Improvements in and relating to tandem mass spectrometry

Abstract

An apparatus fortime-of-flight, TOF, tandem mass spectrometry comprises an ion source for providing precursor ions, a linear ion trap comprising a set of electrodes configured for receiving the precursor ions into the ion trap. A voltage source is configured for applying to the set of electrodes a trapping voltage(s) configured to generate an axial trapping potential field forming a potential barrier to axially trap the received precursor ions within the linear ion trap, and for applying to the set of electrodes an RF voltage(s) configured to generate a radial trapping potential field to radially trap received precursor ions. The voltage source selectively changes the radial trapping potential field to increase the kinetic energy of precursor ions in the ion trapping region so that precursor ions can overcome the potential barrier thereby axially ejecting the selected precursor ions from the linear ion trap. A collision cell is configured to receive the ejected precursor ions and to apply to them a process of collision-induced dissociation to generate product ions therefrom. A mass analyser, such as a time-of-flight, TOF, mass analyser, receives the product ions (and / or any remaining unfragmented precursor ions) and to apply to them a process of mass analysis.

Description

[0001] IMPROVEMENTS IN AND RELATING TO TANDEM MASS SPECTROMETRY Field of the Invention

[0002] The present invention relates to tandem mass spectrometry and particularly, although not exclusively, to tandem mass spectrometry and methods for data independent acquisition (DIA).

[0003] Background

[0004] Data-independent acquisition, DIA, has rapidly grown into a popular untargeted technique for high accuracy mass spectrometry (e.g., q-TOF) and has found wide applications in proteomics and metabolomics. Sequential window acquisition (known in the art as ‘SWATH’) or other similar DIA methods isolate precursor ions with relatively wide m / z windows by a mass filter (known as the ‘MS1 ’ stage) and acquire product ions spectra within a selected precursor m / z range using a mass analyser (known as the ‘MS2’ stage) such as a TOF device or Orbitrap device. In general, the use of two stages (‘MST and ‘MS2’) in mass spectrometry is known as a ‘Tandem’ mass spectrometry method or system.

[0005] A benefit of DIA is that it allows retrospective analysis of the data in both MS1 and MS2 stages. In some applications, DIA is reported to achieve better dynamic range and reproducibility than data dependent methods (known as data-dependent acquisition, ‘DDA’). It is found that DIA is very suitable for analysis of low abundance analytes in complex samples. However, DIA methods suffer from the following drawbacks:

[0006] (1) Low duty cycle or low sensitivity. For example, only precursor ions within the mass transmission window of the mass filter can be transmitted at the MS1 stage and then fragmented to produce mass spectra while at the MS2 stage. The other, non-transmitted precursor ions are discarded and wasted in the precursor ion selection at the MS1 stage. Therefore, this results in low duty cycle, low ion usage and low sensitivity. By narrowing the precursor isolation (ion transmission) window at the MS1 stage, an increase in selectivity and a reduction of interferences in MS2 spectra can be achieved, but this has a drawback in that it leads to more ion loss and thus lower duty cycle of the system in use.

[0007] (2) Slow acquisition speed or long acquisition time. Prior art methods such as SWATH usually need about one second or longer to acquire sufficiently high-quality data. However, requiring one second or longer for the acquisition time can make it difficult to use this method with fast liquid chromatography, LC, sample separation methods because one chromatography spectral peak may not have sufficient width to allow enough sampling data points for acceptably accurate analysis to be performed.

[0008] The present invention has been devised in light of the above considerations.

[0009] Summary of the Invention

[0010] The invention, at its most general, is to use a linear ion trap (LIT) to collect precursor ions from an ion source and to output any of the collected precursor ions selectively according to their mass-to-charge8388035

[0011] 2

[0012] ratio for downstream use in generating product ions therefrom. Desirably, precursor ions are not selected for output by the LIT according to a mass filtering process, which inherently results in a loss of precursor ions (i.e., those “filtered out”) but, instead, the LIT is used to trap all collected precursor ions for subsequent potential selection or isolation (i.e., output). In this way, precursor ion isolation is enabled for any of the collected precursor ions. The linear ion trap may be configured to output precursor ions mass-selectively for downstream use in generating product ions, such as in a tandem mass-spectrometry system. Tandem mass spectrometry (MS / MS) is the process of isolating precursor ions of a specific mass-to-charge ratio (m / z), subjecting them to some physiochemical process (e.g. collision induced dissociation, electron transfer dissociation), and measuring the masses of the product ions in a tandem mass analyser, such as a time-of-flight (TOF) apparatus, to enhance data independent acquisition. The inventors have found that in doing so, a high ion ejection efficiency from the from the MS1 stage can be achieved which leads to faster scan speeds. It has also been found to improve the duty cycle of the system in use, with improvements of up to about one order of magnitude being achievable, and with narrower precursor ion selection windows being possible at the MS1 stage, simultaneously. This can greatly enhance sensitivity for mass analysis. The invention may provide a fast data acquisition method and apparatus. Duty cycle times of less than 0.5 second may be achievable (e.g. for a m / z range from 400 Th to 1200 Th) thereby making the method and apparatus suitable to for use with fast liquid chromatography, LC, sample separation methods.

[0013] Disclosed herein is a method using a linear ion trap, LIT, to collect precursor ions and then to axially eject ions from amongst the collected ions selectively according to their m / z. The method may comprise using the linear ion trap (LIT) as the MS1 stage of a tandem TOF mass spectrometer to collect precursor ions selected by the LIT of the MS1 stage and then to axially eject selected ions from amongst the collected ions according to their respective mass-to-charge ratio (m / z). A mass resolution of the ejected ions may be such that an m / z spectral peak of a precursor ion has a FWHM of between about 5 Th and about 10 Th. Ejection efficiencies exceeding 80% may be achieved. This may be achieved at high scan speeds such as scan speeds exceeding about 5000 Th / s (e.g., at 5100 Th / s scan speed). A set of quadrupole rods may be used as both the mass filter and the LIT. For example, a quadrupole of length 120mm within a buffer gas at a pressure of 0.2 mTorr (e.g., nitrogen) is one example simulated to achieve these benefits.

[0014] In a first aspect, the invention may provide an apparatus for tandem mass spectrometry comprising: an ion source for providing precursor ions;

[0015] a linear ion trap comprising a set of electrodes defining an ion trapping region extending along an ion optical axis configured for receiving the precursor ions into the ion trapping region;

[0016] a voltage source configured for:

[0017] applying to the set of electrodes trapping voltages configured to generate an axial trapping potential field in the ion trapping region forming a potential barrier to axially trap received precursor ions within the linear ion trap; and,

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[0020] applying to the set of electrodes voltages (e.g., RF voltages) configured to generate a radial trapping potential field in the ion trapping region to radially trap received precursor ions within the linear ion trap;

[0021] wherein the voltage source is configured selectively to change the radial trapping potential field to increase the kinetic energy of precursor ions in the ion trapping region so that precursor ions can overcome the potential barrier selectively according to their mass-to-charge ratio, m / z, thereby axially ejecting the selected precursor ions from the linear ion trap;

[0022] a dissociation cell configured to receive the ejected precursor ions and to apply to them a process of ion dissociation to generate product ions therefrom;

[0023] a mass analyser configured to receive the product ions and to apply to them a process of mass analysis. The mass analyser may be configured to receive any remaining unfragmented precursor ions and to apply to them a process of mass analysis.

[0024] Herein, a reference to “AC voltage” includes a reference to a time-varying voltage the instantaneous value of which oscillates, as would be readily understood by the person skilled in the art. Herein, a reference to “RF voltage” includes a reference to a time-varying voltage the instantaneous value of which oscillates with a frequency in the radio-frequency range, as would be readily understood by the person skilled in the art. The mass analyser may be a time-of-flight, TOF, mass analyser configured to apply a process of TOF mass analysis. Alternatively, the mass analyser may be an Orbitrap mass analyser. The dissociation cell may be configured to apply to precursor ions a process of collision induced dissociation or electron transfer dissociation to generate product ions.

[0025] The set of electrodes and the voltage source may be configured, collectively, to generate a quadrupole radial trapping potential field in the ion trapping region whereby the voltage source may be configured to apply to the set of electrodes the RF voltages in a form configured to have a negligible or no massdiscriminating DC voltage component therein. Consequently, the RF voltages may be configured provide negligible or no applied mass filtering upon received precursor ions within the linear ion trap. This maximises the range of masses of precursor ions that the linear ion trap is able to collect and, therefore, improves the duty cycle, the ion usage and the sensitivity of the apparatus.

[0026] The set of electrodes may be configured to provide a multi-polar electrical potential field in which the contribution from potential field components of order higher than quadrupolar, is enhanced at the potential barrier as compared to such contribution at other parts of the multi-polar electrical potential field. The influence of such higher-order components upon ion motion and dynamics at the potential barrier is found to be inversely proportional to the mass-to-charge ratio (m / z) of the ion. As a result, by controlling the kinetic energy of precursor ions, those ions can be made to overcome the potential barrier according to their mass-to-charge ratio. Because the enhancement is inversely proportional to the mass-to-charge ratio (m / z) of an ion, then so too is the ability of an ion to surmount the potential barrier. This improves ion ejection efficiency which leads to faster scan speeds and is discussed in more detail below.

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[0029] The voltage source may be configured to apply to electrodes of the set of electrodes one or more AC auxiliary voltages to generate an excitation potential field in the ion trapping region to excite radially motion of precursor ions therein. This allows selective excitation of the radial component of oscillation amplitude of precursor ions within the trapping region, and mass-selective axial ejection as a result of that.

[0030] The voltage source may be configured to apply to electrodes of the set of electrodes one or more AC auxiliary voltages so as to generate a dipolar electric potential field in the ion trapping region. This may induce dipolar excitation of the radial component of oscillation amplitude of precursor ions within the trapping region. In other examples, the one or more AC auxiliary voltages may be configured so as to generate a quadrupolar electric potential field in the ion trapping region, which may induce quadrupolar excitation of the radial component of oscillation amplitude of precursor ions within the trapping region. The voltage source may be configured to apply AC auxiliary voltages to each of two electrodes forming a pair of electrodes that oppose each other across a longitudinal axis of the ion trapping region. An AC auxiliary voltage, VAux, may be of the form:

[0031] VAux= V'cos a)’t + (f>)

[0032] Having an amplitude V', a frequency, ω', and a phase φ. The amplitude and / or the frequency of the AC auxiliary voltages may differ from the amplitude, VRF, and frequency, ω, of the RF voltages applied simultaneously to the set of electrodes to generate the radial trapping potential field (e.g., quadrupolar field) in the ion trapping region.

