Methods and systems for performing tandem ms / ms / ms mass spectrometry

Abstract

The present teachings are generally related to a method of performing mass spectrometry, which includes dissociating a plurality of precursor ions to generate a first set of product ions, wherein ions with approximately same m / z are associated in a group, and wherein said first set of product ions contains at least two groups of ions with distinct m / z's. The method further includes introducing the first set of product ions into an ion trap; transferring different groups of the first set of product ions during different time intervals from the ion trap to an ion dissociation device so as to cause dissociation of at least a portion of the first set of product ions to generate a second set of product ions, and acquiring a mass spectrum of the second set of product ions.

Description

[0001] METHODS AND SYSTEMS FOR PERFORMING TANDEM MS / MS / MS MASS SPECTROMETRY

[0002] CROSS-REFERENCE TO RELATED APPLICATIONS

[0003] This application claims priority to, and the benefit of, U.S. Provisional Application No. 63 / 534,408, entitled “Ion Processing Device Utilizing Dual RF Circuit,” and filed August 24, 2023, the content of which is incorporated herein by reference in its entirety.

[0004] TECHNICAL FIELD

[0005] The present disclosure relates to mass spectrometry, and more particularly, to methods and systems for generating a controllable axial pseudopotential barrier in multipole rod sets of mass spectrometers.

[0006] BACKGROUND

[0007] The present teachings are generally directed to systems and methods for mass spectrometry, and more particularly, to generation and use of axial pseudo potentials generated via RF fields in mass spectrometry.

[0008] Mass spectrometry (MS) is an analytical technique for determining the structure of test chemical substances with both qualitative and quantitative applications. MS can be useful for identifying unknown compounds, determining the composition of atomic elements in a molecule, determining the structure of a compound by observing its fragmentation, and quantifying the amount of a particular chemical compound in a mixed sample. Mass spectrometers detect chemical entities as ions such that a conversion of the analytes to charged ions must occur.

[0009] In some MS systems, ion traps are employed for enhancing the functionality of the mass spectrometric systems. For example, in some applications, the trapped ions can undergo dissociation, e.g., via electron activated dissociation, to generate product ions that can subsequently be released from the trap. In some applications, the ions trapped within an ion trap can be ejected from the ion trap according to decreasing or increasing m / z ratios of ions. Such mass selective ejection of the ions can provide certain advantages, e.g., it can allow for selective detection of ions, enhanced sensitivity, among others. Notwithstanding various advancements achieved in recent years in ion traps and their use in mass spectrometry, there is still a need for further improvements in techniques for trapping ions in and releasing ions from ion traps.

[0010] SUMMARY

[0011] The present teachings are generally related to generating an axial pseudo potential barrier via an RF field that is non-homogeneous along the axis. As discussed in more detail below, such a pseudo potential barrier can be employed in a variety of different applications. By way of example, such a pseudo potential barrier can be employed for trapping ions within a rod set comprising a plurality of rods arranged in a multipole configuration. In other applications, an adjustment of the height of the pseudo potential barrier established in a rod set together with application of a DC potential between the rod set and an external electrode can be utilized to cause mass selective extraction of ions trapped within the rod set. In yet other applications, such a pseudo potential barrier can be employed in multiplexing approaches for performing mass spectrometry.

[0012] I. Mass selective axial ejection of ions

[0013] In one aspect, a method of performing mass spectrometry is disclosed, which includes applying a first RF voltage to a first pair (groupings comprising more than two 2 rods, e.g., two grouping of three (3) rods as shown in FIGS. IE and IF, can also be used) of a first plurality of rods arranged in a multipole configuration and extending from a proximal end providing an inlet for receiving ions into a volume between the rods to a distal end providing an outlet through which ions can exit the first plurality of rods, applying a second RF voltage to a second pair of the first plurality of rods, wherein said second RF voltage has substantially the same frequency as the first RF voltage. The method further includes establishing a DC electric potential difference between any of said first pair and said second pair of the first plurality of rods and at least one electrode that is axially separated from the distal end of any of said first pair and said second pair of the plurality of rods, and adjusting a difference between at least one of amplitudes and phases of said first RF voltage and said second RF voltage so as to maintain radial confinement of the ions while adjusting an axial pondermotive force in a space between the distal end of the plurality of rods and the at least one electrode such that the combination of the adjusted axial pondermotive force and said DC electric potential causes an m / z-selective axial extraction of the ions through said outlet.

[0014] The DC electrical potential difference can be generated via application of at least a DC voltage to any of the plurality of rods and the at least one electrode.

[0015] In some embodiments, the at least one electrode includes at least one rod of a second plurality of rods that are arranged in a multipole configuration, e.g., a quadrupole configuration.

[0016] In some embodiments, the step of adjusting the difference between amplitudes of the first and the second RF voltages comprises lowering the amplitude difference from an initial value to a final value, where the final value is optionally zero. In some such embodiments, the step of lowering the difference between amplitudes includes ramping down an amplitude of at least one of the first and the second voltages. In some embodiments, the step of lowering the difference between amplitudes includes ramping up the amplitude of at least one of the first RF voltage and the second RF voltage. In some embodiments, the step of adjusting the difference between phases includes varying the difference between phases from an initial phase value to a final phase value that is closer to 180 degrees than the initial phase value. By way of example, the step of adjusting the difference between phases includes varying the difference between phases from about 45 degrees to about 180 degrees, e.g., from about 90 degrees to about 180 degrees.

[0017] In some embodiments, the amplitudes of the first and the second voltages are maintained at substantially constant values while varying the phase difference. The amplitudes of the first and the second RF voltages can be substantially equal. Alternatively, the amplitudes of the first and the second voltages can be different.

[0018] In some embodiments, the step of varying the phase difference includes changing the phase difference continuously over a predefined range. In some embodiments, the step of varying the phase difference includes digitally changing the phase difference over a plurality of values within a predefined range.

[0019] In some embodiments, the first plurality of rods can be in the form of a branched rod set. By way of example, such a branched rod set can include two groups of L-shaped rods that are axially separated from one another and each group includes rods arranged in a multipole configuration, e.g., a quadrupole, a hexapole or an octupole configuration. In a related aspect, a method of performing mass selective extraction of ions from a branched rod assembly comprising a first and a second rod set axially separated from one another to form an ion trapping region therebetween is disclosed, which includes applying RF voltages to the first rod set and the second rod set so as to maintain the branched rod assembly in an asymmetric state thereby generating an axial pondermotive force for facilitating trapping of a plurality of ions within the ion trapping region, establishing a DC electric potential difference between rods of the second rod set and at least one electrode axially separated from the second rod set, and adjusting a difference between at least one of amplitudes and phases of the RF voltages so as to maintain radial confinement of the ions while reducing an amplitude of the axial pondermotive force such that the DC electric potential difference is effective in causing m / z selective extraction of the ions from the second rod set.

[0020] In some embodiments, the plurality of ions present in the ion trap can include a plurality of product ions generated via any of fragmentation and charge reduction of a plurality of precursor ions introduced into the ion trapping region.

[0021] In a related aspect, a method of performing m / z (mass) selective extraction of ions from a rod set having a plurality of rods arranged in a multipole configuration is disclosed, which includes maintaining the rod set in an asymmetric state so as to generate a pondermotive force for trapping a plurality of ions within a volume between the plurality of rods of the rod set, establishing an adjustable DC voltage difference between the rod set and at least one electrode, and adjusting the DC voltage difference so as to cause m / z selective extraction of ions from the rod set via overcoming the trapping provided by the axial pondermotive force.

[0022] In some embodiments, the step of adjusting the DC voltage difference includes increasing an amplitude of the DC voltage difference. By way of example, and without limitation, the step of adjusting the DC voltage difference can include ramping up the amplitude of the DC voltage difference.

