L'invention concerne un appareil et des procédés qui permettent l'interaction d'électrons à faible énergie et de positrons ayant des ions d'échantillonnage qui facilitent la dissociation à capture d'électrons (ECD) et la dissociation à capture de positrons (PCD), respectivement, dans les structures de guidage d'ions multipôle. Il a été découvert récemment que la fragmentation d'ions protonés de plusieurs biomolécules par dissociation à capture d'électrons se produit le long de chemins de fragmentation auxquels d'autres procédés de dissociation n'ont pas accès. Ces chemins mènent à des informations de structure moléculaire qui ne sont pas si faciles à obtenir autrement. Cependant, de telles analyses ont été limitées aux spectromètres de masse à résonance cyclotronique ionique à haut champ et transformée de Fourrier (FTICR) onéreux. La mise en oeuvre de la dissociation de capture d'électrons (ECD) dans des structures de guidage d'ions multipôles utilisées couramment est problématique dû aux effets perturbateurs de champs RF dans ces dispositifs. L'appareil et les procédés décrits surmontent ces difficultés, et permettent d'exécuter la dissociation à capture d'électrons (et dissociation à capture de positrons) dans les guides d'ions multipôles, soit tout seuls, soit combinés aux procédés de fragmentation d'ions conventionnels. L'invention concerne donc l'exécution analytique améliorée et la fonctionnalité de spectromètres de masse qui utilisent des guides d'ions multipôles.

Claims

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



Claims:
1. An apparatus for fragmenting ions of sample substances, comprising:

(a) a first multipole ion guide comprising a first set of rods having a first
entrance
end and a first exit end;
(b) means for producing low-energy electrons;
(c) means for directing said low-energy electrons to a first region proximal
to said
first exit end such that the kinetic energies of said low-energy electrons are
less than about
eV in said first region; and,
(d) means for applying AC or DC voltages to said first set of rods.

2. An apparatus for fragmenting ions of sample substances, comprising:
(a) a first multipole ion guide comprising a first set of rods having a first
entrance
end and a first exit end;
(b) a first enclosure, wherein said first multipole ion guide is enclosed,
said first
enclosure having a first entrance aperture proximal to said first entrance
end, and a first
exit aperture proximal to said first exit end;
(c) means for producing low-energy electrons;
(d) means for directing said low-energy electrons to intersect ions within a
second
region proximal to said first exit aperture and external to said first
enclosure; and,
(e) means for applying AC or DC voltages to said first set of rods.

3. An apparatus for fragmenting ions of sample substances, comprising:
(a) a first multipole ion guide comprising a first set of rods having a first
entrance
end and a first exit end;
(b) a first enclosure, wherein said first multipole ion guide is enclosed,
said first
enclosure having a first entrance aperture proximal to said first entrance
end, said first
enclosure comprising an exit electrode proximal to said first exit end, said
exit electrode
having a first exit aperture;
(c) means for producing low-energy electrons;
(d) means for directing said low energy electrons to intersect ions within a
third
region proximal to said first exit aperture and external to said first
enclosure;

42



(e) means for applying AC or DC voltages to said first set of rods; and,
(f) means for applying a voltage to said exit electrode.

4. The apparatus of claim 1, further comprising:
(a) a second multipole ion guide comprising a second set of rods having a
second
entrance end and a second exit end, wherein said second entrance end is
proximal to said
first region, such that said first region is between said first exit end and
said second
entrance end; and,
(b) means for applying AC or DC voltages to said second set of rods.
5. The apparatus of claim 2, further comprising:
(a) a second multipole ion guide comprising a second set of rods having a
second
entrance end and a second exit end;
(b) a second enclosure, wherein said second multipole ion guide is enclosed,
said
second enclosure having a second entrance aperture, wherein said second
entrance
aperture is proximal to said second region outside said second enclosure, and
wherein said
entrance aperture is proximal to said second entrance end within said second
enclosure,
such that said second region is proximal to and between said first exit
aperture and said
second entrance aperture; and,
(c) means for applying AC or DC voltages to said second set of rods.
6. The apparatus of claim 3, further comprising:
(a) a second multipole ion guide comprising a second set of rods having a
second
entrance end and a second exit end;
(b) a second enclosure, wherein said second multipole ion guide is enclosed,
said
second enclosure comprising an entrance electrode proximal to said second
entrance end,
said entrance electrode having a second entrance aperture proximal to said
third region
outside said second enclosure, and wherein said entrance aperture is proximal
to said
second entrance end within said second enclosure, such that said third region
is proximal
to and between said first exit aperture and said second entrance aperture;
and,
(c) means for applying AC or DC voltages to said second set of rods; and,
(d) means for applying voltage to said entrance electrode.

43



7. An apparatus according to claim 2, 3, 5, or 6, wherein said first enclosure
further
comprises means for adjusting the gas pressure within said first enclosure.

8. An apparatus according to claim 5, or 6, wherein said second enclosure
further
comprises means for adjusting the gas pressure within said second enclosure.

9. An apparatus according to claim 1, 2, 3, 4, 5, or 6, wherein said first set
of rods
comprises a quadrupole.

10. An apparatus according to claim 1, 2, 3, 4, 5, or 6, wherein said first
set of rods
comprises a hexapole.

11. An apparatus according to claim 1, 2, 3, 4, 5, or 6, wherein said first
set of rods
comprises an octapole.

12. An apparatus according to claim 1, 2, 3, 4, 5, or 6, wherein said first
set of rods
comprises more than eight rods.

13. An apparatus according to claim 4, 5, or 6, wherein said second set of
rods
comprises a quadrupole.

14. An apparatus according to claim 4, 5, or 6, wherein said second set of
rods
comprises a hexapole.

15. An apparatus according to claim 4, 5, or 6, wherein said second set of
rods
comprises an octapole.

16. An apparatus according to claim 4, 5, or 6, wherein said second set of
rods
comprises more than eight rods.

17. An apparatus according to claim 1, 2, 3, 4, 5, or 6, wherein said means
for
producing electrons comprises a directly-heated filament.

44



18. An apparatus according to claim 1, 2, 3, 4, 5, or 6, wherein said means
for
producing electrons comprises an indirectly-heated cathode.

19. An apparatus according to claim 1, 2, 3, 4, 5, or 6, wherein said means
for
producing electrons comprises a negative electron affinity surface.

20. An apparatus according to claim 1, 2, 3, 4, 5, or 6, wherein said means
for
producing electrons comprises a multichannel plate.

21. An apparatus according to claim 1, 2, 3, 4, 5, or 6, wherein said means
for
producing electrons comprises an electron field-emission array.

22. An apparatus according to claim 1 or 4, wherein said means for directing
said low-
energy electrons to said first region comprises:
(a) electrodes for focusing and steering said low-energy electrons; and,
(b) means for applying voltages to said electrodes for focusing and steering
said
low-energy electrons.

23. An apparatus according to claim 2 or 5, wherein said means for directing
said low-
energy electrons to said second region comprises:
(a) electrodes for focusing and steering said low-energy electrons; and,
(b) means for applying voltages to said electrodes for focusing and steering
said
low-energy electrons.

24. An apparatus according to claim 3 or 6, wherein said means for directing
said low-
energy electrons to said third region comprises:
(a) electrodes for focusing and steering said low-energy electrons; and;
(b) means for applying voltages to said electrodes for focusing and steering
said
low-energy electrons.

25. An apparatus according to claim 1 or 4, wherein said means for directing
said low-
energy electrons to said first region comprises means for providing an
electron beam path
that is essentially free of electric fields.




26. An apparatus according to claim 2 or 5, wherein said means for directing
said low-
energy electrons to said second region comprises means for providing an
electron beam
path that is essentially free of electric fields.

27. An apparatus according to claim 3 or 6, wherein said means for directing
said low-
energy electrons to said third region comprises means for providing an
electron beam path
that is essentially free of electric fields.

28. An apparatus according to claim 1 or 4, wherein said means for directing
said low-
energy electrons to said first region comprises a magnetic field.

29. An apparatus according to claim 2 or 5, wherein said means for directing
said low-
energy electrons to said second region comprises a magnetic field.

30. An apparatus according to claim 3 or 6, wherein said means for directing
said low-
energy electrons to said third region comprises a magnetic field.

31. An apparatus according to claim 1 or 4, wherein said means for directing
said low-
energy electrons to said first region comprises:
(a) electrodes for focusing and steering said low-energy electrons;
(b) means for applying voltages to said electrodes for focusing and steering
said
low-energy electrons;
(c) means for providing an electron beam path that is essentially free of
electric
fields; and,
(d) a magnetic field.

32. An apparatus according to claim 2 or 5, wherein said means for directing
said low-
energy electrons to said second region comprises:
(a) electrodes for focusing and steering said low-energy electrons;
(b) means for applying voltages to said electrodes for focusing and steering
said
low-energy electrons;

46



(c) means for providing an electron beam path that is essentially free of
electric
fields; and,
(d) a magnetic field.

33. An apparatus according to claim 3 or 6, wherein said means for directing
said low-
energy electrons to said third region comprises:
(a) electrodes for focusing and steering said low-energy electrons;
(b) means for applying voltages to said electrodes for focusing and steering
said
low-energy electrons;
(c) means for providing an electron beam path that is essentially free of
electric
fields; and,
(d) a magnetic field.

34. An apparatus according to claim 31, wherein means for providing an
electron beam
path that is essentially free of electric fields comprises:
(a) a first shield electrode proximal to said first exit end, said first
shield electrode
having a first shield aperture for transmitting ions therethrough;
(b) a second shield electrode proximal to said second entrance end, said
second
shield electrode having a second shield aperture for transmitting ions
therethrough;
(c) means for applying a first shield electrode voltage to said first shield
electrode;
and,

(d) means for applying a second shield electrode voltage to said second shield

electrode;

wherein, said first shield electrode voltage is essentially the same as said
second
shield electrode voltage.

35. An apparatus according to claim 34, wherein said first shield aperture
further
comprises a first conductive grid.

36. An apparatus according to claim 32, wherein means for providing an
electron beam
path that is essentially free of electric fields comprises:
(a) a first shield electrode proximal to said first exit aperture, said first
shield
electrode having a first shield aperture for transmitting ions therethrough;

47



(b) a second shield electrode proximal to said second entrance aperture, said
second shield electrode having a second shield aperture for transmitting ions
therethrough;
(c) means for applying a first shield electrode voltage to said first shield
electrode;
and,
(d) means for applying a second shield electrode voltage to said second shield

electrode;
wherein said second region is located between said first shield aperture and
said
second shield aperture; and, wherein, said first shield electrode voltage is
essentially the
same as said second shield electrode voltage.