[0033] The amplitude of the auxiliary voltage, V, may depend on pressure and scan speed. The ratio V' / VRFcan be a range of 10-4to 10-3; e.g., V' = 3 volts, V = 1180 volts.

[0034] The voltage source may be configured to apply to electrodes amongst the set of electrodes one or more AC auxiliary voltages having a frequency, a>’, differing from the frequency, a>, of the RF voltages and corresponding to a frequency of resonant ion motion in the radial trapping potential field thereby to excite such resonant ion motion. The frequency of the AC auxiliary voltages may be selected to conform to the following relationship:

[0035] ω' = (2l + β)ω / 2; l = 0, ±1, ±2, ±3...

[0036] Here, β is a dimensionless parameter. A value of β ≈ 0.75 may be suitably used. A value of l = 0 may be suitably used ( l = -1 may be used as an alternative). The range of the suitable values of β may be from about 0.4 to about 1.0.

[0037] The amplitude V', a frequency, ω', of the AC auxiliary voltage signal, for ion excitations, may be in a range from about 0.2V to about 20V, and in a range from about 0.05 times to about 0.5 times of the frequency of the main RF trapping (radial trapping) voltage signal. The main RF trapping (radial trapping) voltage signal may have a frequency in a range from about 0.5 MHz to about 3 MHz, such as about 1.2MHz for example.

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[0040] A buffer gas may be present in the trapping region to provide a desired pressure. The buffer gas may be helium, nitrogen, air or argon. A pressure of a buffer gas in the trapping region may be in the range from about 0.01 mTorr to about 1.0 mTorr.

[0041] The voltage source may be configured to apply the RF voltages to the set of electrodes to generate the radial trapping potential field as a pseudopotential field in the ion trapping region. The voltage source may be configured to apply the trapping voltages to the set of electrodes as AC voltages to generate the axial trapping potential field as a pseudopotential field in the ion trapping region thereby forming a pseudopotential barrier to axially trap the received precursor ions within the linear ion trap. Alternatively, the voltage source may be configured to apply the trapping voltages to the set of electrodes as one or more DC voltages to generate a DC axial trapping potential field in the ion trapping region thereby forming a DC potential barrier to axially trap the received precursor ions within the linear ion trap.

[0042] The set of electrodes may be configured to define a fringing field region in which a fringing field is generated collectively by the radial trapping potential field and the axial trapping potential field. The voltage source may be configured to apply the one or more AC auxiliary voltages to at least electrodes of the set of electrodes that are adjacent to or surrounding the fringing field region.

[0043] A spatial arrangement I geometry of electrodes of the LIT may be selected to provide a desired potential barrier (e.g., as a fringing field). For example, the axial separation between adjacent electrodes of the LIT may be from about 0.2roto about r0, where r0is the field radius, or may be from about 0.4roto about 0.6ro. Electrodes of the LIT may comprise cylindrical rods. Cylindrical rods have been found to be able to provide higher-order field components, as compared to other electrode shapes, and the higher order components may improve ejection efficiency. Cylindrical rods may comprise a circular cross-sectional shape or a hyperbolic cross-sectional shape.

[0044] The fringing field region may comprise a combination of a pseudopotential barrier component originating from the radial trapping potential field and either: a pseudopotential barrier component originating from the axial trapping potential field; or, a DC potential barrier component originating from the axial trapping potential field. Because the height of a given pseudopotential barrier component is inversely proportional to the mass-to-charge ratio (m / z) of an ion within the pseudopotential, then so too is the ability of an ion to surmount that barrier. This is discussed in more detail below.

[0045] The linear ion trap may comprise multiple electrode sets (e.g., quadrupole rod sets), including a main electrode set, and a downstream electrode set, each configured to receive a voltage and therewith to generate a potential field configured for one or more of the following processes:

[0046] (a) the trapping, without applied mass selection, of precursor ions to accumulate precursor ions in a predefined maximal mass range supported by the main electrode set, and / or

[0047] (b) cooling the collected precursor ions by collisions with buff gas molecules, and / or

[0048] (c) ejecting trapped precursor ions so as to pass through a potential barrier formed using the downstream electrode set.

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[0051] The downstream electrode set may be axially shorter in length than the axial length of the main electrode set.

[0052] The linear ion trap may comprise a voltage source arranged to apply to the electrodes of the main electrode set and the downstream electrode set a respective DC voltage, or RF voltages, configured to cause the electrode sets to generate respective electrical potentials which collectively form a potential barrier configured for trapping precursor ions within the linear ion trap, and / or for ejecting selected, trapped precursor ions axially from the linear ion trap.

[0053] The voltage source may be arranged to apply to the electrodes of the upstream electrode set, the main electrode set, and the downstream electrode set a respective DC voltage, or RF voltages, configured to cause the electrode sets to generate respective electrical potentials which collectively form a potential well configured fortrapping precursor ions axially between the upstream electrode set and the downstream electrode set. The voltage source may be arranged to apply to the electrodes of the upstream electrode set a respective DC voltage, or RF voltages, configured to cause the electrode set to generate an electrical potential barrier that is lower than an electrical potential barrier simultaneously generated by the downstream electrode set in response to a respective DC voltage, or RF voltages, applied thereto by the voltage source. This may provide a low-sided well wall at the ion inlet side of the linear ion trap and a high-sided well wall at the ion outlet side of the linear ion trap to allow precursor ions to enter the potential well from the ion source without exiting the well downstream, thereby permitting accumulation of precursor ions. The voltage source may be arranged to apply to the electrodes of the downstream electrode set a respective DC voltage, or RF voltages, configured to cause the electrode set to generate an electrical potential barrier that is lower than an electrical potential barrier simultaneously generated by the upstream electrode set in response to a respective DC voltage, or RF voltages, applied thereto by the voltage source. This may provide a low-sided well wall at the ion outlet side of the linear ion trap and a high-sided well wall at the ion inlet side of the linear ion trap to allow precursor ions that have been accumulated within the trapping region to be mass-selectively ejected axially from the potential well in the downstream direction, but not in the upstream direction.

[0054] The downstream electrode set may be configured to generate a potential barrier at an axial position located within or adjacent to the downstream electrode set. If the potential barrier is located at an axial position adjacent to the downstream electrode set, then preferably this axial position is located upstream of the downstream electrode set between the main electrode set and the downstream electrode set. This positioning may be achieved by a suitable control of the respective DC voltages applied to the main electrode set and the downstream electrode set for collectively generating the potential barrier.

[0055] The potential barrier may be generated within or adjacent to the downstream electrode set.

[0056] The voltage source may be arranged to apply to the electrodes of the main electrode set a said RF voltage with a waveform (e.g., alternating) configured to cause at least the main electrode set to generate a quadrupole potential field (e.g., a pseudo-potential) to trap precursor ions in the linear ion trap in conjunction with said axial trapping voltages, and subsequently eject ions from the linear ion trap according to their m / z. The voltage source may be arranged to apply to the electrodes of the main 4154-9954-8199, v. 18388035

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[0058] electrode set a said AC auxiliary voltage with a waveform (e.g., alternating) configured to cause the main electrode set to eject trapped ions from the linear ion trap according to their m / z by changing the amplitude and / or frequency of the AC auxiliary voltage waveform, or the main RF trapping voltage waveform, to values such that selected ions are those possessing a mass-to-charge ratio, m / z, that can receive sufficient kinetic energy to overcome the potential barrier at the downstream electrode set.

[0059] Resonance may occur when the frequency of the AC auxiliary voltage (e.g., dipole excitation) matches the frequency of ion motion determined by the main RF trapping field. Changing either the AC auxiliary or main RF trapping can cause the resonance. In practice, it can be easier to scan the amplitude of the main RF trapping field.

[0060] Optionally, an ion guide may be provided downstream of the downstream electrode set of the ion trap, for receiving selected precursor ions ejected from the linear ion trap.

[0061] The linear ion trap may comprise a voltage source arranged to apply at least to the electrodes of the downstream electrode set an RF (radio-frequency) voltage with a waveform (e.g., alternating) configured to cause at least the downstream electrode set to generate a quadrupole potential field (e.g., a pseudopotential) configured radially trapping ions therein. This may be appropriate when the potential barrier is located axially within or adjacent to the downstream electrode set.

[0062] The linear ion trap may comprise a voltage source arranged to apply to the electrodes of the main electrode set an RF voltage with a waveform (e.g., alternating) configured to cause at least the main electrode set to generate a quadrupole potential field (e.g., a pseudo-potential) fortrapping in the linear ion trap for subsequent selective ejection. The mass analyser may comprise a time-of-flight, TOF, mass analyser configured to receive the product ions (e.g., and / or any remaining unfragmented precursor ions) and to apply to them a process of time-of-flight, TOF, mass analysis.

[0063] In a second of its aspects, the invention may provide a method for tandem mass spectrometry comprising:

[0064] providing precursor ions;

[0065] providing a set of electrodes defining a linear ion trap comprising a trapping region extending along an ion optical axis and receiving the precursor ions into the ion trapping region;

[0066] applying to the set of electrodes trapping voltages configured to generate an axial trapping potential field in the ion trapping region forming a potential barrier to axially trap received precursor ions within the linear ion trap;

[0067] applying to the set of electrodes voltages (e.g., RF voltages) configured to generate a radial trapping potential field in the ion trapping region to radially trap received precursor ions;

[0068] changing the radial trapping potential field to increase the kinetic energy of precursor ions in the ion trapping region so that precursor ions can overcome the potential barrier thereby axially ejecting the selected precursor ions from the linear ion trap;

[0069] applying a process of ion dissociation to the ejected precursor ions to generate product ions therefrom;

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[0072] applying a process of mass analysis (e.g., time-of-flight, TOF, mass analysis) to the product ions. Mass analysis may be applied to any remaining unfragmented precursor ions.

[0073] The method may include generating a quadrupole radial trapping potential field in the ion trapping region and applying to the set of electrodes said RF voltages configured to have a negligible or no massdiscriminating DC voltage component therein.

[0074] The method may include providing a multi-polar electrical potential field in which the contribution from potential field components of order higher than quadrupolar, is enhanced at the potential barrier as compared to such contribution at other parts of the multi-polar electrical potential field.

[0075] The method may include applying to electrodes of the set of electrodes one or more AC auxiliary voltages to generate an excitation potential field in the ion trapping region to excite radially motion of precursor ions therein. The method may include applying to electrodes of the set of electrodes said one or more AC auxiliary voltages so as to generate a dipolar electric potential field in the ion trapping region.

[0076] The method may be such that the amplitude and / or the frequency of a said AC auxiliary voltage differs from an amplitude and / or a frequency, respectively, of a said RF voltage applied simultaneously to the set of electrodes to generate the radial trapping potential field in the ion trapping region.