[0023] In a related aspect, a mass spectrometer is disclosed, which includes at least a first rod set comprising a first plurality of rods arranged according to a multipole configuration so as to provide a volume between the rods, said first plurality of rods extending from a proximal end providing an inlet through which ions can be introduced into the volume between the rods to a distal end providing an outlet through which ions can exit the rod set. The mass spectrometer can further include at least one RF voltage source for applying a first RF voltage to a first pair of the plurality of rods and a second RF voltage to a second pair of the first plurality of rods, wherein each of said first and second pair comprises two radially opposed rods. At least one electrode is axially separated from the distal end of the first plurality of rods. The mass spectrometer further includes at least one DC voltage source for establishing a DC electric potential difference between said at least one electrode and said first plurality of rods and at least one controller that is in communication with the at least one RF voltage source and the at least one DC voltage source. The controller is configured to transmit control signals to the at least one RF voltage source for adjusting a difference between at least one of amplitudes and phases of the first and second RF voltages so as to maintain radial confinement of the ions while adjusting an axial pondermotive force in a space between the distal end of the first plurality of rods and the at least one electrode such that the combination of the adjustment of the axial pondermotive force and the DC electric potential causes m / z-selective axial extraction of ions through said outlet of the first plurality of rods.

[0024] In some embodiments, the DC voltage source is configured to apply a DC voltage to at least one of the first plurality of rods and the at least one electrode.

[0025] Further, in some embodiments, the at least one electrode can include at least one rod of a second plurality of rods arranged in a multipole configuration, such as a quadrupole, a hexapole or an octupole configuration.

[0026] The control signals can cause the at least one RF voltage source to adjust the voltages applied to the rods of the rod set so as to cause a transition of the rod set from an asymmetric operational state into a symmetric operational state.

[0027] In some embodiments, the control signals can cause the at least one RF voltage source to reduce the amplitude difference by ramping up the amplitude of at least one of the first and the second voltage.

[0028] In some embodiments, the control signals can cause the RF voltage source to vary phase difference between the first and the second RF voltages from a first phase value to a second phase value, where the second phase value is closer to 180 degrees than the first phase value. For example, the control signals can cause the RF voltage source to vary the phase difference between the first and the second voltages from about 45 degrees to about 180 degrees, e.g., from about 90 degrees to about 180 degrees.

[0029] Further, in some embodiments, the mass spectrometer’s rod set can include a branched rod set. n. Generation of axial pondermotive force using phase shift change and its use for mass selective axial ejection of ions

[0030] In another aspect, a method of establishing an axial pondermotive force in a multipole rod set comprising a plurality of rods arranged in a multipole configuration to provide an ion passageway extending along an axial direction from an inlet for receiving ions to an outlet through which the ions can exit the passageway is disclosed. The method can include applying a first voltage to a first pair of said plurality of rods, applying a second voltage to a second pair of said plurality of rods, and setting a phase difference between the first and the second RF voltage so as to generate a pondermotive force along said axial direction.

[0031] In some embodiments, the phase difference can be in a range of about 45 degrees and about 180 degrees, e.g., in a range of about 90 degrees to about 180 degrees.

[0032] In a related aspect, in a rod set utilized in a mass spectrometer and comprising a plurality of rods arranged in a multipole configuration providing a passageway extending along an axial direction from an inlet for receiving ions to an outlet through which the ions can exit the passageway, a method for adjusting a pondermotive force along the axial direction is disclosed. The method can include applying a first voltage to a first pair of the plurality of rods, applying a second voltage to a second pair of said plurality of rods, and adjusting a phase difference between the first voltage and the second voltage so as to vary an axial pondermotive force generated via said first and said second voltage.

[0033] In some embodiments, the step of varying the phase difference can include continuously changing the phase difference between an initial and a final phase value, e.g., between about 90 degrees to about 180 degrees so as to reduce the amplitude of the pondermotive force.

[0034] In a related aspect, in a mass spectrometer having a rod set comprising at least one plurality of rods arranged in a multipole configuration with a volume between the rods for receiving ions, said rod set providing an inlet through which ions can enter the volume between the rods and an outlet through which the ions can exit the rod set, a method for performing mass selective ion extraction is disclosed. The method includes applying a first RF voltage between a first pair of rods of said rod set with phase one, applying a second RF voltage between a second pair of rods of said rod set with phase two, establishing a DC electric potential difference between the rods of the second rod set and at least one electrode axially separated from the distal end of the second rod set, and varying at least one of a phase difference between said first and said second voltage and the DC electric potential difference so as to cause mass selective ion ejection through the outlet of the rod set.

[0035] In some embodiments, the step of varying the phase difference can include varying the phase difference between about 45 degrees and about 180 degrees, or a value between 90 degrees and 180 degrees. In some such embodiments, the amplitudes of the first and the second voltages can be maintained substantially constant while the phase difference is varied.

[0036] By way of example, the multipole configuration of the rod set can be any of a quadrupole, a hexapole and an octupole configuration. Further, in some embodiments, the at least one rod set can be in the form of a branched rod set.

[0037] HI. Ion-ion reaction and mutual trapping

[0038] In another aspect, a method for mutual trapping of a plurality of positive and negative ions within a rod set having a plurality of rods arranged in a multipole configuration is disclosed, which includes applying a first voltage to a first pair of the plurality of rods, applying a second voltage to a second pair of the plurality of rods, and selecting a phase difference between the first voltage and the second voltage to operate the rod set in an asymmetric operational state so as to generate an axial pondermotive force to cause mutual trapping of the positive and the negative ions in the rod set.

[0039] In some embodiments, the method can further include introducing a neutral reactive reagent into the rod set and ionizing the reactive reagent to generate the plurality of negatively or positively charged reacting ions. By way of example, the reactive reagent can be ionized outside of the rod set and the resulting ions can be transferred to the rod set. In some embodiments, the ions of first polarity can be introduced into the rod set while the rod set is operating in a symmetric operational mode. In some such embodiments, the analyte ions of a second polarity can be introduced into the rod set subsequent to the step of generating reactive ions with the first polarity.

[0040] In some embodiments, either the positive or the negative ions can be introduced into the rod set while the rod set is in a symmetric operational state. Subsequent to the introduction of either the positive or the negative ions into the rod set, the rod set can be switched from the symmetric operational state to an asymmetric operational state and the ions having the opposite charge polarity can be introduced into the rod set while the rod set is in the asymmetric operational state.

[0041] In some embodiments, the rod set can include an ion-ion reaction region. In some such embodiments, the positive and the negative ions can interact in the ion-ion reaction region to generate a plurality of product ions. In such embodiments, the method can further include releasing the product ions from the rod set. In some cases, the rod set can be a branched rod set.

[0042] In a related aspect, a method for mutual trapping of a plurality of positive and negative ions within a rod set having a plurality of rods arranged in a multipole configuration is disclosed, which includes applying a first voltage to a first pair of the plurality of rods, applying a second voltage to a second pair of the plurality of rods, and using a controller to select at least one of an amplitude difference and a phase difference between the first voltage and the second voltage so as to operate the rod set in an asymmetric operational state in order to cause mutual trapping of the positive and the negative ions in the rod set.

[0043] In a related aspect, a method of performing ion-ion reaction in mass spectrometry is disclosed, which comprises introducing a reactive reagent into an ion-ion reaction region of an ion trap while the ion trap is in a symmetric operational state, ionizing the reactive reagent so as to produce a plurality of reactive ions having a first charge polarity, transitioning the ion trap from the symmetric operational state into an asymmetric operational state, introducing a plurality of precursor ions having a second charge polarity opposite to the first charge polarity of the reactive ions into the ion-ion reaction region of the ion trap while the ion trap is in the asymmetric operational state, where the asymmetric operational state is configured to cause mutual trapping of the first and second plurality of ions. The method can further include any of extracting and releasing the product ions from the ion trap.

[0044] In some embodiments, the step of transitioning the ion trap from the symmetric operational state to the asymmetric operational state can include adjusting at least one of an amplitude difference and a phase difference between the first and the second voltage.

[0045] In a further aspect, a method of establishing an axial pondermotive force in a multipole rod set comprising a plurality of rods arranged in a multipole configuration to provide an ion passageway extending along an axial direction from an inlet for receiving ions to an outlet through which at least some of the ions can exit the passageway is disclosed. The method includes applying a first voltage to a first pair of the plurality of rods, applying a second voltage to a second pair of the plurality of rods, and setting a phase difference between the first and the second voltages so as to generate a pondermotive force along the axial direction.

[0046] In some embodiments, the phase difference can be in a range of about 45 degrees and about 180 degrees.