37. An apparatus according to claim 36, wherein said first shield aperture
further
comprises a first conductive grid.

38. An apparatus according to claim 36, wherein said second shield aperture
further
comprises a second conductive grid.

39. An apparatus according to claim 33, wherein means for providing an
electron beam
path that is essentially free of electric fields comprises:
(a) a first shield electrode proximal to said first exit aperture and outside
said first
enclosure, said first shield electrode having a first shield aperture for
transmitting ions
therethrough;
(b) a second shield electrode proximal to said second entrance aperture and
outside
said second enclusure, said second shield electrode having a second shield
aperture for
transmitting ions therethrough;
(c) means for applying a first shield electrode voltage to said first shield
electrode;
and,
(d) means for applying a second shield electrode voltage to said second shield

electrode;
wherein said third region is located between said first shield aperture and
said
second shield aperture; and, wherein, said first shield electrode voltage is
essentially the
same as said second shield electrode voltage.

48



40. An apparatus according to claim 38, wherein said first shield aperture
further
comprises a first conductive grid.

41. An apparatus according to claim 38, wherein said second shield aperture
further
comprises a second conductive grid.

49

Description

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



CA 02487135 2004-11-24
WO 03/102545 PCT/US03/17436
Title:
Fragmentation methods for mass spectrometry
Field of Invention
This invention relates to the field of mass spectrometry, and specifically to
the
application of electron-capture dissociation (ECD) or positron-capture
dissociation (PCD) within multipole ion guides of mass spectrometers to
facilitate the identification and structure of chemical species.

Background of the Invention:
Mass spectrometers are powerful tools for solving important analytical and
biological problems. For example, mass spectrometers can be used to
determine the molecular weight of an ion by measurement of its mass-to-
charge (m/z) ratio, while its structure may be elucidated by dissociation
methods and subsequent analysis of fragmentation patterns.

The most common useful ion sources for large molecules are atmospheric
pressure chemical ionization (APCI), matrix-assisted laser desorption
ionization (MALDI) and electrospray ionization (ESI) sources. In contrast to
other types of ion sources, such as electron ionization or inductively-coupled
plasma sources, the ionization processes used in MALDI and ESI sources
may be characterized as gentle, in that molecules become charged without
inducing fragmentation, thereby preserving the identity of the sample
molecules. Such gentle ionization can be efficiently achieved with MALDI and
ESI even for relatively large biomolecules such as proteins, peptides, DNA,
RNA, and the like. This capability is in large part responsible for the
important
role that MALDI and ESI, coupled to mass spectrometers, have come to
assume in the advancement of research and development in biotechnology
fields.

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In general, MALDI generates primarily singly charged ions (z=1), while ESI
efficiently produces primarily multiple-charged ions (z>1) (Fenn, et al,
Science
246, 64 (1989)). These different charge-state distributions lead to different
advantages and disadvantages of the two ionization methods. For example,
the analysis of mixtures of components is often more straightforward with
MALDI due to the presence of only single-charge states, versus the more
complicated multiple-charge-state distributions produced by ESI. On the
other hand, specific structural information can be very difficult to obtain
with
MALDI for relatively large molecules (e.g., with mass > 20,000 Da), because
fragmentation methods commonly used to elucidate structure tend to be
relatively inefficient for ions with large m/z values. Detailed information on
the
structure of a molecule is often at least as analytically useful, if not more
so,
than knowledge of the mass of the molecule.

However, even a very large molecule may be analyzed in conventional mass
spectrometers if the molecule can be ionized with multiple charges. For
example, if a protein of molecular weight 30,000 Da acquires 10 charges, its
m/z value is reduced to 3,000, which is readily measurable with essentially
all
commonly used mass spectrometers. The multiple-charge ionization of large
molecules is one prominent capability of the ESI process, which has resulted
in rapid growth of the popularity of ESI sources for the creation of multiple-
charge ions of a variety of biomolecules, including small organic molecules,
peptides, proteins, and other molecular complexes such as DNA derivatives.
Mass spectrometer types that have been configured with ESI sources include
Fourier transform ion-cyclotron resonance (FTICR), magnetic-sector, 2-
dimensional and 3-dimensional quadrupole ion-traps, quadrupole mass filters,
and hybrid instruments consisting of various combinations of these types, as
well as others.

An important application of ESI combined with mass spectrometry is the
structural identification of peptides, proteins, and other biomolecules with
amino-acid residues. Structural analysis is often performed with a so-called
tandem mass spectrometer using a technique referred to as MS/MS analysis.
Essentially, a precursor ion of interest is m/z-selected in a first stage of a

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tandem mass spectrometer, and the selected ion is then fragmented in a
second stage to produce product ions. These product ions are then mlz-
analyzed in a third stage, resulting in a product-ion mass spectrum that
represents a fragmentation pattern of the selected precursor ion. Such
tandem instruments may be configured so that the separate stages are either
sequential in space, such as multiple quadrupole mass filters arranged co-
axially in series, or sequential in time, as with a single three-dimensional
ion
trap.

Deductions about the molecular structure of the precursor ion may then be
made from an analysis of the fragmentation pattern observed in the product-
ion spectrum. For example, the sequence structure of a protein may be (at
least partly) determined from the measured m/z values of the various detected
fragment ions, by deducing the sequence of amino acid residues that would
have had to exist in the protein precursor ion to produce the observed
fragment ions. The ideal situation in this case would be the cleavage of the
amine backbone bonds on either side of each amino acid residue in a protein
or peptide chain.

The success of this approach depends fundamentally on the extent to which
dissociation occurs at such strategically advantageous locations in the
structure of the precursor ion. Whether dissociation occurs by cleavage of
any particular chemical bond in a precursor ion depends on many factors,
including: the nature of the chemical bond; the amount of energy absorbed by
the precursor ion; the modes available in the precursor ion to dissipate
energy; and the mechanism by which energy is deposited. The various
mechanisms by which energy may be deposited in an ion have given rise to a
variety of fragmentation methods, such as collisionally activated dissociation
(CAD), in which energy is deposited in a precursor ion as a result of
collisions
with a target gas; and, infrared multi-photon dissociation (IRMPD) which
involves absorption of infrared photons by the precursor ions.

While distinctly different in approach, both CAD and IRMPD depend ultimately
on the excitation of vibrational and rotational states within the precursor
ion to
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cleave chemical bonds, and so the fragmentation patterns resulting from
either method naturally tend to be dominated by excitation of the lowest-
energy vibrational and/or rotational states. Consequently, cleavage at some
bond sites of a particular precursor ion is typically preferred over others
within
any particular ion. Given that only a limited amount of energy is available
for
`activation' of an ion, and that some energy may be dissipated by exciting
vibrational or rotational modes without bond cleavage, a limitation of CAD and
IRMPD is that the probability for dissociation of a precursor ion by cleavage
at
many of its bond sites may be insignificant relative to that of other, more
energetically-favored, sites. For example, for peptides, cleavage readily
occurs at the N-terminal side of a proline residue or the C-terminal side of
an
aspartic acid, while cleavage seldom occurs at di-sulfide bonds. The net
result is that the structural information provided by fragment ion spectra is
often insufficient to deduce a complete residue sequence.

For small peptide precursor ions, i.e., those consisting of typically less
than
10-15 amino acid residues, the dissipation of energy within an ion without
bond cleavage can be relatively inefficient due to the limited number of
bonds.
In this case, bond cleavage may occur with sufficient probability for most, if
not all, of the strategically important cleavage sites, resulting in a
relatively
comprehensive sequence analysis. In general, though, proteins, peptides,
peptide nucleic acids (PNAs), and other biomolecules can be substantially
larger than such small peptides, and, in fact, can frequently contain hundreds
of amino acid residues. Owing to the much greater ability of such large ions
to absorb and dissipate vibrational and rotational energy, significant
cleavage
with the CAD or IRMPD methods often occur only for the most energetically
favored cleavage sites, resulting in relatively sparse fragmentation spectra.
Consequently, the CAD or IRMPD approaches alone frequently do not
provide sufficient sequence information for a complete structural analysis to
be performed on many molecules.

An alternative approach to CAD or IRMPD was reported recently by Zubarev
et al., in J. Am. Chem. Soc. 120, 3265 (1998), where they teach that multiple-
charged ions dissociate differently upon capture of low-energy electrons than
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they do with CAD. In this process, called electron-capture dissociation
(ECD), low-energy electrons combine with low-energy, multiple-protonated
molecules in the gas phase. Unlike CAD and IRMPD, the energy for
fragmentation is derived from electronic state interactions rather than by
vibrational and/or rotational state excitations. Subsequent to the capture of
a
low-energy electron, a multiple-charged ion is believed to undergo a
structural
rearrangement, leading to structural instability and, ultimately,
fragmentation.
These processes are proposed to be sufficiently fast that competing
processes, such as energy redistribution, are less likely to occur than with
CAD or IRMPD, resulting in bond cleavage that is less dependent on bond
strength than with CAD or IRMPD. Consequently, the fragmentation patterns
generated by ECD exhibit a larger variety of different cleavage patterns than
those generated by CAD or IRMPD.

The advantages of ECD, either alone, or in combination with CAD, have been
amply demonstrated. For example, ECD has been found to cleave peptide
backbone amine bonds, (Ca -N bonds), which cleave infrequently with CAD,
and results in much greater peptide sequence coverage than with CAD.
Additionally di-sulfide bonds of larger proteins readily and selectively
fragment, unlike CAD. Consequently, for example, McLafferty et al., in
Science 284, 1289 (1999), report that, for the 76-residue ubiquitin (8.6 kDa),
data from one CAD and two ECD spectra provided complete sequence
information. Olsen et al., in Rapid Commun. Mass Spectrom., 15, 969 (2001),
report that the combination of CAD and ECD yields similarly powerful
complementary data for sequencing peptide nucleic acids (PNAs). Horn et
al., in Anal. Chem. 72, 4778 (2000) also teach that the combination of CAD
and ECD, whereby ions are subjected to ECD while colliding with background
gas, increases the efficiency of cleavage at least 3-fold for a smaller
protein
(17 kDa) and extends the usefulness of ECD to much larger proteins (>40
kDa). Therefore, it is evident from these and other reports that ECD often
yields nearly complete sequence mapping of small proteins (< 20 kDa) and, at
the least, has been demonstrated to be a powerful complement to
conventional CAD methods, even for larger ions.



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Thus far, however, the success of the ECD technique has only been reported
in conjunction with FTICR mass spectrometers. In an ICR cell, precursor ions
are stored under the influence of magnetic and electric fields; the ions
oscillate at cyclotron frequencies corresponding to their m/z values, and the
Fourier transform of the repetitive signal that such m/z-dependent
oscillations
produce results in the measured m/z spectrum. Although the incorporation of
ECD fragmentation into FTICR instruments has been relatively successful, it
has not been without challenges. The first requirement for reasonable
fragmentation efficiency by ECD is the production of a large flux of low-
energy
electrons in the energy range of <0.2 to about 5 eV. The significance of this
requirement was demonstrated recently by Hakansson et al., in Anal. Chem.,
73, 3605 (2001), who reported two to three orders of magnitude increase in
sensitivity by optimizing the design and operation of their electron source,
and
subsequently by Tysbin et al., in Rapid Commun. Mass Spectrom. 15, 1849
(2001) who demonstrated the potential for rapid analysis enabled by the use
of relative large indirectly heated dispenser type cathodes in the electron
source.