[0077] The method may include applying to electrodes amongst the set of electrodes said one or more AC auxiliary voltages having a frequency that differs from the frequency of a said RF voltage and corresponds to a frequency of resonant ion motion in the radial trapping potential field thereby to excite such resonant ion motion.

[0078] The method may include providing a fringing field region in which a fringing field is generated collectively by the radial trapping potential field and the axial trapping potential field and applying said AC auxiliary voltages to at least electrodes of the set of electrodes that are adjacent to or surrounding the fringing field region.

[0079] The method may include applying said RF voltages to the set of electrodes to generate the radial trapping potential field as a pseudopotential field in the ion trapping region. The method may include applying said trapping voltages to the set of electrodes as AC voltages to generate the axial trapping potential field as a pseudopotential field in the ion trapping region thereby forming a pseudopotential barrier to axially trap the received precursor ions within the linear ion trap. The method may include applying the trapping voltage to the set of electrodes as a DC voltage to generate a DC axial trapping potential field in the ion trapping region thereby forming a DC potential barrier to axially trap the received precursor ions within the linear ion trap.

[0080] The method may include providing the fringing field as a combination of a pseudopotential barrier component originating from the radial trapping potential field and either: a pseudopotential barrier

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[0083] component originating from the axial trapping potential field; or, a DC potential barrier component originating from the axial trapping potential field, or a combination of both the AC pseudopotential barrier and DC voltage barrier.

[0084] The set of electrodes may comprise multiple electrode sets including a main electrode set, and a downstream electrode set, each configured to receive a voltage and therewith to generate a potential field configured for one or more of the following methods:

[0085] (a) the trapping, without applied mass selection, of precursor ions thereby accumulating precursor ions in a predefined maximal mass range supported by the main electrode set, and / or

[0086] (b) cooling the collected precursor ions by collisions with buff gas molecules, and / or

[0087] (c) ejecting trapped precursor ions so as to pass through a potential barrier formed using the downstream electrode set.

[0088] The method may include applying to the electrodes of the main electrode set a said RF voltage with a waveform configured to cause at least the main electrode set to generate a quadrupole potential field to trap said precursor ions in the linear ion trap in conjunction with said axial trapping voltages, and subsequently eject ions according to their m / z from the linear ion trap.

[0089] The method may include applying to the electrodes of the main electrode set a said AC auxiliary voltage with a waveform configured to cause the main electrode set to eject trapped ions from the linear ion trap according to their m / z by changing the amplitude and / or frequency of the main RF voltage trapping waveform or of the AC auxiliary voltage waveform (or of both waveforms) to values such that selected ions are those possessing a mass-to-charge ratio, m / z, that can receive sufficient kinetic energy to overcome the potential barrier at the downstream electrode set.

[0090] The method may include providing an ion guide arranged downstream of the downstream electrode set of the linear ion trap and therewith receiving selected precursor ions ejected from the linear ion trap.

[0091] The method may include applying to the electrodes of the main electrode set and the downstream electrode set a respective DC voltage configured to cause the electrode sets to generate respective electrical potentials which collectively form a potential barrier configured for trapping within the linear ion trap received precursor ions, and / or for ejecting selected trapped precursor ions axially from the linear ion trap.

[0092] The method may include, by the downstream electrode set, generating a potential barrier at an axial position located within or adjacent to the downstream electrode set. The method may include applying at least to the electrodes of the downstream electrode set an RF voltage with a waveform configured to cause at least the downstream electrode set to generate a quadrupole potential field configured for radially trapping ions therein.

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[0095] The invention includes the combination of the aspects and preferred features described except where such a combination is clearly impermissible or expressly avoided.

[0096] Multipole Fields, Pseudo-potentials and Fringing Fields

[0097] Quadrupoles and quadrupole fields

[0098] A quadrupole field is expressed by its linear dependence on the coordinate position. In Cartesian coordinates, the quadrupole electric field is given by:

[0099] E = E0(λx + σy + γz)

[0100] Here, E0, λ,σ,γ are all position-independent, and E0may be a function of time. The electric field is uncoupled in the three cartesian directions. Thus, in a quadrupole electric field, the force on a charged particle increases linearly with displacement from the zero position. The electric field is subject to the constrain of Laplace’s equation such that:

[0101] ∇·E = 0

[0102] This condition is satisfied when λ = − σ,γ = 0. The electrical potential corresponding to this field, obtained by spatially integrating the electric field, is:

[0103] 1 1

[0104] <!’ = — — E0(Ax2+ cry2+ yz2) = — — E0A(x2— y2)

[0105] The equipotential field lines of this electrical potential field are hyperbolae in the x-y plane. Such a potential field may be generated using four parallel hyperbolic cylinders angularly equally-spaced around a common ion optical axis with one pair of the electrodes that oppose across the axis being equally charged and the other pair opposing across the axis being oppositely charged. If the minimum distance between opposing electrodes is equal to 2r0, where r0is the inscribed radius (also referred as the field radius) of a notional cylindrical volume or channel centred on the axis, and the electrical potential difference (voltage) that is between the two pairs of electrodes is Wo, then:

[0106]

[0107] This gives:

[0108] Φ = W0 / 2r02

[0109]

[0110] :2^(x y

[0111] When used as a mass filter, the electrical potential (voltage), Wo / 2, is applied to one of the two pairs of electrodes and the electrical potential (voltage), -Wo / 2, is applied to the other one of the two pairs of electrodes. Here, Wois given by:

[0112] W0= 2[U − Vcos(ωt)]

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[0115] The quantity V is the ground-to-pole voltage zero-to-peak amplitude of a sinusoidal RF potential of angular frequency a>, and the quantity U is the value of a “mass discriminating” DC ground-to-pole potential. This applied voltage results in equations of motion for the ion in the potential field as follows:

[0116] / CZ \

[0117] — - + I - 7 I [U — ycos(ftjt)]x = 0

[0118] at2\mr / )

[0119] d2y [ cz \

[0120] — + — 2_Vcos(wt)]y = o

[0121]

[0122] dt2\mrg J

[0123] Here, the quantity z is the charge of the ion, and e is the elementary charge. By defining the following parameters:

[0124] _ / QzeU \

[0125] dy I 7 2 I

[0126] / 4-zeV \

[0127] Qx = -Qy = ^^^2 J

[0128]

[0129] / =

[0130] The equations of motion reduce to:

[0131] d2u

[0132] — + [au- 2qucos(2f)]u = 0

[0133]

[0134] Here, the symbol u represents either x ory. Only certain values of auand qulead to solutions representing stable ion trajectories within the channel formed by the four electrodes. The so-called “stability diagram” for a quadrupole device is shown schematically in Figure 5. These stable trajectories have values of auand quthat are coordinates constrained to reside within a roughly triangular “stable region” of the “stability diagram”. By controlling the values of the voltages U and V so that the ratio U / V = constant, the result is that the ratio of the ion trajectory parameters, ax yand qxy, becomes axy / qxy= constant. This may be represented as a straight line in a graph of parameter axyversus qxy, with the line passing through the origin of coordinates and having a gradient equal to the value of the “constant" noted above:

[0135] ax y=constant) ■ qxy

[0136] This straight line defines the “mass scan line”. When the value of the quantity U (the “mass discriminating” DC potential) is zero, the quadrupole device acts as an ion guide or a linear ion trap, and the mass scan line is simply a horizontal line for which all axy= 0, and the maximum range qxyof the parameter qxyis possible. However, when operated as a mass analyser, quantity U (the “mass discriminating” DC potential) must be set to a non-zero value, and the mass scan line acquires a positive gradient of value U / V for which the only permissible values of auare those lying within a finite range t axycorresponding to a limited range qxyof permissible values of the parameter qxy. In this sense, the mass analyser is able to discriminate ion masses by transmitting only those selected by the mass scan line.

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[0139] Higher-order fields and frinciinci fields

[0140] The above discussion applies strictly to perfectly quadrupolar fields; that is to say, with electrodes having with perfectly quadrupolar geometry, in receipt of perfectly sinusoidal applied voltages and without the presence of ‘fringing fields’.

[0141] Higher-order Fields

[0142] In the more general case, where multipolar field orders greater than quadrupole are present within the electric field generated by a quadrupole ion guide or ion trap device, the electric potential field present within a volume surrounded by the electrodes of the quadrupole device can be expressed as:

[0143] Z / r \wbnVcos(no) / 2')(t — tn)

[0144]

[0145] N °C0SN~X

[0146] n

[0147] Here, the quantity N is a positive integer indicating the “order” of the spatial field component contributing to the overall spatial structure of the potential field generated by 2N electrode pole pieces. For example, N = 1 corresponds to the potential field generated by a dipole electrode structure, N = 2 corresponds to the potential field generated by a quadrupole electrode structure, N = 4 corresponds to an octopole, and N = 6 to a dodecapole. The terms r and <f> are polar coordinates, ANand bnare weighting factors and cpNand tnare phase factors. In cartesian coordinates, this may be expressed as:

[0148] u - bnVcos(n<x> / 2}(t — tn)

[0149] N '0

[0150] Nz

[0151]

[0152] cp = Re{(x + iy)'v}

[0153] Here, i = V-l and the term Re{z} refers to the real component of the quantity z. Notably, for an ideal quadrupole field, only the terms for N = 2 appear in the equation for the electric potential field <t>, in which we may set A2= b2= 1. All other terms are zero. This gives the quadrupolar potential field structure noted above. Of course, in this example of a quadrupolar rod set, the reduction of the above general multipolar field equation to the much simpler quadrupolar field equation is something of an idealisation in which the quadrupolar rod set is assumed to comprise an array of four rods each of infinite length, of exactly the same shape and dimensions arranged perfectly in parallel and perfectly symmetrically around the central longitudinal axis of the array.

[0154] More generally, deviations from this idealised circumstance lead to the creation of higher-order multipole field terms in the electric potential field of a real quadrupolar rod set. The equations of motion for an ion in a multipolar field generated by a quadrupolar electrode rod set in general may be expressed as:

[0155] d2x ( ze \z / ze\r, V9(PN

[0156] j - Vcos(wt)]^ = - ( — ) [U ~ Vcos(o>t)] ) AN— —

[0157] dt2\mrA w Z_i ox

[0158]

[0159] V U 7N>3

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[0162] d2y ( ze \ rze\1d(i)rj— + j “ Vcos(at)]y = - ( — ) [U - Vcos(a)f)] > AN— — dt2\mrn / \m' t—i dy

[0163]

[0164] Here, higher order field effects influence the equations of motion in the form of the spatial differentials (dpN / dx; dcpN / dy) of multipolar field components, cpN, of order greater than N = 2 (e.g., hexapolar, octopolar, and so on). Note that the influence of the higher-order fields is inversely proportional to the mass-to-chare ratio (m / ze) of the ion. Here, the quantity z is the charge of the ion in question, and e is the elementary charge. These equations return to the idealised case for a perfect quadrupolar rod set when all higher-order terms are neglected such that

[0165]

[0166] = 0 for all N > 2.