[0047] In some embodiments, the phase difference can be in a range of about 90 degrees to about 180 degrees.

[0048] In some embodiments, setting the phase difference further can include selecting the phase difference to operate the multipole rod set in an asymmetric operational state so as to cause mutual trapping of positive and negative ions in the multipole rod set.

[0049] In some embodiments, the method may further include introducing a neutral reactive reagent into the multipole rod set and ionizing the reactive reagent to generate the negatively or positively charged ions.

[0050] In some embodiments, the reactive agent is ionized outside of the multipole rod set and resulting ions are transferred to the multipole rod set.

[0051] In some embodiments, reactive ions of a first polarity can be introduced into the multipole rod set while the multipole rod set is operating in a symmetric operational mode.

[0052] In some embodiments, analyte ions of a second polarity can be introduced into the multipole rod set subsequent to introducing the reactive ions with the first polarity. In some embodiments, the method can further include introducing either the positive or the negative ions into the multipole rod set while the multipole rod set is in a symmetric operational state.

[0053] In some embodiments, the method can further include switching the multipole rod set from the symmetric operational state to the asymmetric operational state subsequent to the step of introducing either the positive or the negative ions into the multipole rod set, and introducing the ions having an opposite charge polarity of a polarity of the ions introduced during the symmetric operational state into the multipole rod set while the multipole rod set is in the asymmetric operational state.

[0054] In some embodiments, the multipole rod set may include an ion-ion reaction region.

[0055] In some embodiments, the positive and negative ions can interact in the ion-ion reaction region to generate a plurality of product ions.

[0056] In some embodiments, the method can further include releasing the product ions from the multipole rod set.

[0057] In some embodiments, the multipole rod set can include a branched rod set.

[0058] In a related aspect, a method of establishing an axial pondermotive force in a rod set utilized in a mass spectrometer and comprising a plurality of rods arranged in a multipole configuration providing a passageway extending along an axial direction from an inlet for receiving ions to an outlet through which the ions can exit the passageway, and for adjusting a pondermotive force along the axial direction is disclosed. The method includes applying a first voltage to a first pair of the plurality of rods, applying a second voltage to a second pair of the plurality of rods, and adjusting a phase difference between the first voltage and the second voltage so as to vary an axial pondermotive force generated via the first and the second voltages.

[0059] In some embodiments, the step of adjusting the phase difference can include substantially continuously changing the phase difference between an initial and a final value.

[0060] In some embodiments, the method can further include using a controller to select at least one of an amplitude difference and the phase difference between the first voltage and the second voltage so as to operate the rod set in an asymmetric operational state to cause mutual trapping of positive and negative ions in the rod set.

[0061] In an additional aspect, a method is disclosed for performing mass-selective ion extraction in a mass spectrometer having a rod set comprising at least one plurality of rods arranged in a multipole configuration with a volume between rods of the rod set for receiving ions, with the rod set providing an inlet through which ions can enter the volume between the rods and an outlet through which the ions can exit the rod set. The method includes applying a first RF voltage between a first pair of the rods of the rod set with phase one, applying a second RF voltage between a second pair of the rods of the rod set with phase two, establishing a DC electric potential difference between the rods of the rod set and at least one electrode axially separated from the distal end of the rod set, and varying at least one of a phase difference between the first and the second RF voltages and the DC electric potential difference so as to cause mass selective ion ejection through the outlet of the rod set.

[0062] In some embodiments, the step of varying the phase difference can include varying the phase difference between about 45 degrees and about 180 degrees, or a value between 90 degrees and 180 degrees.

[0063] In some embodiments, the method can further include maintaining amplitudes of the first and the second RF voltages substantially constant while varying the phase difference.

[0064] In some embodiments, the multipole configuration can include any of a quadrupole, a hexapole and an octupole configuration.

[0065] In some embodiments, the rod set can include a branched rod set.

[0066] In a related aspect, a method of performing ion-ion reaction in mass spectrometry is disclosed, that includes introducing a reactive reagent into an ion-ion reaction region of an ion trap while the ion trap is in a symmetric operational state, ionizing the reactive reagent so as to produce a plurality of reactive ions having a first charge polarity, transitioning the ion trap from the symmetric operational state into an asymmetric operational state, and introducing a plurality of precursor ions having a second charge polarity opposite to the first charge polarity of the reactive ions into the ion-ion reaction region of the ion trap while the ion trap is in the asymmetric operational state. The asymmetric operational state is configured to cause mutual trapping of the plurality of precursor ions.

[0067] In some embodiments, the method further includes any of extracting and releasing product ions from the ion trap.

[0068] In some embodiments, the step of transitioning the ion trap from the symmetric operational state to the asymmetric operational state can include adjusting at least one of an amplitude difference and a phase difference between first and second RF voltages applied to respective sets of rods.

[0069] In a further aspect, a mass spectrometer is disclosed that includes an ion trap to receive a plurality of ions, with the ion trap including at least a rod set comprising a plurality of rods arranged according to a multipole configuration so as to provide a volume between the plurality of rods, the plurality of rods extending from a proximal end providing an inlet through which the plurality of ions is received into the volume between the plurality of rods, to a distal end providing an outlet through which at least some of resultant ions processed by the ion trap exit the ion trap, and at least one RF voltage source for controllably applying RF voltages to one or more rods of the plurality of rods. The mass spectrometer further includes at least one controller to control operations of the ion trap through controllably applying the RF voltages to the one or more rods to perform one or more of a controlled release of the at least some of the resultant ions and / or trapping at least a portion of the plurality of ions.

[0070] In some embodiments, the at least one controller configured to control operations of the ion trap can be configured to cause applying a first voltage to a first pair of the plurality of rods, cause applying a second voltage to a second pair of the plurality of rods, and set a phase difference between the first and the second voltages so as to generate a pondermotive force along an axial direction of the rod set.

[0071] In some embodiments, the phase difference can be in a range of about 45 degrees and about 180 degrees.

[0072] In some embodiments, the controller configured to set the phase difference can be further configured to select the phase difference to operate the rod set in an asymmetric operational state so as to cause mutual trapping of a plurality of positive and negative ions in the rod set.

[0073] In some embodiments, the ion trap can further be configured to receive a neutral reactive reagent into the rod set and to ionize the reactive reagent to generate the negatively or positively charged reacting ions.

[0074] In some embodiments, the reactive agent can be ionized outside of the rod set, and the ionized reactive agent ions can be transferred to the rod set.

[0075] In some embodiments, the ion trap can further be configured to first receive either positive or negative ions into the rod set while the rod set is in a symmetric operational state, and, subsequent to receiving either the positive or the negative ions into the first rod set, the ion trap can be configured to switch the rod set from the symmetric operational state to an asymmetric operational state, and to receive ions, with an opposite polarity of what was first received during the symmetric operational state, into the first rod set while the first rod set is in the asymmetric operational state.

[0076] In some embodiments, the at least one controller configured to control operations of the ion trap can be configured to apply a first RF voltage between a first pair of the first rod set with phase one, apply a second RF voltage between a second pair of rods of the first rod set with phase two, establish a DC electric potential difference between rods of the first rod set and at least one electrode axially separated from the distal end of the first rod set, and vary at least one of a phase difference between the first and the second RF voltages and the DC electric potential difference so as to cause m / z selective ion ejection through the outlet of the first rod set.

[0077] In some embodiments, the at least one controller configured to control operations of the ion trap can be configured to perform ion-ion reaction in mass spectrometry, including to receive at the ion trap a reactive reagent into an ion-ion reaction region of the ion trap while the ion trap is in a symmetric operational state, ionize the reactive reagent so as to produce a plurality of reactive ions having a first charge polarity, transition the ion trap from the symmetric operational state into an asymmetric operational state, and receiving at the ion trap a plurality of precursor ions, having a second charge polarity opposite to the first charge polarity of the reactive ions, into the ion-ion reaction region of the ion trap while the ion trap is in the asymmetric operational state. The asymmetric operational state can be configured to cause mutual trapping of the plurality of precursor ions.