Apart from the production of a healthy flux of low-energy electrons, a second
critical requirement is to be able to transport low-energy electrons into the
mass spectrometer with good efficiency. A third critical requirement is to
retain low-energy electrons in the volume occupied by precursor ions long
enough to allow a significant number of interactions to take place between the
precursor ions and the low-energy electrons. The successful incorporation of
the ECD technique in FTICR instruments is directly related to the relative
ease with which low-energy electrons can be readily transported and retained,
along with precursor ions, due to the stability of the electrons' motion in
the
strong magnetic fields of the ICR cell.

FTICR instruments, however, are currently relatively expensive, and require
specialized skill to operate and maintain. Therefore, it would be of
substantial,
benefit to incorporate the ECD fragmentation technique into more economical,
commonly-used types of mass spectrometers, such as triple quadrupole mass

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spectrometers, quadrupole-time-of-flight mass spectrometers, two-
dimensional quadrupole ion traps, and other similar multipole ion guide-based
mass spectrometers. Unfortunately, in contrast to ICR cells of FTICR
instruments, multipole ion guide-based mass spectrometers typically utilize
only DC and AC (RF) electric fields, that is, without magnetic fields. (For
this
reason, such multipole ion guides are sometimes referred herein as 'RF
multipole ion guides', which is to be understood to encompass ion guides that
employ both DC and RF voltages, as well as RF-only voltages). Generally,
the stability of motion of a charged particle in such electric fields extends
only
over a limited range of particle m/z values. However, the m/z value of an
electron is typically a factor of at least five orders of magnitude less than
ions
with even the lowest m/z value of interest. Therefore, low-energy electrons
and precursor ions are hardly likely to be stable simultaneously within the
fields of an RF multipole ion guide, in contrast to the situation in an FTICR
instrument.

In addition, electrospray ionization readily produces negative ions as well as
protonated positive molecules, and most mass spectrometers have the
capacity to routinely analyze and detect both positive and negative ions. The
ECD method of fragmentation is not useful for negative ions, since the
Coulomb repulsion of same-polarity charge would preclude the close-range
interaction of electrons and negative ions. Nevertheless, a fragmentation
method similar to ECD would prove to be just as useful for structure analysis
of negative ions as ECD appears to be for positive ions. In fact, it is
expected
that the capture of positrons (electron anti-particles) by negative ions
follows a
mechanism similar to electron capture in reaction with positive ions. In
analogy to ECD, the fragmentation of ions due to capture of positrons may be
referred to as 'positron capture dissociation', or PCD. Positrons are stable
but relatively short-lived due to their strong reaction with matter. However,
McLuckey et al., in Rapid Commun. Mass Spectrom. 10, 269 (1996), has
reported that positron capture by organic molecules can occur, and, at
positron energy less than about 3 eV, extensive fragmentation of organic
molecules was observed. They also noted that the fragmentation efficiency
increased as the positron energy decreased, similar to trends observed with

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ECD fragmentation of positive ions, which seems to suggest that similar
mechanisms leading to fragmentation are involved. The apparatus
incorporated a Penning trap where close interaction between positrons and
organic molecules was achieved in the presence of a 1 T magnetic field over
the length of the trap. As with ECD, the incorporation of PCD into RF
multipole ion guide-based mass spectrometers would be of substantial benefit
for ion structure determination by MS/MS analysis, in particular, of negative
ions.

Despite the clear desireability of performing ECD and PCD within RF
multipole ion guide-based mass spectrometers, the means by which this may
be accomplished has not previously been available

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Summary of the Invention:

Accordingly, it is one object of the present invention to provide apparatus
and
methods that enable the fragmentation of ions by the processes of ECD (for
positive ions) and PCD (for negative ions) within RF multipole ion guide
structures.
It is another object of the present invention to provide apparatus and methods
that enable the fragmentation of ions within RF multipole ion guide structures
by the processes of ECD and PCD, simultaneous with, or alternately with,
other conventional fragmentation methods, such as CAD, within the same RF
multipole ion guide structure.

It is still another object of the present invention to provide apparatus and
methods that enable fragmentation of ions by ECD and PCD within a multiple
RF multipole ion guide configuration, wherein ECD and PCD take place in
regions between adjacent multipole ion guides.

It is still another object of the present invention to provide apparatus and
methods that enable fragmentation of ions by ECD and PCD within a multiple
RF multipole ion guide configuration, wherein ECD and PCD takes place in
regions between adjacent ion guides, while other fragmentation methods,
such as CAD, can be performed, either simultaneously, or alternately, within
one or more RF ion guides of the multiple RF multipole ion guide
configuration.

In most conventional mass spectrometers based on RF multipole ion guide
configurations, selection of a precursor ion for fragmentation is most
frequently performed with an RF quadrupole ion guide operated in the so-
called RF/DC mass filter mode. The selected precursor ions are usually
accelerated into a pressurized second multipole ion guide (typically an RF-
only multipole collision cell), where they fragment due to collisions with
target
gas molecules.

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The collision cell multipole can be a quadrupole, hexapole, octapole, etc.
essentially coaxial with the upstream m/z-resolving quadrupole. Typically the
rods are mounted in an enclosure in order to establish the desired target gas
pressure within the collision cell, while maintaining a low pressure in
surrounding regions. Two electrodes with apertures are positioned in the
entrance and the exit of the collision cell to restrict outflow of gas while
allowing ions to pass in and out of the cell.

A third m/z analyzer then measures the m/z spectrum of the resulting
fragment, or product, ions. When this third m/z analyzer is another RF/DC
mass filter, the overall configuration just described is referred to as
a`triple-
quadrupole' configuration. Alternatively, the third m/z analyzer may be a time-

of-flight mass spectrometer (TOF-MS), in which case, the overall configuration
is referred to as a 'QqTOF' configuration. Other types of m/z analyzers may
be used for m/z selection of precursor and product ions, as well.

Clearly, the ECD technique is best incorporated into such multiple ion guide
arrangements in the vicinity of the collision cell, that is, after the
precursor
ions have been selected for dissociation, and before the m/z analyzer that
will
measure the fragment ions. The challenges that need to be surmounted in
order to achieve effective and efficient ECD in a multipole ion guide include
the same ones that were discussed above in conjunction with the
implementation of ECD in an FTICR instrument. Specifically, the first
requirement is the production of a large flux of low-energy electrons in the
energy range of <0.2 to about 5 eV. A second requirement is to be able to
transport such low-energy electrons into the multipole ion guide, or
otherwise,
the region where ECD fragmentation is intended, with good efficiency'.
Alternatively, low-energy electrons may be produced in the intended vicinity
of
fragmentation. A third requirement is to retain low-energy electrons in the
volume occupied by precursor ions long enough to allow a significant number
of interactions to take place between the precursor ions and the low-energy
electrons. Various aspects and embodiments of the present invention that
specifically address each of these requirements will be described briefly
below.



CA 02487135 2007-12-06

A pressurized RF multipole ion guide provides an attractive environment for
efficient ECD
because ions are forced to move with low velocity due to collisional cooling
effects. Douglas,
et al., in U. S. Patent No. 4,963,736, teach that RF multipole ion guides
operating at elevated
pressures provide an effective means to achieve reduced ion kinetic energy.
Ion collisions
with the neutral background gas serve to reduce the radial and axial velocity
components of
the ion due to momentum changing collisions. As the ions lose most of
their.radial and axial
energy due to such collisions in the presence of the RF field, they tend to
coalesce near the
axis of the collision cell. The reduction of ion velocity in a pressurized
collision cell leads to
an increase in low-energy electron capture efficiency. The electron capture
efficiency is also
increased due to the electrostatic potential well created near the collision
cell axis by the
space charge of the coalesced ion population. The space charge well creates an
attractive
potential for the slow electrons and serves to draw them toward the higher
density ions.

The reaction efficiency can be further enhanced by electrostatic trapping in
an RF multipole
ion guide as taught by Whitehouse, et al., in U. S. Patent No. 6,011,259.
During electrostatic
trapping, an axial field gradient is applied that reverses the ion velocity
ions in the regions of
the exit and entrance of an RF multipole ion guide. Reactions are most
efficient when the
ions and electrons have very low relative velocity, which can occur in the
vicinity of velocity
reversal of the ions in the repulsive electric fields.

It is also possible to enhance the low energy flux of electrons on the axis of
the pressurized
RF multipole ion guide by use of a magnetic field coaxial with the ion guide
axis. Electrons
precess around magnetic field lines, which acts to retains electrons that
would otherwise have
been lost. An appropriately-shaped magnetic field can be applied to enhance
the density of
electrons near the axis, while having a negligible effect on the very slow
ions with little
velocity in both the radial and axial direction.

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Utilizing methods of electron reversal in electric fields can produce a high
flux
of low-energy electrons. Electrostatic focussing of the electron beam can be
arranged such that electrons undergo velocity reversal in the RF multipole ion
guide. At these points the electrons have near-zero energy. A preferred
configuration permits overlap in space of the low velocity ions with the near-
zero energy electrons. Methods that incorporate electron reversal for
efficient
low velocity electron/molecule reactions are described by Man, et al., in U.S.
Patent No. 5,670,378, and references therein.

There are numerous approaches to developing high fluxes of electrons, any of
which are included within the scope of the present invention. One approach
utilizes a heated filament and appropriate electron optics. Another approach,
as demonstrated by Zubarev, utilizes an indirectly heated cathode dispenser.
Dispenser cathodes are useful when low temperature, high current density
electron emission is desired, and typically are constructed from doped porous
tungsten metal with oxide coatings. Materials with wide band gaps, including
but not limited to magnesium oxide, silicon carbide, aluminum oxide, and
aluminum nitride, also are used for emission of electrons from surfaces. They
exhibit the property of negative electron affinity (NEA), whereby the vacuum
level of the material lies below the bottom of the conduction band. In this
case
no energy barrier prevents low-energy electrons from escaping into the
vacuum. Lasers of appropriate wavelength can also be used to induce
electron emission from surfaces.

Relatively fewer approaches are known that allow the production of positrons,
but these, as well as others, are considered to be within the scope of the
present invention. High intensity positron sources can be generated using an
particle accelerator, by colliding a high energy electron beam (100 MeV) with
a platinum or tungsten surface. When the electron beam impinges on the
target, it decelerates and generates highly energetic photons. These photons
interact with the electric field of the target nuclei and produces electron-
positron pairs. Then normal optics are used to accelerate positrons and reject
electrons. Low energy positron beams can be produced relatively
inexpensively using radioactive substances such as 22Na. 22 Na emits beta

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particles (with energy of 554 keV). A solution of 22NaCI is deposited on a
thin
layer of Kapton. The layer is encapsulated with tungsten, and reaction occurs
that produces positrons in a range of energies from 0.2 eV to 100 eV.
Conventional fragmentation methods are also provided within the scope of the
present invention, either simultaneously, or in series, with ECD, to achieve
complete, or nearly complete, sequence coverage for structural
characterization of large biomolecules. The present invention also includes a
method to introduce slow positrons for effective positron capture.