[0167] One example of the presence of higher order field effects in a real (non-idealised) quadrupolar rod set is the so-called ‘Fringing Fields’ at and around the terminal ends of the rods. Here, higher-order fields become significant such that AN> 0 for at least some N > 2.

[0168] Fringing Fields

[0169] In the inner regions of a linear quadrupole ion guide, far from a terminal end of the guide, the two-dimensional quadrupole potential can be written as:

[0170] o = - — [U - Vcos(a>t)]

[0171]

[0172] ro

[0173] Here, 2r0is the shortest distance between opposing rods of the quadrupole ion guide, and where the expression: U - Vcos(a)t) is the electric potential (voltage), measured with respect to ground, applied with opposite polarity to each of the two pairs of rods. It is a linear combination of DC (i.e. IT) and RF (i.e. ycos(wt)) components, where is the angular frequency of the RF signal. This is a somewhat idealised circumstance which is a very good approximation in the inner regions of a linear quadrupole ion guide, far from a terminal end of the guide, but is increasingly inaccurate at axial positions along the ion guide increasingly close to a terminal end. Furthermore, the potential of the ion guide also extends outside of the ion guide beyond its terminal ends and does not simply fall away instantaneously to a zero value outside of the terminal ends. Rather, a so-called “fringing field” region exists in which the amplitude or strength of the potential smoothly transitions from the value it would have well within the ion guide to a value it would have well outside of the guide. It can be shown that the exit fringing-field, <t>FF, may be quantified as:

[0174] 2 2

[0175] ‘I’FF = ‘I’ / U) = - IV_Vcos(<x>ty]f(z')

[0176]

[0177] Here, the diminishing term (z) is a smoothly decreasing amplitude or strength function of the axial distance, z, along the ion guide axis on the approach to, and passing beyond, the exit end of the ion guide. As a consequence of the fringing region at the end of an ion guide, ions upon the central axis (i.e. the z-axis) of the ion guide experience a non-zero quadrupole potential outside of the ion guide that diminishes at increasing distance beyond the terminal end of the ion guide, in a direction along the z-axis. It can be shown that, to a good approximation:

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[0180] f(z) = 1 - exp (~a[z - z0] - b[z - z0]2)

[0181] Here a and b are positive constants determined by the geometry of the quadrupole ion guide, and z0is an axial position outside the ion guide at a fixed potential (e.g. earthed). So-called “Enge functions” are also descriptive. This fringing effect applies equally to the pseudo-potential generated by an RF potential, as discussed below. Fringing fields exist in ion guides of other than quadrupole geometry (e.g., hexapole, octopole, decapole etc.). One can see that the effect of the fringing field is to diminish the potential within the ion guide adjacent to, and also at, the terminal end of the guide and to define a non-zero extension of the potential extending a finite distance beyond the terminal end.

[0182] Mass-Selective Axial Ion Ejection

[0183] A method of mass scanning is possible with linear quadrupolar devices (e.g., quadrupole rods) employing quadrupole fields known as mass-selective axial ejection (MSAE). This method uses the fringing field at the exit of the quadrupolar device where the otherwise independent ion motions in the x, y and z directions become coupled by the fringing field. This is due to the significant contribution of higher-order field components present within the fringing field. A quadrupolar device may be operated by applying to the electrodes (e.g., rod set) of the device only an RF voltage. An end plate or exit lens arrangement may be disposed at the exit end of the device and may have a voltage applied to it which is set to a value relative to the potentials applied to the electrodes of the device so as to define a stopping potential, or potential barrier to ions within the device.

[0184] Within the fringing field, radial energy of the ions is converted into axial energy due to the coupling effect of the higher-order field components (i.e., with N > 2) present in the fringing field. If ions have sufficient radial energy then this may be converted into an axial energy sufficient to surmount the potential barrier generated by the end plate or exit lens of the device. Ions possessing a greater radial energy are able to acquire a greater radial displacement which permits those ions to occupy regions of the multipolar field in which the effects of the higher-order field components are relatively larger - as compared to their effects at the central axis of the device - and the consequential coupling or radial motion to axial motion is greater.

[0185] The principle underlying MSAE is to deliberately excite ions within such a device, using bespoke excitation potentials, to increase their radial displacements in a mass-selective manner such that ions with a selected mass-to-charge ratio will achieve the radial displacement necessary for radial-to-axial energy conversion needed to surmount the potential barrier. As a result, axial ejection becomes mass-selective.

[0186] A bespoke excitation potential (voltage) may take the form of auxiliary AC voltages applied either to electrodes of the quadrupolar rod set, in addition to (i.e., superimposed upon) the existing RF potentials applied to the electrodes of the rod set, such as shown in Figure 6, or to separate auxiliary electrodes provided forthat purpose. This manner of the application voltages applies to the arrangements shown in Figures 3(b) and 3(c). Auxiliary electrodes may be disposed between, and aligned parallel to, the main electrodes of the rod set.

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[0189] Typically, the excitation potential (voltage) may be selected so as to generate a dipolar electric potential field at least in the region of the fringing field. This may be achieved by applying an AC excitation voltage to each of two electrodes forming a pair of electrodes that oppose each other across the longitudinal axis of the device. This enables dipole excitation to take place. Figure 6 shows an example of this in which the auxiliary AC excitation voltage, VAux, is of the form:

[0190] VAux= V'cos 't)

[0191] Here, the amplitude V of the auxiliary AC voltage and its frequency, a>', may (and generally do) differ from the amplitude and frequency of the quadrupolar field-generating potentials: U - Vcos(Mt), that are applied simultaneously to the rod set. The motion of a pendulum can serve as a simplified analogy to the radial motion of an ion in the quadrupole field. Just as in the case of a pendulum that has a force applied to it once per period synchronously with the pendulum’s motion, whereby the height of the pendulum swing increase, so too does the amplitude of the ion radial oscillatory motion. Thus, resonant excitation of ions can be achieved in this way by adding the auxiliary excitation voltage of angular frequency a>’ to the basic RF quadrupole field of angular frequency a>. The amplitude V of the excitation voltage may be much less than the amplitude V of the RF voltage which confines ions. In this so-called “dipole excitation” method, the electric potential of the excitation field is directly proportional to the coordinates, and the electric field magnitude does not depend on coordinates. This corresponds to a forced harmonic oscillator and resonant motion occurs when the frequency, a>’, of the applied force coincides with one of the following ion oscillation frequencies:

[0192] w' = (21 + / ?)<z> / 2; I = 0, ±1, ±2, ±3...

[0193] Here, p is a dimensionless parameter. The auxiliary AC voltage may be used to excite this resonant ion motion.

[0194] Ion trajectories are influenced by axial fields in the fringing region. An increasing axial electric field arises at and close to the ends of the quadrupole rods due to a spatial gradient in the diminishing RF quadrupole potential there. Additionally, an exit lens arrangement may be provided which creates an axial field when an electric potential is applied to it. These two axial electric fields may be balanced by applying a suitable static positive DC potential to the exit lens such that the total axial field experienced by an ion, averaged over one RF cycle has the effect of generating a potential barrier at the exit of the rod set. This potential barrier may be surmounted by mass-selective excitation of radial ion motion. The spatial shape and position of the potential barrier is schematically shown as a function of axial position in Figure 7. The loci of points (304, Fig. 7) at which the net spatial gradient, over one RF cycle, of the potential barrier changes sign (i.e., passes through a zero-value at the ‘peak’ of the barrier) is represented by dash-double-dot lines. Ions positioned at points in space axially behind the barrier peak experience a net negative axial force, F, over one RF cycle and are reflected axially back into the rod set unless they are able to overcome the barrier. Conversely, ions positioned at points in space axially in front of the barrier peak, having been able to overcome the barrier, experience a net positive axial force, F, over one RF cycle. When the exit lens DC potential is appropriately chosen, ions with a radial motion having sufficient energy are able to penetrate this potential barrier, and be ejected axially, while all others are reflected axially

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[0197] back into the rod set. Due to the axial shape of the loci of points defining the axial position of the barrier peak, this shape is known as the “cone of reflection”, being rotationally symmetric about the axis of the rod set. The following reference provides additional details: F. A. Londry, James W. Hager, “Mass selective axial ion ejection from a linear quadrupole ion trap”, Journal of the American Society for Mass Spectrometry, Volume 14, Issue 10, 2003, pp 1130-1147. Figure 7 schematically shows a “cone of reflection” 304 formed in the region adjacent to the output end of a quadrupole rod set 300 (two of four rods shown) and an exit lens unit 302 of an ion guide.

[0198] The Pseudo-potential

[0199] The following provides an understanding of the physics of confining charged particles with radio frequency fields, and an outline of the pseudo-potential approach exemplified via the simpler case of the 2D quadrupole mass filter. Consider a counterpart to the purely electrostatic arrangements of ion confinement in RF fields, by considering a mechanical analogue useful for understanding. In particular, consider the trapping of a bead on a rotating saddle surface. The rotating saddle-potential analogue does not exactly correspond to the physics of an RF ion guide / trap, however it will capture the underlying principles in an intuitive and useful way. To confine a particle of mass m stably at a point of space, we require a restoring, i.e., binding force F (cf. Hooke’s law):

[0200] F = — c r

[0201] Here, c is the spring constant, and r the position variable. A conservative force F can always be written in terms of a scalar potential:

[0202] F

[0203]

[0204] =

[0205] Given the force, we can calculate the potential by integrating once:

[0206] < I’(x, y, z) = -(axz+ py + yzz)

[0207]

[0208] where a, / ? and y are constants that play the role ofc in three spatial directions. In anticipation of the discussion of trapping charged particles in electrostatic potentials, choose: a = - / ? = l,y = 0. With this choice, <t> forms a potential that has the shape of a saddle surface:

[0209] < I’(x, y) = -(x2 —T2)

[0210]

[0211] Although potentials of this shape will allow to trap the particle along the x-direction, there exists no stable minimum and the particle could always escape along the y- direction. Hence, stable trapping is not possible with these static potentials. However, as we will show now using the example of a gravitational saddle potential, trapping becomes feasible when we introduce a time variation. In a gravitational potential, we can set:

[0212] mgh0

[0213] We obtain the expression of a gravitational saddle potential:

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[0216] x mgh0

[0217] < P(x,y) =2(x2- y2)

[0218]