[0078] IV. Multiplexing

[0079] In one aspect, a method of performing mass spectrometry is disclosed, which includes introducing a plurality of precursor ions having ion populations with different m / z ratios into a mass filter, where the mass filter is configured to allow passage of at least two populations of the precursor ions having two different m / z ratios. The precursor ion populations exiting the mass filter can be introduced into a mass selective ion extraction device comprising a plurality of rods arranged in a multipole configuration and extending from a proximal end providing an inlet for receiving ions to a distal end providing an outlet through which ions can exit the mass selective ion extraction device, wherein a first RF voltage is applied to one pair of the plurality of rods and a second RF voltage is applied to another pair of the plurality of rods. The mass selective ion extraction device can further include at least one electrode that is axially separated from the plurality of rods and to which a DC voltage can be applied to establish a DC potential difference between the at least one electrode and the plurality of rods. An amplitude difference and / or a phase difference between the first and the second voltage can be adjusted so as to cause, in combination with said DC potential difference, mass selective extraction of said at least two populations of the precursor ions. The ion population extracted during each of the temporal periods can be introduced into an ion dissociation device to generate product ions associated with that ion population. For each ion population, a mass analysis of the respective product ions can be performed. In some cases, a difference in the m / z ratios of the at least two populations of the precursor ions is sufficiently large such that the product ions associated with the two ion populations can be independently detected via the mass analysis.

[0080] In some embodiments, the at least two populations of the precursor ions are extracted from the mass selective ion extraction device in different temporal intervals.

[0081] In some embodiments, the at least two populations of the precursor ions are substantially co-extracted from the mass selective ion extraction device as two partially overlapping ion clouds. In some such embodiments, the product ions corresponding to the at least two populations of the precursor ions exhibit substantially similar temporal profiles with a time offset relative to one another so as to allow correlating each of the product ions with one of the two populations of the precursor ions.

[0082] In some embodiments, the step of adjusting any of the amplitude and the phase difference between the first and the second RF voltage includes varying the phase difference from an initial phase value to a final phase value that is closer to 180 degrees than the initial phase value while maintaining the amplitudes of the first and the second voltages substantially constant. By way of example, and without limitation, the phase difference can be varied from about 90 degrees to about 180 degrees.

[0083] In some embodiments, the step of adjusting any of the amplitude and the phase difference between the first and the second voltage includes lowering the amplitude difference while maintaining the phase difference substantially constant.

[0084] In some embodiments, the amplitude of at least one RF voltage is increased during the step of adjusting any of the amplitude and the phase difference.

[0085] In some embodiments, the at least two distinct populations of ions are transmitted sequentially using a mass filter. In some embodiments, the at least two distinct populations of ions are co-transmitted using a mass filter.

[0086] In some embodiments, the ion dissociation device can include any of an electron activated dissociation device and a collision induced dissociation device.

[0087] Further, in some embodiments, the multipole configuration can be in any of a quadrupole, a hexapole and an octupole configuration.

[0088] In some embodiments, a difference between the m / z ratios of the at least two populations of the precursor ions is equal to or greater than about any of 20, 30, 40, and 50 Da.

[0089] In a related aspect, a mass spectrometer is disclosed, which includes a mass filter configured to receive a plurality of precursor ions having ion populations with different m / z ratios, where the mass filter is configured to allow passage of at least two populations of the precursor ions having two different m / z ratios. The mass spectrometer further includes a mass selective ion extraction device positioned downstream of the mass filter, which includes a plurality of rods that are arranged in a multipole configuration and extend from a proximal end that provides an inlet for receiving the precursor ions exiting the mass filter to a distal end providing an outlet through which ions can exit the mass selective ion extraction device. At least one electrode is positioned downstream of the mass selective ion extraction device and is axially separated from the distal end thereof. The mass spectrometer further includes at least one RF voltage source for applying a first RF voltage to a first pair of the plurality of rods and a second RF voltage to a second pair of the plurality of rods, where each of the first and the second pair includes two radially opposed rods, and at least one DC voltage source for establishing a DC electric potential between the plurality of rods and the at least one electrode. At least one controller is in communication with the at least one RF voltage source and the at least one DC voltage source and is configured to transmit control signals to the at least one RF voltage source for adjusting a difference between at least one of amplitudes and phases of the first and the second RF voltage so as to maintain radial confinement of the ions while causing, in combination with said DC voltage, mass-selective axial ejection of the ions through said outlet of the rod set. Further, an ion dissociation device is positioned downstream of the mass selective ion extraction device to receive ions extracted from the mass selective ion extraction device and to cause dissociation of at least a portion of those ions, thereby generating a plurality of product ions. The mass spectrometer further includes a mass analyzer for receiving the plurality of product ions and generating mass detection signals associated with said product ions.

[0090] By way of example, the multipole configuration can be any of a quadrupole, a hexapole and octupole configuration.

[0091] The mass spectrometer can further include an ion source for generating the plurality of the precursor ions.

[0092] In one aspect, a method of performing mass spectrometry is disclosed, which includes accumulating a plurality of precursor ions in a mass selective ion extraction device comprising a plurality of rods arranged in a multipole configuration and extending from a proximal end providing an inlet for receiving ions to a distal end providing an outlet through which ions can exit the ion extraction device, wherein a first RF voltage is applied to one pair of the plurality of rods and a second RF voltage is applied to another pair of the plurality of rods. The method further includes establishing a DC electric potential difference between an electrode positioned downstream of the mass selective ion extraction device and axially separated from the distal end of the plurality of the rods and said plurality of the rods, adjusting any of an amplitude difference and a phase difference between the first and the second voltage so as to cause, in combination with said DC electric potential difference, mass selective extraction of the accumulated precursor ions from the mass selective ion extraction device, and introducing the extracted ions into a mass filter. The mass filter is adjusted in synchrony with the mass selective extraction of the precursor ions so as to allow passage of ions extracted from the mass selective extraction device and having m / z ratios within a bandpass of the mass filter to pass through the mass filter. The ions passing through the mass filter are introduced into an ion dissociation device to cause dissociation thereof to generate a plurality of product ions. This is followed by performing mass analysis of the plurality of product ions.

[0093] In some embodiments, the mass filter exhibits a greater mass-to-charge resolution than a mass resolution of the mass selective ion extraction device. By way of example, an m / z center of the bandpass of the mass filter can be selected based on previously-obtained temporal profile of mass selective extraction of ions from the mass selective extraction device.

[0094] In some embodiments, the number of ions introduced into the mass selective extraction device is selected so as to reduce potential effect of space charge on the mass ion selective extraction.

[0095] In a related aspect, a mass spectrometer is disclosed that includes a mass selective ion extraction device comprising a first plurality of rods arranged in a multipole configuration and extending from a proximal end providing an inlet for receiving ions to a distal end providing an outlet through which ions can exit the ion extraction device, at least one RF voltage source for applying a first RF voltage to one pair of the plurality of rods and applying a second RF voltage to another pair thereof. An electrode is positioned downstream of the mass selective ion extraction device and is axially separated from the distal end of the first plurality of rods. The mass spectrometer further includes at least one DC voltage source for establishing a DC electric potential between said at least one electrode and said first plurality of rods, and a controller that is in communication with said at least one RF voltage source and said at least one DC voltage source. The controller can be configured to send control signals to the RF voltage source for adjusting any of an amplitude difference and a phase difference between the first and the second voltage so as to cause, in combination with said DC electric potential, mass selective extraction of the precursor ions from the mass selective ion extraction device. A mass filter is positioned downstream of the mass selective ion extraction device for receiving precursor ions extracted from the mass selective extraction device. An ion dissociation device is positioned downstream of the mass filter for receiving ions passing through the mass filter and causing dissociation of at least a portion of the ions to generate a plurality of product ions. The mass spectrometer further includes a mass analyzer positioned downstream of the ion dissociation device for receiving the product ions and providing a mass analysis thereof.

[0096] In some embodiments, the mass filter can include a plurality of rods that are arranged in a multipole configuration.

[0097] In some embodiments, the at least one RF voltage source includes a first RF voltage source for applying RF voltages to the first plurality of rods and a second RF voltage source for applying RF voltages to the second plurality of rods of the mass filter.

[0098] In some embodiments, the at least one DC voltage source includes at least one DC voltage source for applying a DC voltage between the at least one electrode and the first plurality of rods and at least a second DC voltage source for applying a resolving DC voltage to the mass filter.