The invention, as described below, includes a number of embodiments. Each
embodiment comprises a source of electrons or positrons. The source of
electrons includes, but is not limited to, appropriate electron transfer
optics in
combination with: a heated filament; an indirectly heated cathode dispenser;
photosensitive materials in combination with a photon source; wide band-gap
materials in combination with applied voltages; a commercially obtained
electron gun; and any of the electron sources mentioned above. Each
embodiment also contains at least one multipole ion guide, with or without
electrostatic trapping. Each embodiment contains apparatus and methods for
the production of low-energy electrons, the introduction of the low-energy
electrons into a multipole RF ion guide configuration, and the sustained
interaction of low-energy electrons or positrons with positive or negative
ions,
respectively. A two-dimensional multipole ion guide may be comprised of a
set of 4 rods (quadrupole), 6 rods (hexapole), 8 rods (octapole) or greater
numbers of rods arranged symmetrically about a common axis. In some
cases it is preferable to fill the ion guide with background gas. In some
cases
it is preferable to use a quadrupole ion guide, for example, to yield a
narrower
beam of ions on axis, or as another example, to permit mass-to-charge
selection. In cases where a wider beam near axis is beneficial, a higher order
multipole may be used. In some cases it is preferable to trap the precursor
ion
in one or multiple collision cells by applying trapping potentials.

The embodiments of the invention can be interfaced to any kind of ion source,
including atmospheric pressure ion (API) sources or low pressure sources.

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API sources include but are not limited to Electrospray (ESI), Matrix-Assisted
Laser Desorption and Ionization (MALDI), Inductively Coupled Plasma (ICP)
and Atmospheric Pressure Chemical Ionization (APCI) sources. Ion sources
that operate in vacuum or partial vacuum include, but are 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). The
embodiments of the invention can be interfaced to continuous-flow single and
triple quadrupole ion guides, two-dimensional ion traps, three dimensional ion
traps, magnetic sector, FTICR, time-of-flight, and hybrid quadrupole-TOF
mass analyzers, or to any combination of these.

The embodiments described herein utilize the phenomenon of radial and axial
compression in a pressurized RF multipole collision cell. Ions that are
introduced into an RF multipole collision cell experience a dramatic reduction
in their velocity due to momentum changing collisions with the neutral
background gas in the RF field. As the ions lose most of their radial and
axial
velocity in the presence of the RF field, they converge to the centerline of
the
collision cell. The spatial focus of the ions creates an attractive potential
for
slow electrons and serves to draw them toward the higher density ions.

The embodiments described below also utilize the advantages of trapping the
ions in the collision cell. (Trapping is accomplished by providing repulsive
barriers at the exit and entrance). Trapping is utilized for a number of
reasons. First, the ions are given enough time to undergo a large number of
collisions, which is required in order to focus them near the centerline of
the
axis of the RF multipole collision cell, where the RF field is zero. Any
charged particle introduced in or very close to the zero field of the RF field
has
a stable trajectory, because they will not be influenced in any way by the
field.
Second, the electrons can be introduced into the RF multipole collision cell
in
such a way as to permit a focus along the centerline. The attractive forces of
the ions that are localized near the centerline further draw in the electrons.
Electrons that reside in close vicinity to the ions for a sufficient period of
time
undergo reaction. Third, electrostatic lenses can be arranged such that

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velocity reversal of both ions and electrons can be utilized in the trapping
field,
minimizing their relative velocity and enhancing the electron capture
efficiency. Fourth, it is preferable to control the ion-electron encounter
time.
The electron flux may be low and it may be necessary to irradiate the ions
with electrons for a period of time longer than a typical flight through a
pressurized ion guide. Fifth, it is preferable to control the time after the
ion-
electron encounter. Although the reaction time for electron capture is fast,
the
ion may need time to rearrange prior to fragmentation. Thus the yield of
fragments may depend on the excess time given to the fragmenting ion prior
to exiting the collision cell. Finally, trapping the ions is helpful because
it is
sometimes preferable to pulse the focussing optics. For example, it is
sometimes preferable to pulse the RF off temporarily to permit the electrons
to
enter an RF-free multipole collision cell. By first thermalizing the precursor
ions to the center of the cell, more time is required for precursor ions and
their
fragments to respond to the pulsed field.

One embodiment of the present invention includes the pulsed injection of
electrons onto the axis of a pressurized RF multipole collision cell. An
electron source is positioned behind an RF multipole collision cell, between
two lenses, and at an angle from the axis of the collision cell, typically
near 90
degrees. The electrons are pulsed onto the centerline of the RF multipole ion
guide, where the RF field is adjusted to be close to zero. The voltages on the
lenses are adjusted in such a way as to cause the electron to undergo velocity
reversal along the axis of the ion guide. This is accomplished by applying
appropriate DC or pulsed voltages within the electron source, on the RF
multipole electrodes, and on the entrance and exit lenses. Similarly the ions
are trapped within the RF multipole collision cell, and undergo velocity
reversal. Voltages are arranged to permit maximum overlap of the electron
and ion density.

An alternative configuration includes positioning an electron source on axis,
in
the region behind the RF multipole collision cell, in a volume between two
lenses, to enhance the number of electrons with velocity components that are
coaxial with the RF multipole collision cell.



CA 02487135 2004-11-24
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Another embodiment of the invention includes a weak magnetic field of
several milliTesla, along the axis of an RF multipole collision cell. The
magnetic field aids to compress the electron radial velocity, discouraging the
electrons from escaping the centerline.

Yet another embodiment includes the pulsing the RF field off and on at
regular intervals, to reduce electron scattering losses as the electrons are
injected into the RF multipole collision cell.

Yet another embodiment includes a magnetic field aligned radially with
respect to the axis of the RF multipole ion guide. Yet another embodiment
includes adjustment of the RF balance on the multipole ion guide or collision
cell.

Another embodiment of the invention comprises electron sources embedded
within the RF multipole collision cell or three-dimension trap to further
enhance the electron flux on axis.

Another embodiment of the invention comprises sequential collision cells and
injection of electrons in an essentially field-free region between the exit of
the
first collision cell and the entrance of the second collision cell.

Another embodiment of the invention, further enhancing the flux of low-energy
electrons, comprises the injection of an electron or positron beam in the
elongated space between one A pole and one B pole of a quadrupole rod set.
An alternative configuration of this embodiment comprises the injection of an
electron or positron beam in the elongated space between one + pole and one
- pole of a multipole rod set.

Another embodiment comprises collision cell rods with thin wires or meshed
conducting materials, positioning an electron source behind the meshes.
An'other embodiment utilizes a light source or a laser to induce electron

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emission from a photosensitive gas in the RF multipole collision cell. In one
configuration a laser beam is used as a light source, and the laser beam is
transmitted along the axis of the collision cell. In an alternative
configuration
the laser beam is transmitted orthogonal to the axis, through space between
the electrodes. In these configurations, the laser beam can be passed
through the cell in a multi-pass fashion to enhance the overlap of the
electrons, generated by ionization, with the precursor ions. '

Another embodiment comprises a light source or a laser to induce electron
emission from a photosensitive surface in the RF multipole collision cell. A
laser beam is aimed at the surface, preferably at an angle to permit multiple
passes. In an alternative configuration, the surface is positioned behind the
collision cell and the laser strikes the surface orthogonal to the axis of the
RF
multipole collision cell.

Another embodiment utilizes a fast ion beam source is used to eject electrons
from a surface.

Another embodiment comprises the injection of an ion beam into the multipole
volume and the simultaneous injection of an electron beam into the volume, at
some angle between 0 and 90 degrees.

Another embodiment comprises an orthogonal ion source positioned behind
the RF multipole collision cell, useful for ion-ion interactions. The ions are
turned and directed inward, to the center of the collision cell.

Another embodiment comprises an orthogonal ion source positioned in
between two RF multipole collision cells, useful for ion-ion interactions in a
continuous flow device. The ions are produced and injected orthogonal to the
axis, and undergo collision with the precursor ion beam in a cross-beam
fashion.

The invention involves the utilization of a pressurized RF multipole ion
guide.
The pressure within the ion guide also impacts the yield of electron capture.
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The yield depends on the specific conditions employed, including but not
limited to the precursor ion to be fragmented, the required electron flux, and
whether CAD is desired to occur simultaneously. Therefore, in the inventions
described below, the pressure can vary over the range such that the number
of ion-neutral collisions varies from 1 to >50.

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Brief Description of the Figures

Figure 1A illustrates an overview of a preferred embodiment, whereby a low-
energy electron beam is produced orthogonal to the axis of a, RF multiple
ion guide collision cell and injected inward.

Figure 1 B illustrates the four rod structure of a RF quadrupole ion guide
collision cell.

Figure 1 C illustrates a solenoid encompassing an RF multipole collision cell,
providing an axial magnetic field.

Figure 1 D illustrates a preferred embodiment, whereby a low-energy electron
beam is produced behind but coaxial with a RF multiple ion guide collision
cell
and drawn inward.

Figure 2 illustrates in detail a preferred embodiment, comprising a tandem
mass spectrometer equipped with an ESI source, a resolving quadrupole, a
RF multipole collision cell designed for ECD and CAD, and a TOF mass
spectrometer.

Figure 3 illustrates an alternative configuration whereby ECD is performed in
an RF multipole ion guide positioned directly behind the RF multipole
collision
cell.

Figure 4 illustrates an RF multipole collision cell arrangement whereby an
electron source such as an indirectly heated cathode dispenser is embedded
in the exit and entrance lenses of an RF multipole collision cell.

Figure 5 illustrates two RF multipole collision cells separated by a field
free
region whereby a low-energy electron beam is produced orthogonal to the
axis and intersected with the ion beam at an angle of 90 degrees.

Figure 6A illustrates an RF multipole collision cell configuration wherein an
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electron beam source is mounted in the space above a pair of oppositely
charge rods, and electrons are injected through the elongated space between
the rods.

Figure 6B illustrates a top-down view of the electron source configuration.
Figure 6C illustrates the four-pole configuration of an RF quadrupole
collision
cell.

Figure 6D illustrates the electron beam source configuration of figure 4a with
four filaments.

Figure 6E illustrates the oscillating nature of the electric fields between
the
rods.

Figure 7A illustrates a multipole array constructed from mesh,wire, through
which electrons are injected.

Figure 7B illustrates from another angle a multipole array constructed from
mesh wire, through which electrons are injected.

Figure 8A illustrates the use of a laser, transmitted through an RF multipole
collision cell in a coaxial configuration, used to resonantly ionize molecules
to
generate slow electrons.
Figure 8B illustrates the use of a laser, transmitted through an RF multipole
collision cell in an orthogonal configuration, used to resonantly ionize
molecules to generate slow electrons.