[0219] zr0

[0220] Here, m is the mass of the bead, g the Earth’s gravitational acceleration, and h0and r0are parameters that shape the curvature of the potential. It is possible to rotate the saddle with a angular frequency around the vertical axis (z-axis), without applying any other motion to it, in order to ‘balance’ the bead within the saddle. This angular rotation transforms the static gravitational potential into a time-varying potential that can be described by writing the potential in terms of rotating axes x',y‘ as follows:

[0221] (x,y) = — ^- (x2- y2)

[0222]

[0223] zr0

[0224] The rotating saddle potential may be described in the laboratory frame by applying the standard coordinate transformation given by the rotation matrix:

[0225] x'\ > / cos(cot) — sin(cot)\ / x\

[0226] y' J \sin(cot) cos(cot) / \y)

[0227] This gives:

[0228] < I’(x,y, t) =2° {(x2— y2)cos(cot) — 2xysin(cot)}

[0229]

[0230] zr0

[0231] Pictorially, one may visualise the time-variation of this potential as a rotation of the saddle surface around the vertical axis, with a frequency co prevents the bead from rolling off the saddle surface. The faster the saddle rotates, the better the bead is confined within the saddle surface (i.e., gravitational potential surface). It can be shown that the bead may follow stable trajectories confined to the saddle surface if the rotation is fast enough. Although the rotating saddle potential intuitively illustrates the basic physics of trapping particles with a rapidly oscillating potential, it must be noted that the electrical potentials used in in ion trapping / guiding are not exactly of the mathematical form shown above for the gravitational potential saddle surface <t>(x,y, t). Rather, electric potentials in ion guides / traps are typically of a form:

[0232] cf

[0233] < I’(x, y, t)~ ~ (x2— y2)cos(cot)

[0234] Pictorially, the time-variation of this potential representation would rather resemble a flapping potential, where the curvature oscillates with time and the walls of the saddle potential flap like the wings of a bird. The constant c' is dependent on the voltage that is applied to the ion trap / guide electrodes.

[0235] Rapidly oscillating potentials like the “rotating-saddle” potential or the “flapping” potential can be used to confine particles and this is understood via the concept of the “pseudo-potential”. In the pseudo-potential approximation, one considers the average potential that acts on a particle in a rapidly oscillating potential as an effective potential. It is calculated by taking the time-average over one period of the fast oscillation. To analyse the trajectory of the particles in such potentials, we may write down the equations of motion of the particle in the potential:

[0236] F = mr = —z7< P(r)

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[0239] Here z is the charge of the particle with mass m. A generic type of electrical potential for ion confinement consists of a stationary, slowly changing orquasi-static part, U(r), and a fast time-dependent oscillating part, V(r) cos{a>t) which oscillates with a frequency a>

[0240]

[0241] = t / (r) + V(r) cos (cot)

[0242] Assume that the frequency of the oscillating part is much larger than the inverse time scale of one period of motion T the particle would carry out only under the influence of U(r), i.e. D » 1 / T. As a result of this assumption, we obtain:

[0243] mf = — z7(t / (r) + V(r) cos lt)) = —zVU(r) — z V(r) cos(a>t) = F0(r) + FRF(r) cos(cot) The smooth particle trajectory due to the force F0(r) is modulated by an oscillating force FfiF(r) at frequency co.

[0244] Thus, we may write the total trajectory r(t) as a sum of a smooth part 7?(t) and rapidly oscillating part £(t):

[0245] r(t) = F(t) + (t)

[0246] Typically, the amplitude of the oscillations will be much smaller than the smooth part of the trajectory R, i.e. | | « |7?|. This permits us to expand the forces F0(r) and FfiF(r) in a Taylor series up to lowest order in the parameter, as follows:

[0247] F

[0248]

[0249] 0(R + 0 = F0(F) + f + ■ ■ ■

[0250] FRF(F + 0 = FRF(R) + ■ FFRF(R) + ■ ■ ■

[0251] Omitting negligible parts of the series, the equation of motion becomes:

[0252] m(F(t) + (t)) = F0(R + £(t) ■ FF0(R + [FRF(F) + £(t) ■ VFRF(R)'] cos{c t The result of the equation of motion for the oscillating part of the trajectory is given approximately by:

[0253] m^(t) = FRFcos(cot)

[0254] The solution to this equation is:

[0255] f

[0256]

[0257] (t)

[0258] By calculating the time average over: m(F(t) + ’(t)), over one period 2n / co, we obtain an expression for a time-averaged pseudo-potential. In doing so, note that terms containing cos(wt) will time-average to zero and only terms with [cos(wt)]2remain. Namely:

[0259] (m(F(t) + (t))> = F0(R + < (t)> ■ VF0(R) + <[FRF(7?) + £(t) ■ VFRF(R ] cos(a>t)) Given that:

[0260]

[0261] = 0, this reduces to:

[0262] ... {cos2(cot))

[0263] mR{t) = F0(R) - FRF(R) ■ VFRF(R)

[0264]

[0265] Remembering that F is a conservative force, and (7 x FRF(R = 0) this means that:

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[0268] 1 FRF(R) ■ VFRF(R) = FRF(R) ■ VFRF(R) + FRF(R) X (7 X FRF(R)) = - V(FRF(R) ■ FRP(R))

[0269]

[0270] As a result, and noting that ( cos2c t ) = 1 / 2, we may write:

[0271] 1

[0272] mR(t) = Fsec= F0(R) - = ~zVU

[0273]

[0274] sec

[0275] This means that a “secular” force (Fsec) may be defined as the time-averaged force acting on a particle of charge z in the rapidly oscillating RF potential. In other words, the secular force is proportional to the spatial gradient of a secular potential (Usec)

[0276] (FRF)2

[0277] u

[0278]

[0279] -= u°+^ =Uo + Ups

[0280] Here,

[0281] U

[0282]

[0283] ps4mco2

[0284] This is the “pseudo-potential” created by the RF field. The time-averaged equation of motion over one period of the fast oscillation shows that, when time-averaged, the secular potential can be written as a sum of the stationary potential and the “pseudo-potential”. For quadrupolar fields etc., the “pseudopotential” is proportional to the square of the magnitude of the oscillating part of the potential because FfiFoc uRF, and is also inversely proportional to the particle mass-to-charge ratio: mlz. Note also that because FRFOC Z, then \Jpsoc z2, and the resulting force is independent of the sign of the charge on the charged particle.

[0285] Summary of the Figures

[0286] Embodiments and experiments illustrating the principles of the invention will now be discussed with reference to the accompanying figures in which:

[0287] Figure 1A schematically shows a configuration of a tandem mass spectrometer according to an example of the invention.

[0288] Figures 1 B to 1 D show examples of an axial profile of a potential field along the axis of a linear ion trap (LIT) according to an example of the invention.

[0289] Figure 2 schematically shows a configuration of a tandem mass spectrometer according to an example of the invention.

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[0292] Figure 3 schematically shows a scheme for application of (a) DC and (b) RF trapping potentials, and (c) AC excitation voltages for the operation of a LIT according to an example of the invention.

[0293] Figure 4 shows a graph of the simulated output of precursor ions from a linear ion trap of an example of the invention, for having m / z values of m / z = 609 and m / z = 619 at under a buffer gas pressure of 0.2 mTorr (nitrogen) and subject to a m / z scan speed about 5100 Th / s. The results show the detection output of a virtual ion detector located immediately downstream of the downstream electrode set of the linear ion trap.

[0294] Figure 5 shows a “stability diagram” for a quadrupole device.

[0295] Figure 6 shows a schematic diagram of a quadrupole device provided with a power unit configured to supply an RF voltage and a mass-discriminating DC voltage and configured to supply an auxiliary RF voltage forexcitation of radial ion motion.

[0296] Figure 7 shows a “cone of reflection” for a quadrupole device comprising an end plate or exit lens arrangement.

[0297] Detailed Description of the Invention

[0298] Aspects and embodiments of the present invention will now be discussed with reference to the accompanying figures. Further aspects and embodiments will be apparent to those skilled in the art. All documents mentioned in this text are incorporated herein by reference.

[0299] The following disclosures, include examples of apparatuses and methods forTOF mass spectrometry including the use of a quadrupole linear ion trap to enhance data independent acquisition, DIA, performance of TOF mass spectrometry.

[0300] Conventional data independent acquisition, DIA, methods employ a quadrupole mass filter to perform precursor (known as ‘MST in the art) isolations with wide mass-to-charge, m / z, windows. Such methods suffer from low duty cycles and slow data acquisition speed (e.g., data acquisition times exceeding 1 second). The following examples of the invention describe methods to improve the performance of quadrupole TOF methods and systems by using a linear ion trap, LIT, to perform precursor isolations. Of course, optionally, the linear ion trap can also be operated as a mass filter in other data acquisition methods so that the normal functions of q-TOF are not affected and giving versatility to the apparatus. Examples herein describe a method to use a quadrupole linear ion trap with axial ejection for precursor ion isolation in a tandem TOF system with axial ejection. The linear ion trap may axially eject of ions with

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[0303] modest mass resolution (e.g., m / z spectral peaks with full width at half maximum, FWHM, of about 5 Th to 10 Th). Higher ion ejection efficiency may also be achieved at fast m / z scan speeds, in use. As a result, performance can be greatly enhanced and the other functions and operations of q-TOF are not affected. The duty cycle (or sensitivity) of a TOF mass spectrometry system can be improved significantly in this way, as disclosed herein. In addition, narrower precursor m / z isolation windows may become possible resulting in higher selectivity. In some examples, the data acquisition time can be reduced to less 0.5 second thereby allowing better coupling of the apparatus with fast liquid chromatography, LC, or other separation methods.

[0304] EXAMPLE 1:

[0305] Figure 1 schematically illustrates a first embodiment of an apparatus according to the invention. It is to be understood that this example illustrates components of an apparatus for TOF mass spectrometry in which certain components, such as a vacuum pump serving the vacuum chamber 102, are omitted from the illustration merely to aid clarity but are to be understood as being present.

[0306] The apparatus comprises a time-of-flight, TOF, tandem mass spectrometry system comprising an ion source 101 for providing precursor ions of a sample understudy, an ion optics assembly 103 arranged to receive precursor ions output by the ion source and to guide the received precursor ions along a central longitudinal axis 106 of the apparatus to an entrance opening of a linear ion trap (105, 107, 109). The linear ion trap comprises an upstream electrode set 105 axially positioned separately upstream of a main electrode set 107, and a downstream electrode set 109 axially positioned separately downstream of the main electrode set. Each of these electrode sets is arranged around the central longitudinal axis of the linear ion trap structure. The upstream electrode set 105 is positioned and configured for receiving the precursor ions from the ion optics assembly 103 into the ion trap.