[0099] In some embodiments, the controller is configured to send control signals to the second RF voltage source and the second DC voltage source of the mass filter to adjust the mass filter in synchrony with said mass selective extraction of the precursor ions so as to allow passage of ions extracted from the mass selective extraction device and having m / z ratios within a bandpass of the mass filter to pass through the mass filter.

[0100] V. MS3Spectrometry

[0101] In some aspects, the present disclosure provides methods and systems for performing tandem triple mass spectrometry.

[0102] In some embodiments, such a method of performing mass spectrometry can include dissociating a plurality of precursor ions to generate a first set of product ions, with ions with approximately same m / z being associated in a group, and with said first set of product ions contains at least two groups of ions with distinct m / z’s. The method further includes introducing the first set of product ions into an ion trap; transferring different groups of the first set of product ions during different time intervals from the ion trap to an ion dissociation device so as to cause dissociation of at least a portion of the first set of product ions to generate a second set of product ions, and acquiring a mass spectrum of the second set of product ions.

[0103] In some embodiments, the method can further include correlating each of the second set of product ions to one of said different groups of the first set of product ions.

[0104] In some embodiments, the step of transferring the first set of product ions can include m / z selectively extracting the first set of product ions from the ion trap.

[0105] In some embodiments, m / z selectively extracting the first set of product ions can include introducing the plurality of precursor ions into an upstream ion dissociation device to cause dissociation of at least a portion of the plurality of precursor ions so as to generate at least the first set of product ions, directing said first set of product ions into the ion trap, wherein the ion trap comprises a plurality of rods arranged in a multipole configuration providing an inlet to receive the first set of product ions, and an outlet through which resultant ions processed by the ion trap exit, wherein a first RF voltage is applied to at least one pair of the plurality of rods and a second RF voltage is applied to at least another pair of the plurality of rods, establishing a DC electric potential between at least one electrode positioned downstream of the plurality of rods and axially separated from a distal end thereof and said plurality of rods, and controllably adjusting any of an amplitude and a phase difference between the first and the second RF voltages so as to cause, in combination with said DC electric potential, an ordered m / z selective extraction of the different groups of the first set of product ions, during the different time intervals, according to respective different one or more m / z ratios associated with the each of the different groups of the first set of product ions.

[0106] In some embodiments, controllably adjusting any of the amplitude and the phase difference between the first and the second RF voltages so as to cause the ordered m / z selective extraction of the different groups of the first set of product ions can include controllably adjusting any of the amplitude and the phase difference between the first and the second RF voltages to cause m / z selective extraction from high to low of the one or more m / z ratios associated with the different groups of the first set of product ions. In some embodiments, the method can further include introducing input source ions into a mass filter located upstream of the upstream ion dissociation device, with the mass filter being configured to allow passage of precursor ions having an m / z ratio of interest, and wherein the precursor ions correspond to the plurality of ions introduced to the upstream ion dissociation device.

[0107] In some embodiments, the upstream ion dissociation device and said ion trap can be implemented as a single device.

[0108] In some embodiments, the ion trap can exhibit a mass extraction resolution equal to or greater than an m / z separation of ions forming groups with adjacent m / z.

[0109] In some embodiments, acquiring the mass spectrum of the secondary product ions can include a time-of-flight mass analyzer. However, other mass analyzers may also be suitable, and include, a 3D ion trap, a linear ion trap, a quadrupole, an Orbitrap, and an FTICR (Fourier transform ion cyclotron resonance) mass analyzer.

[0110] In a related aspect, a mass spectrometer is disclosed that includes a first ion dissociation device for receiving a plurality of ions and causing dissociation of at least a portion thereof to generate a first set of product ions, with ions with approximately same m / z being associated in a group, and with said first set of product ions contains at least two groups of ions with distinct m / z’s. The mass spectrometer further includes an ion trap to receive the first set of product ions and to transfer different groups of the first set of product ions during different time intervals to a second ion dissociation device so as to cause dissociation of at least a portion of the first set of product ions to generate a second set of product ions; and a mass analyzer to acquire a mass spectrum of the second set of product ions.

[0111] In some embodiments, the mass spectrometer can further include an analysis module to correlate each of the second set of product ions to one of said different groups of the first set of product ions.

[0112] In some embodiments, the ion trap configured to transfer the first set of product ions can be configured to m / z selectively extract the first set of product ions from the ion trap. In some embodiments, the ion trap configured to m / z selectively extract the first set of product ions can include at least a first plurality of rods arranged in a multipole configuration and extending from a proximal end providing an inlet for receiving at least the first set of product ions, to a distal end providing an outlet through which resultant ions processed by the ion trap, at least one electrode positioned downstream of said ion trap and axially separated from a distal end of said plurality of rods, at least one RF voltage source to apply a first RF voltage to one pair of the plurality of rods and apply a second RF voltage to another pair thereof, at least one DC voltage source to establish a DC electric potential between said at least one electrode and said plurality of rods, and a controller. The controller is in communication with the at least one RF voltage source and said at least one DC voltage source, with the controller configured to send control signals to said RF voltage source for adjusting any of an amplitude and a phase difference between the first and the second RF voltages so as to cause, in combination with said DC electric potential, an ordered m / z selective extraction of the different groups of ions during the different time intervals, resulting from operations of the ion trap on the at least the first set of product ions, according to respective one or more different m / z ratios associated with the different groups of ions.

[0113] In some embodiments, the controller configured to send signals to adjust any of the amplitude and the phase difference between the first and the second RF voltages so as to cause the ordered m / z selective extraction of the different groups of the first set of product ions can configured to controllably adjust any of the amplitude and the phase difference between the first and the second RF voltages to cause m / z selective extraction from high to low of the one or more different m / z ratios associated with the different groups of the first set of product ions.

[0114] In some embodiments, the controller can be configured to send control signals to adjust the phase difference between the first and the second RF voltages while maintaining the amplitude difference to cause m / z selective extraction of said different groups of product ions, according to the respective different m / z values associated with the different groups of product ions, from the ion trap.

[0115] In some embodiments, the controller can be configured to send control signals to adjust the amplitude difference between the first and the second RF voltages while maintaining the phase difference substantially constant so as to cause m / z selective extraction of said different groups of product ions.

[0116] In some embodiments, the controller configured to send control signals to adjust any of the amplitude and the phase difference between the first and the second RF voltages so as to cause the ordered m / z selective extraction of different groups of ions can be configured to send control signals to adjust any of the amplitude and the phase difference between the first and the second RF voltages to cause m / z selective extraction from high to low m / z ratios, during the different time intervals, for the different groups of ions.

[0117] In some embodiments, the mass spectrometer can further include a mass filter located upstream of the first ion dissociation device and configured to receive a plurality of precursor ions and to allow passage of a subset of the plurality of the precursor ions having an m / z ratio of interest through the mass filter, with the precursor ions corresponding to the plurality of ions received by the first ion dissociation device.

[0118] In some embodiments, the mass analyzer can include any of a time-of-flight mass analyzer, a quadrupole mass analyzer, an Orbitrap mass analyzer, and an FTICR (Fourier transform ion cyclotron resonance) mass analyzer.

[0119] In some embodiments, the ion trap can exhibit a mass extraction resolution equal to or greater than an m / z separation of said first set of product ions and said second set of product ions.

[0120] In a related aspect, a method of performing mass spectrometry is disclosed that includes introducing a plurality of ions into a mass filter, where the mass filter is configured to allow passage of precursor ions having an m / z ratio of interest, introducing the precursor ions passing through the mass filter into a first ion dissociation device to cause dissociation of at least a portion of the precursor ions so as to generate at least a first and a second set of primary product ions, and introducing the first and the second set of the primary product ions into a mass selective ion extraction device, which comprises a plurality of rods arranged in a multipole configuration providing an inlet for receiving ions and an outlet through which ions can exit the ion extraction device, where a first RF voltage can be applied to one pair of the plurality of rods and a second RF voltage can be applied to another pair of the plurality of rods. The method further includes establishing a DC electric potential between the plurality of rods and at least one electrode that is positioned downstream of the plurality of rods and is axially separated from the distal end thereof. Any of an amplitude and a phase difference between the first and the second RF voltages can be adjusted so as to cause, in combination with said DC electric potential, mass selective extraction of the first and the second set of the product ions from the mass selective ion extraction device. Each of the sets of the primary product ions extracted from the mass selective ion extraction device can be introduced into a second ion dissociation device to cause dissociation of at least a portion thereof so as to generate a secondary set of product ions associated with that set. The secondary product ions can be detected and each of the detected secondary product ions can be assigned to a respective one of the first and the second set of the primary product ions.