Figure 8C is a representation of a mirror arrangement that can be used to aid
multi-passing.

Figure 9A illustrates a RF multipole collision cell arrangement whereby a
photosensitive material is embedded in an exit lens, and a laser is used to
induce electron emission.



CA 02487135 2004-11-24
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Figure 9B illustrates an enlarged view of the electron source.

Figure 9C illustrates a similar arrangement whereby the photosensitive
material is positioned at right angles to the ion axis.

Figure 10 illustrates an RF multipole collision cell arrangement whereby the
electron beam and primary ion beam are injected into the collision cell at a
relative angle greater than zero degrees and less than 90 degrees.

Figure 11A illustrates an ion source suitable for ion-ion interactions, and
injected inward toward the centerline of an single RF multipole collision
cell.
Figure 11 B illustrates an ion source suitable for continuous flow
applications,
whereby an ion beam is directed into the space between two RF multipole
collision cells, and intersects with a precursor beam in a cross-beam fashion.

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Detailed Description of the Invention and the Preferred Embodiments

One embodiment of the present invention is illustrated in FigurelA. Ions are
produced in atmospheric pressure ion (API) source 1, and are transported
through: various vacuum stages 6 of decreasing pressure; RF multipole ion
guide 7; RF/DC quadrupole mass filter 2; RF multipole collision cell 3
containing target gas 4; RF multipole ion guide 24; and TOF m/z analyzer 6.
Mass filter 2 is driven by RF/DC power supply 8. A set of ions of one
particular m/z is selected and transmitted into RF multipole collision cell 3,
typically held at an elevated pressure with respect to mass filter 2. RF
multipole collision cell 3 is powered by an RF power supply 9 that provides
oscillating voltage to the pairs of electrodes. For example, RF multipole
collision cell 3 may comprise a quadrupole rod set 10 containing four
cylindrical electrodes with rounded surfaces, illustrated in Figure 1 D. Rod
set
is electrically configured such that the electrodes positioned 180 degrees
are electrically connected and form an electrode pair, for example electrodes
13 form a pair and electrodes 14 form a pair. The two electrode pairs have
opposite RF polarity; for example, if negative voltage is applied to electrode
pair 13, then a voltage equal in magnitude but positive in polarity is applied
to
electrode pair 14. A common DC bias voltage 15 defines the reference
voltage for the RF waveforms applied to the rods. Capacitance device 16 is
used to adjust the RF balance on the electrodes, to optimize the RF field. The
DC potential on centerline 17 is determined by DC bias voltage 15. Ideally
the RF field on centerline 17 is zero.

RF multipole collision cell 3 is equipped with lens 11 at the collision cell
entrance and lens 12 at the collision cell exit. The voltage on lens 11 is
adjusted to transfer ions from mass analyzer 2 into the collision cell 3. At
time t=1, the voltage on lens 12 is set repulsive with respect to DC bias
voltage 15 to prevent the ions from exiting RF multipole collision cell 3
through
an orifice in lens 12. After a small fill time, most of the ions are nearly
thermalized to the room temperature of the collision gas 4. The pressurized
collision cell is held at a potential given by the DC bias voltage 15. The
pressure of collision gas 4 is variable from 0.01 mTorr to 200 mTorr. At time

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t=2, lens 11 is set repulsive with respect to the DC bias voltage15 such that
ions can neither enter nor exit the RF multipole collision cell 3. The ions
then
traverse the length of the RF multipole collision cell 3 in a multi-pass
fashion
and compress to a volume along centerline 17 where the RF field is zero. A
capacitance device 16 may be required to perfectly balance, or optimize, this
field. The DC field on centerline 17 is repulsive to the ions near lens 11 and
lens 12, yielding ion velocity reversal near points 18 and 19. The DC voltages
applied to lens 11 and lens 12 determine the location of the points. Lens 20
is
positioned behind lens 12, with gap 21 of sufficient width to contain electron
source 5 yet still prevent ion losses during ion extraction into RF multipole
ion
guide 24. Gap 21 may be held at a lower pressure than that of RF multipole
collision cell 3. Lens 20 is set to the same voltage as lens 12.

In one configuration, an electron source 5 of appropriate diameter is
positioned orthogonal but close to the centerline 17. Casing 22 surrounds the
electron source and is held at the same potential as lens 12 and lens 20. The
electron source may be of a type that includes, but is not limited to: a
heated
filament; an indirectly heated cathode dispenser; photosensitive materials in
combination with a photon source; a commercially obtained electron gun; and
so on. Preferably the electron source is configured to optimize the flux of
low-
energy electrons directed toward the centerline 17.

Electrons emitted from the electron source enter the field free region defined
by lens 12, lens 20 and enclosure 22. At some time t = 3 the electrons are
injected into the RF multipole collision cell 3 by pulsing the voltage on lens
20
to a value slightly more negative potential to that on lens 12. Electrons with
appropriate velocity are pulsed near centerline 17 of RF multipole collision
cell
3 and are focussed on centerline 17 by the voltage combination of lens 12
and DC bias voltage 15 on RF multipole collision cell 3. The value of the
voltage on lens 20 determines the extent to which the ions are accelerated
into the field, and can be chosen such that, at some turning point 23, the
field
on axis 17 becomes repulsive to the electrons. In regions near this point the
ECD yield is high. It is preferable to optimize turning point 23 such that it
overlaps with points near turning points 18 or 19 of the ion beam. Lens 12

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and lens 20 are constructed of mesh lenses or aperture lenses. Alternative
lens arrangements can be employed in this region to optimize the flux of low-
energy electrons in this region.

Lens 20 is pulsed at a high rate, typically 1-5 MHz. The voltages on lens 20
and lens 12, and the DC bias voltage 15, may be varied in a repetitive fashion
to permit overlap between the low energy electron beam and low energy ion
beam at different points along centerline 17. In some cases it may be
preferable to transmit a continuous beam of electrons onto centerline 17, for
example if the physical dimensions of the electron source are very small such
that the electrons are produced very close to centerline 17.

After some time t=4, reaction has taken place. Referring again to Figure 1A,
the voltage on lens 12, lens 20 and enclosure 22 are adjusted to release the
ions from RF multipole collision cell 3, where they are focused into RF
multipole ion guide 24 and mass analyzed by TOF-MS 5.

Another configuration of a preferred embodiment is illustrated in Figure 1 C,
and includes the addition of a magnetic field to enhance the axial capture of
slow electrons. Electrons are introduced by means of electron source 25.
Solenoid 26 of several thousand turns/m is wound around an RF multipole
collision cell enclosure 27 producing magnetic field 28. The material of
enclosure 27 is transparent to the magnetic field. A current of several amps
is
passed through the solenoid to generate magnetic field 28 on the order of 5-
milliTesla. The magnetic field is directed parallel to centerline 17 of the RF
multipole collision cell. The current applied depends on the radial dispersion
of the electron beam. Electrons with velocity perpendicular to the magnetic
field vector rotate about the magnetic field lines. Solenoid 26 is optimized
to
produce an electron orbit radius of less than 0.5 mm. Heat may be removed
from the solenoid by use of a small portion of cooling gas into inlet 29. The
ions are sufficiently slow that their orbit radius is very small, sub-micron,
and
are essentially not affected by the magnetic field.

Another mode of operating the preferred embodiment illustrated in Figure 1A
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includes the ability to rapidly turn the RF voltage off during the injection
of the
electrons. This prevents possible repulsion from the axis of electrons with
radial velocity components. For example, the RF voltage can be reduced to
zero in a relatively short time (commercially available RF power supplied are
available, e.g., from R.M. Jordan Co., that can reduce the RF voltage to
essentially zero in 1/2 of an RF cycle). While the RF voltage is off,
electrons
may enter the collision cell and react with ions. The RF voltage may then be
turned back on after several us, for a period of time permitting the fragments
to thermalize and be focused on centerline 17. This sequence may be
repeated for a number of cycles, after which the resulting fragment ions are
release for mass analysis.

Another configuration of the preferred embodiment above includes magnetic
field confinement in axial and radial directions. This configuration also
includes the ability to inject electrons into RF multipole collision cell 3
prior to
injecting the ions. The RF voltage on the RF multipole collision cell 3 is
held
off during the injection of electrons. During this time the electrons are
compressed axially by the magnetic field in three dimensions. After a
sufficient fill time of electrons, the ions are then injected into RF
multipole
collision cell 3 and the RF voltage is slowly ramped on to provide confinement
for the precursor and fragment ions.

Figure 1 D illustrates yet another configuration of the preferred embodiment
above, whereby electron source 30 is positioned close to lens 20 behind lens
12. A spray of electrons is released from electron source 30 and voltages are
arranged such that the electrons are focused on centerline 17 and undergo
velocity reversal near turning point 23.

A detailed illustration of the preferred embodiment of Figure 1 is illustrated
in
Figure 2. Referring to Figure 2, liquid sample is introduced into ES probe 31
using a liquid delivery system, for example a separation system such as liquid
chromatography. The ES source 32 is operated by applying potentials to
cylindrical electrode 33, endplate electrode 34 and capillary entrance
electrode 35. Counter current drying gas 36 is directed to flow through heater



CA 02487135 2004-11-24
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37 and into the ES source chamber through endplate nosepiece 38 opening
39. Bore 40 through dielectric capillary tube 41 comprises an entrance orifice
42 and exit orifice 43. Ions enter and exit the dielectric capillary tube with
potential energy roughly equivalent to the entrance and exit electrode
potentials respectively. To produce positive ions, negative kilovolt
potentials
are applied to cylindrical electrode 33, endplate electrode 34 with attached
electrode nosepiece 38 and capillary entrance orifice 42. ES probe 31
remains at ground potential during operation. To produce negative ions, the
polarity of electrodes 33, 34 and 38 are reversed with ES probe 34 remaining
at ground potential.

With the appropriate potentials applied to elements in ES source 32,
electrosprayed charged droplets are produced. The charged droplets exiting
ES probe tip 44 are driven against the counter current drying gas 36 by the
electric fields formed by the relative potentials applied to ES probe 31 and
ES
chamber electrodes 33, 34, and 38. A nebulization gas 45 can be applied
through a second layer tube surrounding the sample introduction first layer
tube to assist the formation of droplets. As the droplets evaporate, ions are
formed and a portion of these ions are swept into vacuum through capillary
bore 40. The droplets are entrained in neutral background gas that forms a
supersonic jet, expanding into vacuum from capillary exit orifice 43. A
portion
of the ions entering first stage vacuum 46 is directed through the skimmer
orifice 47 and into second vacuum stage 48. Ions are transported through RF
multipole ion guide 7 into a third vacuum stage 50 and into resolving RF/DC
quadrupole mass filter 2. In this configuration, a particular m/z value (or
set of
values) is selected from the ion beam, and ions of other m/z values are
ejected. The selected ion is then transported into the pressurized RF
multipole collision cell 3 where they are trapped by proper adjustment of lens
11 and lens 12. They are collisionally damped to centerline 17. Electron
source 5 generates low-energy electrons that are injected along the axis of
RF multipole 3 as discussed above. The ion undergoes electron capture
reaction induced by the injection of low-energy electrons into RF multipole
collision cell 3. The ion may also undergo conventional collisionally
activated
dissociation (CAD) such as axial acceleration CAD, whereby the ions are

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accelerated into a high pressure region, typically as they are transported
through collision cell 3. This is achieved by applying acceleration potential
between mass filter 2 and RF multipole collision cell 3. The ions may undergo
conventional CAD followed by electron capture, or the ion may proceed
without further fragmentation. Additional methods of fragmentation, including
additional stages of fragmentation, such as resonant excitation as taught by
Whitehouse, et.al. may also be accomplished in the RF multipole collision cell
3.