[0307] A voltage source 104 is configured to apply to the upstream electrode set 105 and the downstream electrode set 109, a trapping voltage configured to cause the electrodes to generate a trapping potential field along and around the longitudinal axis 106 of the linear ion trap forming potential barriers at the upstream electrode set 105 and the downstream electrode set 109 to axially trap the received precursor ions within the main electrode set 107. Figure 1B shows an example of a profile of the axial potential along the central longitudinal axis 106 of the apparatus during the step of precursor ion accumulation or injection, whereby precursor ions are received into the trapping region of the apparatus. In this circumstance, the voltage source 104 is configured to apply to different voltages to the upstream electrode set 105, the main electrode set 107, and the downstream electrode set 109, to cause the electrodes of the upstream electrode set 105, the main electrode set 107, and the downstream electrode set 109 to generate, respectively, an upstream trapping potential field 105B, a main trapping potential field 107B, and an downstream trapping potential field 109B. The upstream trapping potential field 105B has a potential that is slightly larger than (e.g. by 1 Volt) the potential of the main trapping potential field 107B so as to create a low inlet potential barrier for ions within the main trapping potential field 107B. The downstream trapping potential field 109B has a potential that is significantly larger than (e.g. by 10 Volts) the potential of the main trapping potential field 107B so as to create a high outlet potential barrier for ions

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[0310] within the main trapping potential field 107B. This configuration permits precursor ions to be received, or injected, from the ion source 101 into the trapping region 107B and to be prevented by the downstream potential barrier 109B from exiting the trapping region thereby allowing accumulation of precursor ions to take place. Thus, an asymmetric potential well is formed with a relatively low upstream well wall / barrier height.

[0311] Figure 1C shows an example of a profile of the axial potential along the central longitudinal axis 106 of the apparatus during the step of precursor ion cooling following the step of precursor ion injection or accumulation. Here the voltage source 104 is configured to apply to the upstream electrode set 105, a potential that is significantly larger than (e.g. by 10 Volts) the potential of the main trapping potential field 107C so as to create a high inlet potential barrier for ions accumulated within the main trapping potential field 107C. The inlet potential barrier has the same height as the outlet potential barrier 109C. The voltages applied to the main electrode set 107, and the downstream electrode set 109, remain the same as those applied during the precursor ion accumulation step described above with reference to Figure 1B. This configuration permits received precursor ions to be retained and cooled in the trapping region 107C and to be prevented by both the upstream and downstream potential barriers, 105C and 109C, from exiting the trapping region thereby allowing the cooling of accumulated precursor ions to take place. Thus, a symmetric potential well is formed with equally high upstream and downstream well wall / barrier heights.

[0312] Figure 1D shows an example of a profile of the axial potential along the central longitudinal axis 106 of the apparatus during the step of precursor ion mass-selective axial ejection. Here the voltage source 104 is configured to maintain at the upstream electrode set 105, and the main electrode set 107, respectively, the potentials applied during the precursor ion cooling step: these potentials being such that the inlet potential barrier remains significantly larger than (e.g. by 10 Volts) the potential of the main trapping potential field 107D, so as to maintain the high inlet potential barrier for ions accumulated within the main trapping potential field 107D. The voltage source 104 is configured to apply to the downstream electrode set 109 a reduced trapping potential field 109D has a potential that is slightly larger than (e.g. by 1 Volt) the potential of the main trapping potential field 107B so as to create a low outlet potential barrier for ions within the main trapping potential field 107B. Thus, an asymmetric potential well is formed with a relatively low downstream well wall / barrier height. This configuration permits received precursor ions to be selectively axially ejected from the trapping region 107C in the manner described above, by application of an auxiliary voltage to the main electrode set thereby to excite radial enhanced radial motion (increased kinetic energy) of precursor ions in the trapping region, sufficient to overcome the downstream potential barriers 109C to exit the trapping region, depending on the mass-to-charge, m / z, ratio of the precursor ion. The potential barrier 105D formed at the upstream electrode set 105, which is much higher than the potential barrier 109D at the downstream electrode set 109 during mass-selective axial ejection such that the auxiliary voltage can be sufficient cause mass-selective axial ejection of precursor ions through the downstream electrode set 109, but be insufficient to cause mass-selective axial ejection of precursor ions through the upstream electrode set 105.

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[0315] The voltage source 104 is further configured to apply to the main electrode set 107, an AC auxiliary voltage configured to generate a radial excitation potential field to excite precursor ion motion radially to an extent depending on a mass-to-charge ratio, m / z, of the trapped precursor ions. This results in an increase in the radial component of the spatial orbital motion of the precursor ions within the radial trapping potential field which allows an increase in the coupling of radial ion motion to axial ion motion as caused by the higher-order (i.e., multipole, such as quadrupole at least) field components present in the fringing field region containing a ‘cone of reflection’, created in the axial space between the main electrode set and the downstream electrode set, as discussed in detail above. The voltage source is operable to selectively to axially eject precursor ions from the linear ion trap by application of the AC auxiliary voltage to electrodes of the main electrode set 107 to excite this radial motion of trapped precursor ions to an extend depending on their mass-to-charge, m / z, ratio.

[0316] A collision cell 113 is positioned axially downstream of the linear ion trap and is configured to receive the ejected precursor ions and to apply to them a process of collision-induced dissociation to generate product ions therefrom. It is to be understood that other ion dissociation methods, such as electron transfer dissociation, or other, may be used in place of the collision cell 113. A time-of-flight, TOF, mass analyser 115 is positioned axially downstream of the collision cell and is configured to receive the product ions generated by the collision cell and to apply to them a process of time-of-flight, TOF, mass analysis. The linear ion trap in this example comprises electrode sets each comprising a quadrupole rod set. The main quadrupole rod set 107, and the downstream quadrupole rod set, are each configured to receive a voltage from the voltage source 104 and therewith to generate a potential field configured for one or more of the following processes:

[0317] (a) the trapping, without applied mass selection, of precursor ions to accumulate precursor ions in a predefined maximal mass range supported by the main electrode set, and / or

[0318] (b) cooling the collected precursor ions by collisions with buff gas molecules, and / or

[0319] (c) ejecting trapped precursor ions so as to pass through a potential barrier formed using the downstream electrode set.

[0320] The voltage source is arranged, during the trapping process (a) noted above, to apply to the electrodes of the upstream electrode set 105, the main electrode set 107, and the downstream electrode set 109 a respective DC voltage, or RF voltages, configured to cause the electrode sets to generate respective electrical potentials which collectively form a potential well (Figs.lB, 1C, 1D) configured fortrapping precursor ions axially between the upstream electrode set and the downstream electrode set. The voltage source is arranged to apply to the electrodes of the upstream electrode set 105 a respective DC voltage, or RF voltages, configured to cause the upstream electrode set to generate an electrical potential barrier 105B that is lower than an electrical potential barrier 109B simultaneously generated by the downstream electrode set 109 in response to a respective DC voltage, or RF voltages, applied thereto by the voltage source. This provides a low-sided well wall at the ion inlet side of the linear ion trap and a high-sided well wall at the ion outlet side of the linear ion trap to allow precursor ions to enter the potential well from the io 4154-9954-8199, v. 18388035

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[0322] source without exiting the well downstream, thereby permitting accumulation of precursor ions as discussed above with reference to Figure 1B.

[0323] The voltage source is arranged, during the ejecting process (c) noted above, to apply to the electrodes of the downstream electrode set 109 a respective DC voltage, or RF voltages, configured to cause that electrode set to generate an electrical potential barrier 109D that is lower than an electrical potential barrier simultaneously generated by the upstream electrode set 105 in response to a respective DC voltage, or RF voltages, applied thereto by the voltage source. This provides a low-sided well wall 109D at the ion outlet side of the linear ion trap and a high-sided well wall 105D at the ion inlet side of the linear ion trap to allow precursor ions that have been accumulated within the trapping region to be mass-selectively ejected axially from the potential well in the downstream direction, but not in the upstream direction.

[0324] The downstream electrode set 109 is axially shorter in length than the axial length of the main electrode set and is configured to generate a potential barrier at an axial position located within or adjacent to the downstream electrode set. If the potential barrier is located at an axial position adjacent to the downstream electrode set 109, then this axial position is located upstream of the downstream electrode set 109 between the main electrode set 107 and the downstream electrode set 109.

[0325] The voltage source is arranged to apply to the electrodes of the main electrode set 107 RF voltages with a waveform (e.g., alternating) configured to cause at least the main electrode set to generate a quadrupole potential field (e.g., a pseudo-potential) to trap precursor ions in the linear ion trap in conjunction with said axial trapping voltages, and with a waveform (i.e., concurrent auxiliary voltage waveform) configured to eject ions from the linear ion trap according to their m / z. Accordingly, the voltage source is arranged to apply to the electrodes of the main electrode set 107 an AC auxiliary voltage with a waveform (e.g., alternating) configured to cause the main electrode set to eject trapped ions from the linear ion trap according to their m / z. This is done by changing the amplitude and / or frequency of the AC auxiliary voltage waveform, or the main RF trapping voltage waveform, to values such that selected ions are those possessing a mass-to-charge ratio, m / z, that can receive sufficient kinetic energy to overcome the potential barrier ( and the ‘cone of reflection’) at, or adjacent to, the downstream electrode set 109. An ion guide 113 is provided downstream of the downstream electrode set 109 for receiving selected precursor ions ejected from the linear ion trap.

[0326] The voltage source may be arranged to apply at least to the electrodes of the downstream electrode set 109 an RF (radio-frequency) voltage, instead of a DC voltage, with a waveform (e.g., alternating) configured to cause at least the downstream electrode set 109 to generate a quadrupole potential field (e.g., a pseudo-potential) configured for radially trapping ions therein. This may be appropriate when the potential barrier is located axially within or adjacent to the downstream electrode set.

[0327] Note that Fig.1 shows one possible embodiment of a tandem mass spectrometer system according to this invention. As noted above, it comprises of an ion source 101, ion optics to transfer ions from an atmospheric pressure region to the vacuum region 103, multiple quadrupole rods (including upstream rods 105, main rods107 and downstream rods 109), a fragmentation device 113 that fragments the 4154-9954-8199, v. 18388035

[0328] 25

[0329] precursor ions and a high resolution TOF mass analyser 115. The ion source 101 could be ESI, APCI, APPI, DESI, and so on. The ion optics 103 can include one or more than one ion guides, e.g., multipole rods or stack ring ion guides. Differential pumping can be used (using vacuum pumps not shown) to produce a pressure gradient along the longitudinal axis 106 of the apparatus from atmospheric pressure at an ion input end of the vacuum chamber 102 to a vacuum pressure downstream, for the operation of the device.