[0121] In some embodiments, the first ion dissociation device and the mass selective ion extraction device are implemented as a single device.

[0122] In some embodiments, a mass spectrum of the secondary product ions can be acquired and analyzed.

[0123] In some embodiments, the mass selective ion extraction device exhibits a mass extraction resolution equal to or greater than an m / z separation of the first and the second set of the primary product ions.

[0124] In some embodiments, the step of acquiring the mass spectrum of the secondary product ions includes utilizing any of a time-of-flight, a quadrupole, an Orbitrap and an FTICR (Fourier transform ion cyclotron resonance) mass analyzer.

[0125] In a related aspect, a mass spectrometer is disclosed, which includes a mass filter configured to receive a plurality of precursor ions and to allow passage of a subset of the plurality of the precursor ions having an m / z ratio of interest through the mass filter. A first ion dissociation device is positioned downstream of the mass filter for receiving the precursor ions passing through the mass filter and causing dissociation of at least a portion thereof so as to generate at least a first and a second set of primary product ions. The mass spectrometer further includes a mass selective ion extraction device comprising at least a first plurality of rods arranged in a multipole configuration and extending from a proximal end providing an inlet for receiving ions to a distal end providing an outlet through which ions can exit the mass selective ion extraction device. At least one electrode is positioned downstream of the mass selective ion extraction device and is axially separated from the distal end of the plurality of rods. The mass spectrometer further includes at least one RF voltage source for applying a first RF voltage to one pair of the plurality of rods and applying a second RF voltage to another pair thereof and at least one DC voltage source for establishing a DC electric potential between the at least one electrode and the plurality of rods. A controller in communication with the at least one RF voltage source and the at least one DC voltage source is configured to send control signals to the RF voltage source for adjusting any of an amplitude and a phase difference between the first and the second voltage so as to cause, in combination with the DC electric potential, mass selective extraction of the first and the second set of the primary product ions from the mass selective ion extraction device. Further, a second ion dissociation device is positioned downstream of the mass selective ion extraction device to receive, in separate temporal intervals, the first and the second primary product ions and cause dissociation of each of said first and the second set of the primary product ions into a plurality of secondary product ions. A mass analyzer is positioned downstream of the second ion dissociation device for receiving said plurality of secondary product ions and generating a mass spectrum thereof.

[0126] In some embodiments, a controller is configured to adjust the phase difference between the first and the second voltage while maintaining the amplitude difference substantially constant so as to cause mass selective extraction of the first and the second set of the product ions from the mass selective ion extraction device.

[0127] In some embodiments, the controller is configured to adjust the amplitude difference between the first and the second voltage while maintaining the phase difference substantially constant so as to cause mass selective extraction of the first and the second plurality of the primary product ions.

[0128] Further understanding of various aspects of the present teachings can be obtained with reference to the following detailed description in conjunction with the associated drawings, which are described briefly below. BRIEF DESCRIPTION OF THE DRAWINGS

[0129] FIGS. 1A and IB schematically depict a quadrupole rod set in a balanced and an unbalanced operational state, respectively,

[0130] FIGS. 1C and ID schematically depict a quadrupole rod set having a plurality of L- shaped rods operating in a balanced and an unbalanced operational state, respectively,

[0131] FIGS. IE and IF schematically depict a another rod set having a plurality of rods operating in a balanced and an unbalanced operational states, respectively

[0132] FIG. 2A shows an example of variation of the amplitude of an RF voltage applied to one pole (designated in this figure as pole A) of a quadrupole rod set, such as that depicted in FIGS. 1A - 1D,

[0133] FIG. 2B shows an example of variation of the amplitude of an RF voltage applied to another pole (designated in this figure as pole B) of the quadrupole rod set such that the combined variation of the amplitudes results in generation of an axial RF field,

[0134] FIG. 2C shows that the amplitude of an axial RF field generated due to an asymmetry between the amplitudes of the RF A and RF B voltages decreases as the degree of the RF A and RF B voltage difference decreases such that the axial RF field vanishes when the RF A and RF B amplitudes are the same,

[0135] FIG. 3A shows three panels in which panel A shows that a phase difference of 90 degrees between the RF A and RF B voltages, panel B shows a phase difference of 180 degrees between the RF A and RF B voltages, and panel C shows that a transition of the phase difference from 90 degrees to 180 degrees results in progressive reduction in the amplitude of an axial RF field reaching a vanishing amplitude at a phase difference of 180 degrees,

[0136] FIG. 3B shows graphs corresponding to axial and radial field strengths as a function of phase difference between RF A and RF B voltages,

[0137] FIG. 4 is a flow chart depicting various steps in an embodiment of a method for mass selective extraction of ions from a multipole rod set,

[0138] FIG. 5 schematically depicts an electron reaction device according to an embodiment, FIG. 6A is a flow chart depicting various steps of a method according to an embodiment for mutual trapping of positively- and negatively-charged ions in an ion trap,

[0139] FIG. 6B schematically depicts an ion-ion reaction device according to an embodiment of the present teachings operating in a symmetric operational mode during which a reactive reagent is introduced into the device and is exposed to an electron beam to generate a plurality of negatively- charged reacting ions,

[0140] FIG. 6C schematically depicts the ion-ion reaction device of FIG. 6B operating in an asymmetric operational mode during which positive precursor ions are introduced into the device to be mutually trapped with the negatively-charged reacting ions within an ion trapping region of the device,

[0141] FIG. 6D schematically depicts the ion-ion reaction device of FIG. 6A operating in a symmetric operational mode during which product ions generated via interaction of the positively-charged precursor ions and the negatively-charged reacting ions are allowed to exit the device,

[0142] FIG. 7 is an example of a system that can be utilized for introducing a reactive reagent from a reservoir into the ion-ion reaction device depicted in FIGS. 6B - 6D,

[0143] FIG. 8A schematically depicts a charge reaction device according to an embodiment of the present teachings operating in a symmetric operational mode during which a reactive reagent is introduced into the device and is exposed to an electron beam to generate a plurality of negatively- charged reacting ions,

[0144] FIG. 8B schematically depicts the ion-ion reaction device of FIG. 8A operating in an asymmetric operational mode during which positive precursor ions are introduced into the device to be mutually trapped with the negatively-charged reacting ions within an ion trapping region of the device such that the interaction of the negatively-charged reacting ions and positive precursor ions results in a charge reduction of the positive precursor ions to generate a plurality of product ions, FIG. 8C schematically depicts the charge reduction device of FIG. 8A operating in an asymmetric operational mode during which the high m / z product ions are allowed to exit the device, while precursor ions are retained in the trap,

[0145] FIG. 9A is a flow chart depicting various steps in a method according to an embodiment of the present teachings for performing mass spectrometry,

[0146] FIG. 9B is a schematic view of a mass spectrometer according to an embodiment of the present teachings,

[0147] FIG. 9C shows a hypothetical example of a plurality of precursor ions,

[0148] FIG. 9D shows a hypothetical example of m / z transmission widows of a mass filter employed in the mass spectrometer shown in FIG. 9B,

[0149] FIG. 9E schematically depicts the ion populations accumulated in the mass selective ion extraction device of the mass spectrometer of FIG. 9B, subsequent to the passage of those ions through the mass filter,

[0150] FIG. 9F shows the mass dependent transmission profile of the mass selective ion extraction device between an initial m / z ratio setting and a final m / z ratio setting,

[0151] FIG. 9G schematically depicts two ion clouds corresponding to two precursor ions that have been extracted from a mass selective ion extraction device and introduced into a downstream collision cell,

[0152] FIG. 9H schematically shows the temporal profiles of product ions generated via dissociation of the precursor ions illustrated in FIG. 9G,

[0153] FIG. 91 schematically depicts correlating mass spectral lines of the product ions generated via fragmentation of the precursor ions depicted in FIG. 9G with the respective precursor ions,