The resulting fragment and precursor ions are extracted from RF multipole
collision cell 3 and are transported through RF multipole ion guide 24, which
is
positioned in two vacuum stages, 50 and 51, and serves as a conductance
limiting tube separating stage 50 and 51. Pressure continually drops across
its length. The ions may be trapped in RF multipole ion guide 24, and rapidly
pulsed out, to improve duty cycle as taught by Whitehouse. Alternatively,
other forms of CAD may be carried out in this region, for example resonant
excitation CAD or even ECD. The ions are focused through lens 120 and
orifice 121 into the TOF 5 and TOF pulsing region 122. The TOF is
positioned in another vacuum region 123. The product ions are transported
into the pulser region 122 and pulsed into the flight region 123, where they
are
separated in time and detected by microchannel plate 124. The resulting
signal is sent to a digital signal averager 125 for amplification and
analysis.
Another preferred embodiment is illustrated in Figure 3. This embodiment
comprises injection of low-energy electrons into RF multipole ion guide 52,
which is positioned behind RF multipole collision cell 3. RF multipole ion
guide 52 is constructed of appropriate diameter and length to restrict the
conductance between RF multipole collision cell 3 held at pressure 56, and
the evacuated region 57. The junctions 58 and 59 are vacuum seals.
Similarly, RF multipole ion guide 52 restricts flow from evacuated region 57
into evacuated region 62. The junctions 60 and 61 are vacuum seals. Low-
energy electrons generated by source 53 are injected along the axis of RF
multipole ion guide 52. Voltages are arranged on lenses 55, 54, and electron
source 53, DC voltage bias on RF multipole ion guide 52, and DC voltage bias

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15 on RF multipole collision cell 3 such that electron velocity reversal
occurs
near point 76. Near point 76, there are still a sufficient number of
collisions to
contain the fragment ions in RF multipole ion guide 52. Other electron source
configurations as described above can be utilized, such as injection of
electrons through the space between the rods on RF multipole ion guide 52.
This embodiment has the advantage of producing thermalized precursor ions
in RF multipole collision cell 3, and efficiently transporting them RF
multipole
ion guide 52 where low-energy electrons are injected in a lower pressure
region 58.

Another preferred embodiment, as illustrated in Figure 4, comprises electron
sources 62 and 63 positioned within RF multipole collision cell 3. In this
preferred embodiment electron sources 62 and 63 are positioned close to the
lens 12 and lens 11, respectively, of RF multipole collision cell 3. A spray
of
electrons is injected toward centerline 17. Voltages are arranged on lenses
11, 12, 64 and 65, bias voltage 15, and on the casing of electrons sources 62
and 63, such that low-energy electrons are focussed onto centerline 17 and
undergo velocity reversal near points 23 and 66.

Figure 5 illustrates still another embodiment of the invention. In this
preferred
embodiment, two RF multipole ion guides 203 and 214 are positioned so that
ions exiting ion guide 203 move in the direction toward the entrance of ion
guide 214, and will cross gap 225 accordingly. Ion guide 203 is an integral
component of collision cell 205, which comprises enclosure 204, entrance
electrode 201 with entrance aperture 202, exit electrode 206 with exit
aperture
207, as well as multipole ion guide 203. The gas pressure within collision
cell
205 may be adjusted by leaking in gas from an external gas source (not
shown) through a valve (not shown) connected to a gas inlet (not shown) to
the enclosure 204.

Assembly 216 comprises enclosure 215, entrance electrode 212 with
entrance aperture 213, exit electrode 217 with exit aperture 218, and
multipole ion guide 214. Assembly 216 may or may not be utilized as a
collison cell. When assembly 216 is usd as a collision cell, the gas pressure

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within assembly 216 may be adjusted independently from the adjustment of
the gas pressure of collision cell 205, by leaking in gas from an external gas
source (not shown) through a valve (not shown) connected to a gas inlet (not
shown) to the enclosure 215.

Also shown schematically in Figure 5 is RF/DC quadrupole mass filter
assembly 200. The exit of mass filter 200, which is typically a so-called
Brubaker lens assembly comprising a short RF-only section following the
actual mass filter assembly, is positioned immediately adjacent to the
entrance aperture 202 of entrance electrode 201 of collision cell 205.
Precursor ions that are m/z-selected in mass filter 200 are accelerated
(gently, so as to avoid CAD) through aperture 202 and enter ion guide 203,
which is operated as in RF-only mode for transmitting a wide range of m/z
values. Due to low-energy collisions with background gas as the ions
traverse ion guide 203, the ions lose kinetic energy and, by the time the ions
reach exit aperture 207, the thermal energy of the ions is typically
equilibrated
to the temperature of the background gas.

Typically, in order to maximize the transport efficiency of ions through the
exit
aperture, ions are accelerated on their approach to exit aperture 207 due to
potential difference between the DC offset bias of ion guide 203 and the
voltage of exit electrode 206. However, in order to optimize the process of
ECD in region 224, the kinetic energy of the ions needs to be reduced
following this extraction acceleration. For this purpose, the ions are then
decelerated as they pass through exit aperture 207 toward opening 209 in
electrode 208 due to a retarding field between electrode 206 and electrode
208 established by their different applied voltages.

The kinetic energy of the ions will have been reduced to a relatively low
level
by the time they pass through opening 209. Opening 209 may be a simple
aperture, or may comprise a highly transparent mesh (e.g., a 70 line/inch
mesh with 90% transparency is available commercially from Buckbee-Meers
Corporation), as depicted in Figure 5, in order to maintain region 224 field-
free. As described below, a beam of low-energy electrons is provided in

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region 224-as well. The precursor ions and low-energy electrons overlap and
interact in region 224, resulting in fragmentation of precursor ions via ECD.
The resulting product ions, as well as any remaining precursor ions, continue
through field-free region 224 and pass through opening 211 in electrode 210.
They are then accelerated by an electric field due to a difference in the
voltages applied to electrodes 210 and 212, and continue through aperture
213 into the entrance region of ion guide 214.

Ion guide 214 may be an RF/DC mass filter, which may be used for m/z
analysis of the precursor and product ion m/z distribution. In this case, a
detector that produces a signal in response to a flux of ions exiting through
aperture 218 in exit electrode 217 would be located proximal to the ion beam
exit side of aperture 218. A record of this signal as a function of the m/z
value
of the ions transmitted by the mass filter would constitute the measured
product ion spectrum (along with any remaining precursor ions.

However, the assembly 216 may also be used as a collision cell. In this case,
target gas would be admitted into enclosure 215 to the desired pressure, ion
guide 214 would be operated in RF-only mode, and the ions would experience
collisional cooling as described above. The ions exit ion guide 214 via exit
aperture 218 in exit electrode 217, and, hving a reduced kinetic energy and
energy spread due to collisional cooling, may be optimally focussed into a
subsequent m/z analyzer, such as another RF quadrupole mass filter, a TOF-
MS, etc., for analysis of the ECD product ion m/z distribution.

Turning now to the production of the beam of low-energy electrons, electrons
are produced by electron emitter 219, which is shown schematically in Figure
as a filament, but could also be any of a number of well-known electron
emitters, all of which are within the scope of the present invention.
Electrons
emitted by electron emitter 219 are accelerated through emission aperture
226 in Wehnelt electrode 220 due to the potential difference between the
electron emitter 219 and extraction electrode 227. The voltage applied to the
Wehnelt electrode 220 may be positive or negative with respect to the bias
voltage of the emitter 219, as needed, to properly regulate the electron



CA 02487135 2004-11-24
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emission current. The electrons are then focused into a beam and steered by
electric fields established by voltages on electrodes 221, 222, 208, and 210,
as is well-known to those skilled in the art. As the electrons travel from
emitter 219 to the region 229 enclosed by electrodes 208 and 210, the
electrons are first accelerated to a relatively high energy, i.e., at least a
few
tens of electron-Volts (eV) in order to attain maximum electron transport
efficiency. However, the electron energy ultimately needs to be reduced to
the energies required for performing ECD, i.e., from about 0.2 eV upwards of
eV or so. Thus, the electrons are decelerated to their final low kinetic
energy upon reaching the essentially field-free region 229 enclosed by
electrodes 208 and 210. The kinetic energy of the electrons upon reaching
the field-free region 229 is determined by the potential difference between
the
potential at region 229, as defined primarily by the voltages applied to
electrodes 208 and 210, and the bias voltage applied to the emitter 219. The
space enclosed by electrodes 208 and 210 extending from region 229 to
region 224 and beyond is maintained field-free to ensure that no additional
external forces act to divert the low-energy electrons from the path between
region 229 and region 224. Region 224 is the region where ECD of precursor
ions will occur. A small differential between the voltage applied to electrode
208 and the voltage applied to electrode 210 may sometimes be beneficial in
optimizing the overlap between the electron distribution and the precursor ion
distribution. Electrons that do not interact in region 224 continue on to
region
230. Region 230 is located near electrode 223 which has a voltage applied
that is slightly negative with respect to the electron emitter bias.
Therefore,
electrons reaching the vicinity of electrode 223 will not quite have enough
kinetic energy to surmount the potential barrier that this slightly negative
potential represents for these electrons. Thus, they will reverse their
trajectories, and, if not lost to the surfaces of surrounding electrodes due
to
field de-focusing effects, will return to region 224, where they will again
have
the opportunity to interact with precursor ions.

The nominally field-free beam path from region 229 to region 224 ensures that
many low-energy electrons reach region 224 successfully. Nevertheless, the
transport efficiency for electrons of such low energy is reduced by a number
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of effects that are difficult to control, such as space-charge broadening in
the
electron beam, local charging of surfaces along the beam path, residual
magnetic fields, as well as the earth's magnetic field, etc. Therefore, a
number of improvements over the embodiment sketched in Figure 5 are
envisioned, all being within the scope of the present invention. One such
improvement would be to arrange the beam forming and transport electrodes,
and the voltages applied to them, along the electron beam path from the
emitter to immediately before region 224, such that the kinetic ene'rgy of the
electrons in the beam remained high until just arriving at region 224, at
which
point they are rapidly decelerated to their final low energy immediately upon
arriving at region 224. This may easily be accomplished by the addition of
grids that separate the two regions of different potential, according to
methods
that are known to those skilled in the art.