[0330] Regarding the potential barrier formed by the fringing field, Figure 1D shows the potential barrier formed by DC voltages applied to the main electrode set 107 and the downstream electrode set 109 for ion axial ejection. The potential barrier for axial ejection of ions can also be a pseudopotential provided by the RF or AC fields. The main RF trapping voltages applied to the main electrode set 107 and the downstream electrode set 109 can have the same frequency and a phase difference; in some embodiments, their phase difference can be zero but is not limited to zero.

[0331] The amplitudes of the two main RF trapping voltages applied to the main electrode set 107 and the downstream electrode set 109 can be same or different. For example, the RF amplitude applied to the downstream electrode set 109 can be higher than that applied to the main electrode set 107 such that a higher RF pseudopotential is formed in the downstream electrode set 109 than in the main electrode set 107 at a given (x, y), where:

[0332] x2+ y2≤ r02

[0333] The difference between two RF pseudopotentials can provide a potential barrier for axial ejection of ions, which works similarly as the DC potential barrier illustrated in Figure 1D. Alternatively, another AC voltage (that is other than the excitation AC auxiliary voltage) having different frequency of the main RF trapping voltage can be applied to the four rods of downstream electrode set 109, which can provide an AC pseudopotential that works as a potential barrier for ion ejection. It may be more preferable to combine DC voltages and a pseudopotential provided by AC or RF to generate an optimal potential barrier for axial ejection of ions.

[0334] The shape of potential barrier in the fringing field between the main electrode set 107 and the downstream electrode set 109 may differ from that employed in a conventional MSAE application (e.g., see Hager, J. W., “A New Linear Ion Trap Mass Spectrometer”; Rapid Commun. Mass Spectrom, 2002; 16:512-526). In other words, the boundary shape of reflection in this method may differ from the “cone of reflection” shown in Figure 7 due to the difference of the electrode geometry. For example, the angle between the boundary shape of reflection and ion optical axis 106 is greater than that in a conventional MSAE. The main electrode set 107 and the downstream electrode set 109 are both quadrupole rods and thus the fringing field between them has a quadrupole field as the main component and the other higher order components are much smaller than a standard MSAE apparatus using a quadrupole with an end plate or exit lens arrangement. The invention, in examples, permits a geometry design that allows ions to be axially ejected with a smaller threshold of radial kinetic energy than is possible using a conventional MSAE. Therefore, this invention may provide much higher ejection efficiency, and the kinetic energy of ejected ions may also be lower.

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[0337] The multiple quadrupole rods of the (including upstream rods 105, main rods107 and downstream rods 109) may comprise electrodes (or at least parts of electrodes) with geometries of either hyperbolic shapes or cylinder shapes that can provide good quadrupole potential field. The fragmentation device 113 may comprise multipole rods or stack ring ion guides. Herein it is referred as a collision cell where product ions are produced from fragmentations of precursor ions at relative high pressure. A high resolution TOF mass analyser 115 may take the form of an orthogonal extraction type arrangement 115 comprising a pusher region 115a, and ion mirror 115b and a TOF detector 115c. Other TOF types and other high resolution mass analysers (e.g. orbitrap, FTICR) could also be used for this improved DIA method.

[0338] EXAMPLE 2:

[0339] Figure 2 schematically illustrates a second embodiment of an apparatus according to the invention. As between Example 1 and Example 2, like items are assigned like reference symbols.

[0340] Example 2 is similar to the apparatus described above for Example 1, with the difference that the configuration includes an ion guide 211 arranged downstream of the linear ion trap for receiving selected precursor ions ejected axially from the linear ion trap and for guiding those ions to the collision cell 113. The other parts in common with Example 1 have been described above. The ion guide 211 is implemented between the downstream rods 109 and the fragmentation device 113. This ion guide 211 is provided to cool the ejected ions from LIT and transfer these cooled ions into the fragmentation device 113. This cooling process can reduce ion loss of precursor ions selected by LIT and improve the sensitivity. The use of the ion guide 211 can also allow better tuning of the potential barrier formed within or near the downstream rods 109 and can improve the performance of the LIT. Nitrogen, air or argon can be used as a buffer gas at a pressure in a range from 0.02 mTorrto 2 mTorr. Simulated results shown in Fig. 4 used nitrogen as a buffer gas at a pressure of 0.2 mTorr. The axial length of the main rod set 107 of the ion guide may be from about 60 mm to about 200 mm to achieve ab effective cooling step noted as step (b) above.

[0341] Figure 3 schematically shows applications of DC and RF trapping voltages to electrode sets of the linear ion trap, as well as AC auxiliary (excitation) voltages, to operate quadrupole rods of the trap for ion trapping and axial ejection.

[0342] Ions are radially trapped by applying RF voltages (e.g., 1 MHz frequency) out of phase to two pairs of rods. Dipole excitation can be performed by applying two phases of AC auxiliary voltage waveforms to one pair of electrodes. Other excitation methods by application of appropriate auxiliary voltages, e.g., quadrupole excitation, boundary excitations (i.e., ion excitations at the Mathieu stability diagram boundary. See Fig. 5) and so on, are not illustrated as examples in Fig.3, but they are also possible to allow this axial ejection method.

[0343] Ions are axially trapped in the main rods by 107 by setting appropriate DC offsets (‘DCT, ‘DC2’, ‘DC3’) for the upstream, main and downstream rod sets (105, 107 and 109). For positive ions, the DC voltage value ‘DC2’ should be lower than ‘DCT and ‘DC3’. The upstream rods 105 could be replaced by an ion optic

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[0345] 27

[0346] lens if desired, In practice, however, the upstream rod set 105 is preferred as supporting the mass filtering operation of the LIT.

[0347] The downstream ion guide 211 is optional but preferred for the better performance. A potential barrier can be formed within or near to the downstream rods 109 for axial ejection of selected (resonantly excited) precursor ions. Voltages applied to the main and downstream rod sets 107, 109 and to the rod electrodes of the ion guide 211, can contribute to this potential barrier, and the main contribution is preferably from the voltages applied to the downstream rod set 109.

[0348] The potential barrier may be a DC potential barrier, or a pseudopotential barrier formed by AC voltages, or a combination of DC potentials and pseudopotential of AC voltages. It should be typically between 0.2V to 20V in height / size. The geometry of the downstream rods 109 is preferably a quadrupole geometry, but other multipole rod geometries (e.g. hexapole, octupole, and so on) may be used.

[0349] The length of the downstream rods 109 is preferably between O.5ro to 5ro, where ro is the field radius of a quadrupole field, which preferably has a value: 1mm < ro < 20mm.

[0350] The process of resonantly selecting precursor ions, applied by the linear ion trap by application of auxiliary voltages as described in detail above, may take the form of a mass analysis and can be performed by scanning the amplitude of the AC auxiliary voltages, or of the main RF trapping voltages, applied to rod sets of the linear ion trap (LIT) to bring ions to be reasonably excited with a dipole auxiliary AC signal. The voltage supply 104 may comprise an RF power supply used for this mass analysis function via the scanning of the main RF trapping voltage applied to the LIT. Digital waveform and frequency scanning may be used for this. Precursor ions can be resonantly excited increasingly or decreasingly according to their m / z during the mass scanning. The excited ions gain kinetic energies in radial directions that can be transferred into kinetic energies in axial direction due to the coupling of radial-to-axial ion motion caused by the presence of multipole field components in the fringing field region between the main electrode set 107 and the downstream electrode set 109, as described above, as well as due to collisions with a buffer gas provided in the linear ion trap.

[0351] A potential barrier is formed near the downstream rods 109 to allow trapping of unexcited ions and the axial ejection of excited ions with high efficiency and modest mass resolution. The optimal potential barrier and the optimal amplitude of dipole AC is found to depend on m / z of ions and scan speeds of LIT; ideally, these parameters can be scanned during a mass analysis of LIT or can be set as comprised static values for a specific mass range and scan speeds. The main electrode set 107 is not working as a mass filter in the method described herein. Rather, the main electrode set 107 is working as linear ion trap that can trap and accumulate ions with a large m / z range; the unexcited ions remain present inside 107 when excited ions are ejected. For example, precursor ions can be ejected from low to high m / z from LIT, when ions of 200 Th are ejected, ions of 300 Th are still present in LIT and will be ejected afterwards.

[0352] The operation of the linear ion trap may include the following steps:

[0353] STEP 1: Inject precursor ions into the linear ion trap and accumulate precursor ions with a wide range of m / z. This may require a time of e.g., about 5 - 1000 msec);

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[0356] STEP 2: Cool the injected ions (e.g., requiring about 5 msec);

[0357] STEP 3: Perform a mass scan via the linear ion trap to axially eject precursor ions according to their m / z (e.g., requiring about 100 - 1000 msec); and,

[0358] STEP 4: Empty the linear ion trap and its upstream device, such as an ion source, (e.g., requiring about 5 msec).

[0359] The preferred potential barrier formed at or near the downstream electrodes 109 may be set only during the step of mass scanning (i.e., STEP 3). Axial ejection is the central feature of the mass analysis, and it occurs in the STEP 3 rather than STEP 4. STEP 4 is an emptying step that is purely optional and but is recommended when the ion beam intensity is too strong which can over-fill the ion trap. Whether or not to include STEP 4 can depend on different applications. In general, it is recommended to include STEP 4. An alternative method to operate the linear ion trap (LIT) may omit the “empty” step (i.e., STEP 4) mentioned above and perform ion accumulations using an ion guide that is placed upstream of the LIT during the mass scanning of the LIT in STEP 3; these accumulated ions could be used in the next cycle of mass scanning to allow the best use of ions. In practice, the alternative operation should be used at very fast scan speeds, when no mass discrimination occurs in the ion accumulation and the number of accumulated ions has not reach the ion capacity of the LIT; the alternative operation can further increase duty cycle to about 100% in the ideal case.

[0360] For an improved DIA mode, it is desired to operate the instrument in following two steps for data acquisition: in the first step, quadrupole rods 105, 107 and 109 are operated as RF only ion guides and DC voltages are set to avoid dissociations of precursor ions, allowing high resolution TOF mass analyser 115 to acquire precursor mass spectra (also known as MS1 spectra or spectra for survey scans); in the second step, rods 105, 107 and 109 are operated as a linear ion trap (LIT) to perform precursor isolation over the targeted mass range. The ejected precursor ions are fragmented in the fragmentation device 113, and the fragmented ions (i.e., product ions), and / or any remaining unfragmented precursor ions, are mass analysed by high resolution TOF 115.

[0361] In some applications, it may be preferred to repeat the second step several times for average to improve the data quality. After the second step is completed, the instrument goes back to the first step and starts the next cycle of data acquisition. In some application, the first step can be skipped, and such operation should still be considered as a DIA method.