[0154] FIG. 10 is a flow chart depicting various steps of a method according to an embodiment for performing mass spectrometry,

[0155] FIG. 11 A is a schematic view of a mass spectrometer according to an embodiment of the present teachings, FIG. 11B schematically depicts an example of an ion transmission profile of the mass selective ion extraction device employed in the mass spectrometer of FIG. 11A as a function of time, indicating that the precursor ions are extracted in a high m / z to low m / z order,

[0156] FIG. 11C schematically depicts an example of the transmission profile of the mass filter employed in the mass spectrometer of FIG. 11A as a function of time in the m / z space,

[0157] FIG. 11D schematically shows the synchrony between the change in the m / z ratio at the center of the ion transmission window of the mass filter and the change, as a function of time, in the m / z ratio of ions being extracted from the mass selective ion extraction device,

[0158] FIG. 12 is a schematic view of a mass spectrometer according to an embodiment for performing triple tandem mass spectrometry,

[0159] FIG. 13A is a flow chart depicting various steps in a method according to an embodiment for performing triple tandem mass spectrometry,

[0160] FIG. 13B is a flowchart of another example procedure to perform triple stage mass spectrometry, and

[0161] FIG. 14 is an example of implementation of a controller according to an embodiment of the present teachings.

[0162] DETAILED DESCRIPTION

[0163] It will be appreciated that for clarity, the following discussion will explicate various aspects of embodiments of the applicant’s teachings, while omitting certain specific details wherever convenient or appropriate to do so. For example, discussion of like or analogous features in alternative embodiments may be somewhat abbreviated. Well-known ideas or concepts may also for brevity not be discussed in any great detail. The skilled person will recognize that some embodiments of the applicant’s teachings may not require certain of the specifically described details in every implementation, which are set forth herein only to provide a thorough understanding of the embodiments. Similarly, it will be apparent that the described embodiments may be susceptible to alteration or variation according to common general knowledge without departing from the scope of the disclosure. The following detailed description of embodiments is not to be regarded as limiting the scope of the applicant’s teachings in any manner.

[0164] As used herein, the terms "about" and "substantially equal" refer to variations in a numerical quantity that can occur, for example, through measuring or handling procedures in the real world; through inadvertent error in these procedures; through differences in the manufacture, source, or purity of compositions or reagents; and the like. Typically, the terms "about" and "substantially" as used herein means 10% greater or less than the value or range of values stated or the complete condition or state. For instance, a concentration value of about 30% or substantially equal to 30% can mean a concentration between 27% and 33%. The terms also refer to variations that would be recognized by one skilled in the art as being equivalent so long as such variations do not encompass known values practiced by the prior art.

[0165] As used herein the term "and / or" includes any and all combinations of one or more of the associated listed items and may be abbreviated as

[0166] The term “a longitudinal axis of a rod set,” as used herein, refers to an axis (direction) extending along a length of the rods of the rod set. The term “a radial axis of a rod set,” as used herein, refers to an axis (direction) that is orthogonal to the longitudinal axis.

[0167] The term “phase” as used herein has its customary meaning and denotes the position of a periodically varying signal at a point in time during a cycle of the signal’s periodicity.

[0168] The term similar periodic signals, as used herein, is defined as if one signal can be converted to the other either by scaling and shifting in its amplitude domain or by shifting one signals phase.

[0169] The term phase difference and the extent of signal being out of phase are used here interchangeably to refer to the smallest phase shift necessary to convert one signal to another with an appropriate scaling. For example, two RF voltages are 180 degrees out of phase when the maximum value of one voltage occurs at a time corresponding to the minimum value of the other voltage for two sinusoidal signals. By way of further illustration, for two sinusoidal waveforms, two RF voltages are 90 degrees out of phase when the maximum value of one voltage occurs at a time corresponding to a zero value of the other voltage. In this disclosure, the phase difference between two voltages varies from zero to 180 degrees.

[0170] The terms “a symmetric operational state” and “a symmetric operational mode” as well as “a balanced operational state” and a “balanced operational mode” are used herein interchangeably to refer to an operational state of a rod set in which the amplitudes and phases of RF voltages applied to the rods are such that substantially no pondermotive force, e.g., caused by an axial RF field, is generated on axis of the rod set in the proximity of distal ends.

[0171] The terms “an asymmetric operational state” and “an asymmetric operational mode” as well as “an unbalanced operational state” and “an unbalanced operational mode” are used herein interchangeably to refer to an operational state of a rod set in which the amplitudes and / or phases of RF voltages applied to the rods are such that a pondermotive force, e.g., caused by an axial RF field, is generated on axis in the proximity of distal ends

[0172] The term “mass resolution” or “mass-to-charge resolution” of the device as used herein interchangeably, refers to a measure of the ability to distinguish two peaks of different mass-to- charge ratios AM, in a mass spectrum, when the mass spectral analysis is performed by said device.

[0173] The present disclosure relates generally to methods and systems for performing mass spectrometry in which a controllable pseudopotential barrier is generated along a longitudinal axis of a multipole rod set, by controlling either the relative amplitudes of RF voltages applied to the rods of the rod set and / or their relative phase differences. Such a pseudopotential barrier can be generated via a pondermotive force, e.g., caused by an inhomogeneous axial RF field. Such a pseudopotential barrier can be utilized, for example, to enable mutual trapping of positively and negatively charged ions, mass selective ion ejection, among others. As discussed in more detail below, in various embodiments, unbalanced RF voltages (herein also referred to as asymmetric RF voltages) can be employed to generate pondermotive force via axial RF fields for providing trapping of positively and negatively charged ions. Further, a transition of the RF voltages from an asymmetric operational state to a symmetric operational state, together with the establishment of a DC electric potential between the rod set and an external electrode, can be used to cause mass selective extraction of ions from the rod set. The conventional use of unbalanced RF fields in mass spectrometry presents several shortcomings. For example, typically an unbalanced RF field for driving multipole ion guides is achieved using a common tank coil circuit wherein each respective pole circuit has differing capacitance to the ground. In this case, the signals are 180 degrees out of phase and the amplitude unbalancing is achieved by providing a different capacitance for each pole circuit to the ground. The capacitance difference can be achieved using permanent and variable capacitors. The first approach does not allow for the adjustment of unbalancing and the second approach does not allow for a quick adjustment of the extent of the unbalancing. In a conventional alternative approach, two independent circuits of different frequencies are used, one having a common tank coil to supply balanced RF voltages and the other having a single tank coil to supply unbalanced RF voltages to one set of multipole rods. In the latter case, the primary radial confinement is achieved by either of the two signals, and the other signal can induce quadrupolar excitation, e.g., in a manner discussed in an article entitled “Observation of higher order quadrupole excitation frequencies in a linear ion trap,” by Collings el al., published in Journal of the American Society for Mass Spectrometry, November 2000, pp. 1016-1022.

[0174] This property of the setup can lead to significant ion losses across a wide mass range especially when switching from one signal to another is performed for primary ion confinement. In addition, the use of two frequencies typically employed for driving circuits that generate such unbalanced fields can lead to an increase, e.g., a doubling, in the number of higher order resonance frequencies that are capable of exciting ions in fringing fields leading to undesirable losses. Further, in some such conventional systems in which the ion extraction is performed using a transition between unbalanced and balanced RF fields, low m / z ions can experience micromotion and as a result be lost or fragmented in the fringing fields. Further, such systems typically fail to provide for good balancing of RF fields, which can be desirable for electronbased fragmentation.

[0175] In various embodiments, the present teachings solve such shortcomings of conventional systems. As discussed in more detail below, the generation of an axial RF field in a multipole rod set can be achieved by providing a difference in the amplitudes of two RF channels supplying RF voltages to different pairs of a multipole rod set or alternatively by selecting a phase shift between the two RF channels or combination of the two approaches (e.g., using different amplitudes for the RF voltages and selecting a particular phase shift between the RF voltages). In some embodiments, the phase shift between the two RF channels can be selected such that the variation of the axial RF field amplitude through a target volume of the multipole rod set is linear.