Another improvement is the addition of a relative weak magnetic field (a few
hundred gauss or so) arranged so the the magnetic field lines are more-or-
less along the electron beam path and extend from the electron emitter to at
least the axis of the collision cell. This is a well-known approach often used
in
the design of electron-impact ion sources for enhancing electron transport
efficiency, since electrons of low energy tend to follow such magnetic field
lines in spite of the presence of mild electric fields. Such a weak magnetic
field is expected to have negligible effect on the transport of ions in region
224
due to their much larger m/z value and much lower velocity.

Still another enhancement of the electron transport efficiency from region 229
to region 224 is to arrange the voltage differential between the electron
emitter 219 and the field free region 229 such that the electron kinetic
energy
at region 229 is still relatively high. The kinetic energy of the electrons
may
be reduced substantially by maintaining the volume enclosed by electrodes
208 and 210 at a relatively high gas pressure, so that collisions between the
energetic electrons and background gas molecules result in sufficient kinetic
energy by the time they arrive at the region 224. For this purpose, the volume
that includes regions 229, 224, and 230 may be more completely enclosed
than is indicated in Figure 5, which would result in elevated gas pressure due

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to gas flowing from the collision cells through orifices 207 and 213.
Additionally, a separate gas source may be configured to elevate the gas
pressure in this volume.

Even one more additional enhancement to the arrangement depicted in
Figure 5 is to position the electron source and associated electron beam
transport optics as close to region 224 as possible. This enhancement may
be realized in a straightforward fashion by configuring enclosures 204 and
215 to include a re-entrant cavity or recess wide enough and deep enough to
accommodate electron source 219 and associated beam formation and
transport electrodes 220, 227, 221, and 222, within the recess. This has the
effect of reducing the distance over which the low-energy electron beam must
traverse before arriving at region 224, resulting in a greater low-energy
electron transmission efficiency.

The relatively high efficiency that is expected from this arrangment stems
from
the combination of a number of unique and novel features: 1) the substantial
reduction in ion kinetic energy due to the previous collisional cooling
results in
a longer interaction time with low-energy electrons; 2) the establishment of
an
interaction region that is free of electric fields results in longer residence
times
for both low-energy electrons and ions, and allows mutual Coulomb attraction
forces to be more significant in increasing the frequency and effectivenes of
interactions between the ions and electrons; 3) the establishment of an
interaction region in close proximity to the exit region of the collision cell
implies that cooled precursor ions have very little time to disperse due to
space charge effects once they leave the confining action of the RF fields of
the collision cell, resulting in a greater probability of interaction with low-

energy electrons; 4) in case a magnetic field aligned with the electron beam
is used to prevent distortion and dispersion of the low-energy electrons
before
they arrive at the ion-electron interaction region 224, more electrons
arriving
at this region results in greater interaction efficiency.

The collision cells 205 and/or 216 of the embodiment illustrated in Figure 5
may also be operated in trapping mode. In this way, the ions are provided
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sufficient time to collide with the collision gas and cool to the temperature
of
the target gas before reaction. The RF multipole collision cell 216 may be
pressurized by addition of the same or different collision gas as the first RF
multipole collision cell 205. Fragment ions in RF multipole collision cell 216
can continue their migration through collision cell 216, or they may be
trapped, cooled and/or even further fragmented, before being released for m/z
analysis.

Another preferred embodiment is illustrated in Figures 6A through 6E, and
comprises the introduction of an electron beam between the electrode
structures of an RF multipole collision cell, with the electron source
positioned
above and/or between the poles of the electrode structure. Ions are
generated, transported and mass-selected conventionally as described
above. Electron source 77 is configured to provide emission along the length
of the electrodes. Electrons are injected in the space between the rods, and
along the length of the rods, as illustrated in Figures 6A and 6B. In this
schematic representation, an RF quadrupole ion guide is utilized, as shown in
Figures 6C and 6D, although, again, an RF ion guide with a different number
of rods could be used as well. The collision cell quadrupole consists of 4
rods
78, 79, 80 and 81 (round or hyperbolic) mounted coaxial with a circumscribed
radius 82, as illustrated in Figure 6C. One set of opposite pairs of rods 79
and
81 is connected together to form the A pole and the other set of rods 78 and
80 is connected to form the B pole. As usual, an RF voltage is applied to
each pole with a 180-degree phase shift producing a quadrupolar field. The
potential at point 83 in the center of the rods is adjusted to be close to
zero,
(assuming the DC reference voltage is zero).

The RF voltage alternates from Vp to 0 to -Vp and back again, on the A pole,
and from -Vp to 0 to Vp, and back again, on the B pole. Consider the electric
field at point 117 between rod 79 and rod 80. At some points in time, when
the RF voltage on rod 79 is attractive with respect to the electron source 77
in
Figure 6B, the electrons strike the rod 79. At other points in time, when the
RF voltage on rod 80 is attractive with respect to the electron source, the
electrons strike rod 80. When the voltages on the poles are close to or at

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zero, the electric field at point 117 is also close to or near zero. These
nodes
are illustrated at points 84 on curves 85 and 86 in Figure 6D, which plots RF
voltage vs. time for the A and B pole, respectively. Voltages on electron
source 77 can be configured such that at times near points 84, low-energy
electrons traverse centerline 85 in Figure 6C.

Typical RF frequencies are in the range of 250 kHz to 2 MHz. For example
for a 250 kHz frequency, the voltage repeats its cycle every 4 us, and
achieves a field-free or nearly field-free region within the ion guide volume
every 2 us. Lines 87 on Figure 6D illustrate the window of time 8t for which
electrons can pass through the rods and traverse centerline 85. A sinusoidal
field is given by Vosin (92t) and the rate of change of the voltage is -
QVocos(S2t). The duty cycle in the case of a 250 kHz frequency is St/2us. It
is
possible to optimize St by adjustment of maximum RF voltage (effectively
adjusting the Mathieu q-parameter), and to permit a spread in electron energy
of several volts. Duty cycles on the order of 1-2% are achievable. Although
the duty cycle is small, the injection volume can be very large since
electrons
can be injected over the length of the electrodes, illustrated by line 86 in
Figure 6B. Figure 6E illustrates utilizing four electron sources 88, 89, 90
and
91 to further enhance the injection efficiency.' As discussed in a previous
embodiment, it is possible to pulse the RF frequency off and on for a short
duration of time to enhance the electron' injection efficiency.

Another preferred embodiment of the invention comprises a multipole rod
structure constructed of semi-transparent thin wires or meshed conducting
materials 92. This is illustrated in Figures 7A and 7B. The mesh assembly 93
comprises 4 electrodes, 94,95,96 and 97. As above, opposite pairs of
electrodes are electrically connected to form the pairs A pole and B pole.
Electron source 98 is positioned within the mesh rods. The alternating nature
of the RF voltage is utilized for introduction of the electron beam into the
RF
collision cell. The potential difference between the voltage on electron
source
98 and the potential surface near centerline 17 determines the kinetic energy
of the electron as it traverses inward, toward centerline 17. The voltages



CA 02487135 2004-11-24
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applied to the poles determine the potential surface near centerline 17. It is
possible to arrange voltages to reduce the velocity of the electron as it
traverses along axes 118 toward centerline 17, or to configure the potential
surface such that there are velocity reversals near centerline 17. For
example, for one length of time, electron source 98 is positioned behind an
electrode with a negative polarity. Outside the electrode surface near point
99
in Figure 7B, the potential rapidly changes from the negative value at the
electrode surface, to close to zero at the centerline. This generates an
attractive field for electrons. Voltages on electron source 98 can be
configured such that electrons exit through the mesh and accelerate toward
centerline 17. Slow electrons will be available when the electrode voltage
nears zero. Similarly, at another point in time, the electrode has a positive
polarity. Outside the electrode surface near point 99 in Figure 7B, the
potential rapidly changes from the positive value at the electrode surface, to
close to zero at the centerline. This field is repulsive to the electrons, and
they decelerate as they move toward centerline 17. The voltages of electron
source 98 are adjusted differently for the two cases, and also take into
account the DC bias voltage 15 on RF multipole collision cell 3 from Figure 1,
to maximize the density of low-energy electrons near centerline 17. Similarly,
the balance of the electrode pairs can be adjusted using capacitance device
16 of Figure 1 to optimize the electric fields near centerline 17.

Another embodiment of the invention comprises an RF multipole collision cells
and a light source such as an ultraviolet (UV) laser to induce resonant
ionization of molecules, generating low-energy electrons. Two configurations
are, illustrated in Figures 8A, 8B and 8C. An ultraviolet light source is
tuned to
the transition of a dopant molecule in the collision cell. This molecule may
be
Nitrogen gas, which is plentiful and which has a high cross section for
resonant multiphoton ionization. One photon is tuned to excite an
electronically excited state. The second photon induces ionization from that
excited state. Typically, low-energy electrons can be ejected in this manner.
The highest yield occurs when laser beam overlaps the ion beam on
centerline 17. Figure 8A illustrates a configuration whereby laser beam 118 is
introduced to the mass spectrometer through a high transmission window 100

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at one end of the mass spectrometer. The laser beam is focused on
centerline 17 and transported into RF multipole collision cell 3 through
several
orifices. Laser beam 118 ionizes gas phase molecules along centerline 17
within RF multipole collision cell 3. Figure 8B illustrates an alternative
approach whereby the laser beam 101 is introduced to the RF multipole
collision cell 3 orthogonal to centerline 17, through the space between the
adjacent poles of RF multipole collision cell 3. Laser beam 101 is swept along
axis 102 by means of a rotating a mirror 103. An additional mirror 104 can be
positioned below the ion guide to permit multiple passing of laser beam 101
as illustrated in Figure 8C.

Another embodiment of the invention is illustrated in Figures 9A, 9B, and 9C,
and comprises a light source or a laser to induce electron emission from a
photosensitive surface. The light source may be oriented as shown in Figures
9A and 9B. Alternatively, it may be introduced at an angle to the RF multipole
collision cell 3. This is illustrated in Figure 9C. Photosensitive surface 103
is
embedded in lens 11 and 12 of RF multipole collision cell 3. Focusing lens
104 aids in directing electrons toward centerline 17. The photosensitive
material is fabricated to provide a high yield of electron emission when
impinged upon by high-energy ions or photons or electrons and may be
obtained commercially and fabricated for this application. Laser beam 105
from laser source 106 is introduced at an angle 107 with respect to axis 119,
striking surface 103, as illustrated in Figure 9B. Some fraction of photons
are
absorbed, causing an electronic transition within the material to occur. An
electron is ejected whose energy is approximately equal to the photon energy
minus the energy of the state that absorbed the photon. The system is
configured to permit multiple passes of laser beam 105 by reflecting it off
surface 103 positioned at an angle 107. An alternative configuration utilizing
a photosensitive surface placed orthogonal to centerline 17 is illustrated in
Figure 9C. This configuration is similar to those outlined above.
Photosensitive surface 108 is mounted below centerline 17 in the space
between lens 12 and lens 20. Laser beam 110 impinges directly on
photosensitive surface 108. As previously described, ions can be trapped in
RF multipole collision cell 3. Voltages are arranged on lenses, including lens

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12, 20, surface 108, RF multipole collision cell 3, DC bias voltage 15, and
lens
11, to direct low-energy electrons onto centerline 17 and to induce electron
velocity reversal near point 120.