[0362] Fig.4 shows simulation data of the ejected ions of m / z 609 and m / z 619. LIT is operated at a scan speed of 5100 Th / s at 0.2 mTorr nitrogen. A 120 mm long main rods are used with cylinder shapes (the radius of the cylinder is 1.126 ro, where ro is the field radius and equals to 5 mm). The amplitude of 1 MHz cosine RF is scanned increasingly from 1180 V with a step of 0.1089 mV every 10 nanosecond, the amplitude and the frequency of dipole AC are 3V and 0.376953 MHz (corresponding to q=0.84 for ion excitation). Under these conditions, the ejection efficiency of 83% is achieved and FWHM for m / z 609 ions is about 6.4 Th. The median kinetic energy of ejected ions is about 20 eV, which is suitable for collisional induced dissociations. When this LIT is operated at scan speed of 1000 Th / s, it can give >95% ejection efficiency 4154-9954-8199, v. 18388035

[0363] 29

[0364] and FWHM of 5.2 Th. It is also possible to increase its mass resolution for a narrow precursor window (e.g. FWHM < 2 Th) at the cost of ejection efficiency epically at slow scan speed. In DIA mode, it is usually desired to operate this LIT at fast scan speeds to increase duty cycle and acquisition speed. It may be useful to operate the LIT at slow scan speed for a narrow precursor window in some scenarios. The features disclosed in the foregoing description, or in the following claims, or in the accompanying drawings, expressed in their specific forms or in terms of a means for performing the disclosed function, or a method or process for obtaining the disclosed results, as appropriate, may, separately, or in any combination of such features, be utilised for realising the invention in diverse forms thereof.

[0365] While the invention has been described in conjunction with the exemplary embodiments described above, many equivalent modifications and variations will be apparent to those skilled in the art when given this disclosure. Accordingly, the exemplary embodiments of the invention set forth above are considered to be illustrative and not limiting. Various changes to the described embodiments may be made without departing from the spirit and scope of the invention.

[0366] For the avoidance of any doubt, any theoretical explanations provided herein are provided for the purposes of improving the understanding of a reader. The inventors do not wish to be bound by any of these theoretical explanations.

[0367] Any section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.

[0368] Throughout this specification, including the claims which follow, unless the context requires otherwise, the word “comprise” and “include”, and variations such as “comprises”, “comprising”, and “including” will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integers or steps.

[0369] It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Ranges may be expressed herein as from “about” one particular value, and / or to “about” another particular value. When such a range is expressed, another embodiment includes from the one particular value and / or to the other particular value. Similarly, when values are expressed as approximations, by the use of the antecedent “about,” it will be understood that the particular value forms another embodiment. The term “about” in relation to a numerical value is optional and means for example + / - 10%.

[0370] References

[0371] A number of publications are cited above in order to more fully describe and disclose the invention and the state of the art to which the invention pertains. Full citations for these references are provided below. The entirety of each of these references is incorporated herein.

[0372] US6177668B1

[0373] 4154-9954-8199, v. 18388035

[0374] 30

[0375] Hager, J. W., “A New Linear Ion Trap Mass Spectrometer”; Rapid Commun. Mass Spectrom, 2002; 16:512-526.

[0376] US10068753

[0377] F. A. Londry, James W. Hager, “Mass selective axial ion ejection from a linear quadrupole ion trap”, Journal of the American Society for Mass Spectrometry, Volume 14, Issue 10, 2003, pp 1130-1147.

[0378] 4154-9954-8199, v. 1

Claims

838803531Claims:

1. An apparatus for tandem mass spectrometry comprising:an ion source for providing precursor ions;a linear ion trap comprising a set of electrodes defining an ion trapping region extending along an ion optical axis configured for receiving the precursor ions into the ion trapping region;a voltage source configured for:applying to the set of electrodes trapping voltages configured to generate an axial trapping potential field in the ion trapping region forming a potential barrier to axially trap received precursor ions within the linear ion trap; and,applying to the set of electrodes RF voltages configured to generate a radial trapping potential field in the ion trapping region to radially trap received precursor ions within the linear ion trap;wherein the voltage source is configured selectively to change the radial trapping potential field to increase the kinetic energy of precursor ions in the ion trapping region so that precursor ions can overcome the potential barrier selectively according to their mass-to-charge ratio, m / z, thereby axially ejecting the selected precursor ions from the linear ion trap;a dissociation cell configured to receive the ejected precursor ions and to apply to them a process of ion dissociation to generate product ions therefrom;a mass analyser configured to receive the product ions and to apply to them a process of mass analysis.

2. An apparatus according to any preceding claim wherein the set of electrodes and the voltage source are configured to generate a quadrupole radial trapping potential field in the ion trapping region wherein the voltage source is configured to apply to the set of electrodes said RF voltages configured to have a negligible or no mass-discriminating DC voltage component therein.

3. An apparatus according to any preceding claim wherein the set of electrodes are configured to provide a multi-polar electrical potential field in which the contribution from potential field components of order higher than quadrupolar, is enhanced at the potential barrier as compared to such contribution at other parts of the multi-polar electrical potential field.

4. An apparatus according to any preceding claim wherein the voltage source is configured to apply to electrodes of the set of electrodes one or more AC auxiliary voltages to generate an excitation potential field in the ion trapping region to excite radially motion of precursor ions therein.

5. An apparatus according to claim 4 wherein the voltage source is configured to apply to electrodes of the set of electrodes said one or more AC auxiliary voltages so as to generate a dipolar electric potential field in the ion trapping region.

6. An apparatus according to claim 4 of claim 5 wherein the amplitude and / or the frequency of a said AC auxiliary voltage differs from an amplitude and / or a frequency, respectively, of a said RF voltage 4154-9954-8199, v. 1838803532applied simultaneously to the set of electrodes to generate the radial trapping potential field in the ion trapping region.

7. An apparatus according to any of claims 4 to 6 wherein the voltage source is configured to apply to electrodes amongst the set of electrodes said one or more AC auxiliary voltages having a frequency that differs from the frequency of a said RF voltage and corresponds to a frequency of resonant ion motion in the radial trapping potential field thereby to excite such resonant ion motion.

8. An apparatus according to any preceding claim wherein the set of electrodes is configured to define a fringing field region in which a fringing field is generated collectively by the radial trapping potential field and the axial trapping potential field, wherein the voltage source is configured to apply said AC auxiliary voltages to at least electrodes of the set of electrodes that are adjacent to or surrounding the fringing field region.

9. An apparatus according to any preceding claim wherein the voltage source is configured to apply said RF voltages to the set of electrodes to generate the radial trapping potential field as a pseudopotential field in the ion trapping region.

10. An apparatus according to any preceding claim wherein the voltage source is configured to apply said trapping voltages to the set of electrodes as AC voltages to generate the axial trapping potential field as a pseudopotential field in the ion trapping region thereby forming a pseudopotential barrier to axially trap the received precursor ions within the linear ion trap.

11. An apparatus according to any of preceding claims 1 to 9 wherein the voltage source is configured to apply the trapping voltage to the set of electrodes as a DC voltage to generate a DC axial trapping potential field in the ion trapping region thereby forming a DC potential barrier to axially trap the received precursor ions within the linear ion trap.

12. An apparatus according to any preceding claim when dependent upon claim 8 wherein the fringing field comprises a combination of a pseudopotential barrier component originating from the radial trapping potential field and either: a pseudopotential barrier component originating from the axial trapping potential field; or, a DC potential barrier component originating from the axial trapping potential field.

13. An apparatus according to any preceding claim wherein the set of electrodes comprises multiple electrode sets including a main electrode set, and a downstream electrode set, each configured to receive a voltage and therewith to generate a potential field configured for one or more of the following processes:the trapping, without applied mass selection, of precursor ions thereby accumulating precursor ions in a predefined maximal mass range supported by the main electrode set, and / or; cooling the collected precursor ions by collisions with buff gas molecules, and / or;4154-9954-8199, v. 1838803533ejecting trapped precursor ions so as to pass through a potential barrier formed using the downstream electrode set.

14. An apparatus according to claim 13 wherein the voltage source is arranged to apply to the electrodes of the main electrode set a said RF voltage with a waveform configured to cause at least the main electrode set to generate a quadrupole potential field to trap said precursor ions in the linear ion trap in conjunction with said axial trapping voltages, and subsequently eject ions according to their m / z from the linear ion trap.

15. An apparatus according to claim 14 wherein the voltage source is arranged to apply to the electrodes of the main electrode set a said AC auxiliary voltage with a waveform configured to cause the main electrode set to eject trapped ions from the linear ion trap according to their m / z by changing the amplitude and / or frequency of the AC auxiliary voltage waveform, and / or a waveform of the RF voltages, to values such that selected ions are those possessing a mass-to-charge ratio, m / z, that can receive sufficient kinetic energy to overcome the potential barrier at the downstream electrode set..

16. An apparatus according to any preceding claim when dependent upon claim 13 comprising an ion guide arranged downstream of the downstream electrode set of the linear ion trap to receive selected precursor ions ejected from the linear ion trap.

17. An apparatus according to any preceding claim when dependent on claim 13, wherein the voltage source is arranged to apply to the electrodes of the main electrode set and the downstream electrode set a respective DC voltage configured to cause the electrode sets to generate respective electrical potentials which collectively form a potential barrier configured for trapping within the linear ion trap received precursor ions, and / or for ejecting selected trapped precursor ions axially from the linear ion trap.

18. An apparatus according to any preceding claim when dependent on claim 13, wherein the downstream electrode set is configured to generate a potential barrier at an axial position located within or adjacent to the downstream electrode set.

19. An apparatus according to any preceding claim when dependent on claim 13, wherein the voltage source is arranged to apply at least to the electrodes of the downstream electrode set an RF voltage with a waveform configured to cause at least the downstream electrode set to generate a quadrupole potential field configured for radially trapping ions therein.

20. An apparatus according to according to any preceding claim wherein the mass analyser comprises a time-of-flight, TOF, mass analyser configured to receive the product ions and to apply to them a process of time-of-flight, TOF, mass analysis.4154-9954-8199, v. 183880353421. A method for tandem mass spectrometry comprising:providing precursor ions;providing a set of electrodes defining a linear ion trap comprising a trapping region extending along an ion optical axis and receiving the precursor ions into the ion trap;applying to the set of electrodes trapping voltages configured to generate an axial trapping potential field in the trapping region forming a potential barrier to axially trap received precursor ions within the linear ion trap;applying to the set of electrodes RF voltages configured to generate a radial trapping potential field in the trapping region to radially trap received precursor ions;changing the radial trapping potential field to increase the kinetic energy of precursor ions in the ion trapping region so that precursor ions can overcome the potential barrier thereby axially ejecting the selected precursor ions from the linear ion trap;applying a process of collision-induced dissociation to the ejected precursor ions to generate product ions therefrom;applying a process of mass analysis to the product ions.4154-9954-8199, v. 1

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