An alternative configuration of the above-mentioned embodiment includes a
similarly configured surface that emits electrons when struck by high-energy
ions, or high-energy electrons. In this configuration, high-energy ions with
several kV (or more) can be introduced externally by acceleration of an ion
generated by the ion source, for example oxygen ions. High-energy electrons
may be produced by any of the high-energy electron sources well-known by
those skilled in the art. The high-energy ions (or electrons) readily overcome
the low voltage trapping barriers. They enter RF multipole collision cell 3
with
a sufficient divergence to strike the surface and emit low-energy electrons
due
to inelastic scattering processes within the surfaces.

Another embodiment is illustrated in Figure 10. This embodiment comprises
the injection of an ion beam 110 from ion source 111 into RF multipole
collision cell 3 and the simultaneous injection of electron beam 112 into the
volume, at angle 113 between 0 and 90 degrees. Ion beam 110 is generated
by normal means, i.e., utilization of ion source 1 in transport region 6 and
RF
multipole ion guide 7 and mass analyzer 2 in Figure 1. These ions can then
be mildly accelerated and injected into RF multipole collision cell 3 at angle
113. In this configuration, the RF field is set at sufficiently high q to
capture a
large fraction of the ions, after which point they are trapped. Low energy
electron beam 112 is injected coaxial to RF multipole collision cell 3.

In another preferred embodiment, ions of opposite polarity to the precursor
ions are injected into RF multipole collision cell 3 in order to induce
fragmentation. Figure 11A illustrates the configurations whereby an
orthogonal injection source is coupled to RF multipole collision cell 3. Ions
are
produced in source region 113 rather than electrons. For example, negative
ions are chemically produced in source region 113 by means of chemical
reactions . The ions are directed upward toward centerline 17 using optics
configuration 114. Precursor ions may be trapped 'in RF multipole collision

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cell 3, as described earlier. Voltages are adjusted to turn the ions into RF
niultipole collision cell 3 and direct the ions onto centerline 17, as
described
earlier.

An alternative embodiment is illustrated in Figure 11 B. The ions of opposite
polarity intersect in a cross beam fashion, as the precursor ion flows from RF
multipole collision cell 115 to RF multipole collision cell 116. As in Figure
11A, ions are produced ion source 113, directed toward centerline 17 by use
of optics configuration 114. Fragment ions are contained by RF multipole
116, and may undergo further steps of CAD.

Numerous approaches can be undertaken to optimize the electrostatic and
magnetic focusing and trapping of the electron beam in RF multipole collision
cell 3 and this invention includes but is not limited to those described in
the
above embodiments. Also it is within the scope of the invention to pulse on
and off the magnetic field and the electric field for any above-mentioned
embodiment.

Usually sinusoidal waveforms are applied to RF multipole ion guides, however
it is sometimes preferable to use alternative waveforms for RF including but
not limited to square waveforms or triangular waveforms. These alternative
waveforms are within the scope of the invention.

All embodiments described above relate to the combination of electrons and
ions. All embodiments that utilize electron sources such as cross beam
devices are equally applicable to positron sources.

All embodiments provide for a means to adjust the RF balance on the
multipole rods. For example, for a quadrupole ion guide, it is important that
there is a means to adjust the ratio A/B in order to optimize the yield of
electron capture. This is necessary because the RF field on axis needs to be
optimized. In most cases no offset is desirable. Nonetheless it is a parameter
that needs to be optimized for all configurations and experimental conditions.

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All embodiments described above relate to the combination of electrons and
ions in an RF multipole ion guide. The volume may be pressurized, for
example as in an RF multipole collision cell. The pressure range is typically
near 1 mTorr but can range from 0.01 mTorr to 200 mTorr. In many cases, a
multipole collision cell consists of a set of rods that are encased by some
enclosure. This permits containment of gases within the RF multipole ion
guide. However, it is within the scope of this invention to utilize the
embodiments in a high-pressure RF multipole ion guide that is not specifically
enclosed. In these instances the RF multipole ion guide may reside in a
pressurized vacuum chamber, and it may be positioned contiguous to other
ion guides residing in the same pressurized region. These other ion guides
may serve as mass analyzers, collision cells, or transporter guides.
Combinations of the embodiments of the present invention are within the
scope of this invention. Also, the placement of electron sources at multiple
locations using multiple configurations is within the scope of the invention.
For example, an electron source may be positioned at the entrance and exit of
the multipole ion guide simultaneously with the space between the A and B of
an RF quadrupole collision cell, both directed toward the axis, and is also
included within the scope of the invention.

Combinations of RF multipole ion guides and collision cells are within the
scope of the invention. For example, in some cases it is preferable to first
set
conditions for CAD and then perform electron capture. For example a single
collision cell can be used to permit simultaneous performance of CAD and
ECD. Alternatively, multiple collision cells can be used to permit
conventional
low energy CAD and ECD to be performed one after the other (in sequence).
Combinations of the embodiments described above in conjunction with other
mass spectrometers such as three-dimensional ion traps are within the scope
of this invention. For example a three-dimensional ion trap may be placed in
series with the embodiments of this invention.

As stated above, the electron source is suitable for operation in the mTorr


CA 02487135 2004-11-24
WO 03/102545 PCT/US03/17436
range and can include but is not limited to a heated filament; an indirectly
heated cathode dispenser; photosensitive materials in combination with a
photon source; a commercially obtained electron gun; and so on. As shown
above, the electron source may be configured close to the axis of the RF
multipole collision cell or RF multipole ion guide, or displaced from the axis
with appropriate use of electron transfer optics. The electron sources are
configured to give a range of energy from 0.2 to 10 eV with reference to the
axis of the multipole RF collision cell or ion guide.

The embodiments as stated above require optimization of all the electrode
voltages within the electron source, RF multipole collision cells, and RF
multipole ion guides. The electric fields are determined in part by the
relative
sizes of the structures and therefore it is within the scope of this invention
to
include rod diameters, lengths, circumscribed diameters and configurations of
a variety of sizes and poles numbers.

Having described this invention with regard to specific embodiments, it is to
be understood that the description is not meant as a limitation since further
modifications and variations may be apparent or may suggest themselves to
those skilled in the art. It is intended that the present application cover
all
such modifications and variations as fall within the scope of the appended
claims.

41

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

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Administrative Status

Title Date
Forecasted Issue Date 2009-01-27
(86) PCT Filing Date 2003-05-30
(87) PCT Publication Date 2003-12-11
(85) National Entry 2004-11-24
Examination Requested 2004-11-24
(45) Issued 2009-01-27
Expired 2023-05-30

Abandonment History

There is no abandonment history.

Payment History

Fee Type Anniversary Year Due Date Amount Paid Paid Date
Request for Examination $800.00 2004-11-24
Application Fee $400.00 2004-11-24
Maintenance Fee - Application - New Act 2 2005-05-30 $100.00 2005-01-26
Registration of a document - section 124 $100.00 2005-11-09
Maintenance Fee - Application - New Act 3 2006-05-30 $100.00 2006-05-19
Maintenance Fee - Application - New Act 4 2007-05-30 $100.00 2007-05-10
Maintenance Fee - Application - New Act 5 2008-05-30 $200.00 2008-05-07
Final Fee $300.00 2008-10-31
Maintenance Fee - Patent - New Act 6 2009-06-01 $200.00 2009-03-05
Registration of a document - section 124 $100.00 2010-02-23
Expired 2019 - Late payment fee under ss.3.1(1) $50.00 2010-06-04
Maintenance Fee - Patent - New Act 7 2010-05-31 $200.00 2010-06-04
Maintenance Fee - Patent - New Act 8 2011-05-30 $200.00 2011-05-02
Maintenance Fee - Patent - New Act 9 2012-05-30 $200.00 2012-04-30
Maintenance Fee - Patent - New Act 10 2013-05-30 $250.00 2013-04-30
Maintenance Fee - Patent - New Act 11 2014-05-30 $250.00 2014-05-27
Maintenance Fee - Patent - New Act 12 2015-06-01 $250.00 2015-05-26
Maintenance Fee - Patent - New Act 13 2016-05-30 $250.00 2016-05-23
Maintenance Fee - Patent - New Act 14 2017-05-30 $250.00 2017-05-30
Maintenance Fee - Patent - New Act 15 2018-05-30 $450.00 2018-05-29
Maintenance Fee - Patent - New Act 16 2019-05-30 $450.00 2019-05-24
Maintenance Fee - Patent - New Act 17 2020-06-01 $450.00 2020-05-07
Maintenance Fee - Patent - New Act 18 2021-05-31 $459.00 2021-05-05
Maintenance Fee - Patent - New Act 19 2022-05-30 $458.08 2022-04-06
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.
COUSINS, LISA
GHOLAMREZA, JAVAHERY
RAKOV, SERGEY
WELKIE, DAVID G.
WHITEHOUSE, CRAIG M.
Past Owners that do not appear in the "Owners on Record" listing will appear in other documentation within the application.
Documents

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Document
Description 
Date
(yyyy-mm-dd) 
Number of pages   Size of Image (KB) 
Abstract 2004-11-24 2 95
Claims 2004-11-24 8 306
Drawings 2004-11-24 18 774
Description 2004-11-24 41 1,975
Representative Drawing 2004-11-24 1 49
Cover Page 2005-02-03 1 45
Description 2007-12-06 41 2,006
Claims 2007-12-06 8 267
Representative Drawing 2009-01-19 1 40
Cover Page 2009-01-19 1 70
Fees 2008-05-07 1 37
Fees 2006-05-19 1 28
PCT 2004-11-24 1 54
Assignment 2004-11-24 3 99
Correspondence 2005-01-31 1 26
Fees 2005-01-26 1 29
Assignment 2010-02-23 7 258
Assignment 2005-11-09 6 257
Correspondence 2006-02-22 4 131
Correspondence 2006-03-07 1 12
Correspondence 2006-03-07 1 15
Prosecution-Amendment 2007-06-06 2 82
Fees 2007-05-10 1 31
Prosecution-Amendment 2007-12-06 15 524
Correspondence 2008-10-31 2 37
Fees 2009-03-05 1 39
Correspondence 2010-01-22 4 102
Correspondence 2010-02-08 1 14
Correspondence 2010-02-09 1 28
Correspondence 2010-06-11 1 13
Fees 2010-06-04 1 32
Correspondence 2010-06-15 4 139
Correspondence 2010-06-21 1 27