[0176] FIGS. 1A and IB show a rod set 10 that includes four rods 12, 14, 16, and 18 that are arranged in a quadrupole configuration such that the pair of rods 12 and 14 are radially opposed relative to one another and the pair of rods 16 and 18 are radially opposed relative to one another. The rod set 10 extends along a longitudinal axis (LA) from an inlet through which ions can enter a volume between the rods of the rod set to an outlet through which the ions can exit the rod set. For ease of description, the pair of rods 12 and 14 is herein referred to as pole A and the pair of rods 14 and 16 is herein referred to as pole B of the rod set. The same RF voltages are applied to the rods of each pole.

[0177] The application of RF voltages to the rods of the rod set can generate an RF electromagnetic field within the volume between the rods. As discussed in more detail below, the rod set can be operated in a symmetric or an asymmetric operational mode (herein also referred to as a symmetric or an asymmetric operational state).

[0178] FIG. 1A shows the rod set in a symmetric operational state. In this state, the amplitudes of the RF voltages applied to the rods are substantially equal. Further, the phase of the RF voltages applied to pole A is 180 degrees different from the respective phase of the RF voltages applied to pole B (the RF voltages applied to the rods of each pole have the same phase).

[0179] In contrast, FIG. IB shows the rod set 10 in an asymmetric operational state, which can be obtained in various embodiments in two possible ways. In one asymmetric operational state, the amplitudes of the RF voltages applied to pole A and pole B can be different. More specifically, in such embodiments, the RF voltages applied to the rods of each rod pair (12 / 14) and (16 / 18) have the same amplitude but the amplitude of the RF voltages applied to the rod pair (12 / 14) is different from the amplitude of the RF voltages applied to the rod pair (16 / 18). The phase relationships between the RF voltages are, however, the same as that discussed above in connection with the symmetric operational state. Further, it has been discovered that selecting the phase relationship between the voltages applied to pole A and pole B from 180 degrees to another phase difference (typically 90 degrees in the following embodiments) can also place the rod set in an asymmetric operational state. In an asymmetric operational state, a pondermotive force can be generated via an axial RF field in a volume between the rods of the rod set.

[0180] The rods utilized in the rod set 10 can have a variety of different shapes and cross- sectional profiles. By way of example, the rods can be straight or can have an L-shaped profile. For example, FIGS. 1C and ID show a rod set 20 that includes four L-shaped rods 22, 24, 26 and 28 that are arranged in a quadrupole configuration. The rod pair (22 / 24) forms one pole (herein referred to as pole A) and the rod pair (26 / 28) forms another pole (herein referred to as pole B). As discussed in more detail below, two sets of such L-shaped rods can be placed in tandem with an axial gap separating them to form a rod set assembly that can be utilized in a variety of mass spectrometric applications, e.g., as an ion dissociation device.

[0181] FIG. 1C shows the rod set 20 in a symmetric operational state where the RF voltages applied to pole A and pole B have the same amplitude and are 180 degrees out of phase. In contrast, FIG. ID shows the rod set 20 in an asymmetric operational state. By way of example, in various embodiments, the asymmetric operational state of the rod set 20 can be achieved via (a) changing the amplitude of the RF voltages applied to at least one of the poles (i.e., pole A, pole B or both) such that there is a difference between the amplitudes of the RF voltages applied to pole A and pole B, or (b) changing the phase shift between the RF voltages applied to pole A and pole B from 180 degrees to a value less than 180 degree (e.g., 90 degrees), or a combination of (a) and (b).

[0182] While the description provided herein discusses pairs of rods, it will be appreciated that the rod sets can be placed in groupings with more than 2 rods each. For example, FIGS. IE and IF show another rod set in a hexapole arrangement having a plurality of cylindrical rods operating in a balanced and an unbalanced operational states, respectively. Each of the six rods are divided into groupings of three (3) rods each. However, for the purpose of illustration and clarity, the remaining discussion provided herein will focus on pair groupings of rods (i.e., groupings comprising two rods each). As noted above, it has also been discovered that an axial RF field can also be generated by changing the phase difference between the different rod pairs from 180 degrees to another phase difference while maintaining the same, or different, RF voltage amplitudes among the rods. By way of example, rather than having a 180-degree phase difference between two pairs of the rods, a phase difference of 90 degrees can be employed between the respective rod pairs.

[0183] By way of illustration, FIGS. 2A and 2B show an example of transitioning a rod set, such as the above rod set 10, from an asymmetric operational state into a symmetric operational state. Initially, the amplitudes of the RF voltages applied to the pole A and pole B of the rod set (herein designated as RF A and RF B) are unequal (and the phase difference between RF A and RF B is 180 degrees in this example), resulting in the operation of the rod set assembly in an asymmetric operational state. At time 11, in order to transition the rod set assembly from the asymmetric operational state into a symmetric operational state, the amplitude of the RF B voltage is increased and the amplitude of the RF A voltage is decreased over a time period between ti and t2 such that, in this example, at time t2 the amplitude of the RF A and RF B voltages are substantially equal and the rod set has transitioned from the initial asymmetric operational state to a symmetric operational state. In this example, the concurrent ramping down of the RF A voltage and ramping up of the RF B voltage provides substantially the same radial confinement of ions during the period in which the RF A and RF B voltages are changed. In other embodiments, only RF B voltage may be ramped up.

[0184] The amplitude difference between the RF A and the RF B voltages results in the rod set assembly operating in an asymmetric operational state. FIG. 2C shows the resultant amplitude of the axial RF field. As shown in FIG. 2C, the axial RF field is generated when the rod set is operating in the asymmetric operational state. As the RF A and RF B voltages begin to decrease and increase, respectively, the amplitude of the axial RF field continues to decrease until the RF axial field vanishes when the rod state is transitioned fully into the symmetric operational state.

[0185] With reference to FIG. 3 and as noted above, in a symmetric operational state, RF voltages applied to pole A and pole B of a rod set, such as the above rod set 10, have a phase difference of 180 degrees, which in combination with equal amplitudes of the RF voltages, leads to a vanishing axial RF field. In contrast, an asymmetric operational state can be generated by changing the phase shift between the RF voltages applied to pole A and pole B of the rod set from 180 degrees to another phase value. In particular, in this example, the phase shift between the RF voltages applied to pole A and pole B has been selected to be 90 degrees so as to generate an asymmetric operational state.

[0186] As shown in panel A of FIG. 3A, a phase shift of 90 degrees in this example results in generation of an axial RF field, which can provide a pondermotive force that can generate a pseudopotential barrier, which can in turn be employed to trap a plurality of ions in the rod set.

[0187] As shown in panels B and C of FIG. 3A, as the phase difference between the RF voltages applied to pole A and pole B is changed from 90 degrees to 180 degrees the amplitude of the axial RF field decreases until at the phase shift of 180 degrees, the axial RF field vanishes.

[0188] By way of further illustration, FIG. 3B shows an example of simulated variation of the axial and radial field strengths as a function of the phase difference between RF A and RF B voltages.

[0189] In some embodiments, such a change in the phase shift can be employed for causing mass selective extraction of ions from the rod set. For example, a DC voltage difference established between an electrode and the rod set can cause the mass selective extraction of ions from the rod set as the rod set is transitioned from the asymmetric operational state to the symmetric operation state. In particular, as the pondermotive force generated by the axial RF field decreases, the DC potential can allow certain ions to overcome the pseudopotential barrier generated by the axial RF field and exit the rod set.

[0190] In various embodiments, although the intensity of the RF radial field also changes as a function of the phase change, this change is not as drastic as that of the axial RF field. In fact, in various embodiments, the RF radial field remains sufficiently strong while the axial RF field changes to ensure that the ions of interest remain radially confined within the rod set.

[0191] The present teachings can be utilized in a variety of mass spectrometric applications, such as those discussed below.

[0192] I. Mass selective extraction

[0193] A typical cycle of mass selective ion extraction can include the following steps: (1) ion loading, (2) ion cooling, and (3) axial ion ejection. During each step, the ions need to be radially confined. In some conventional systems using multipole ion rod sets, such radial confinement of the ions can be achieved by applying balanced (symmetric) RF voltages to the multipole electrodes. To constrain the ions in the axial direction, a DC potential is typically used.

[0194] In various embodiments, the transition of a multipole rod set (e.g., a rod set functioning as an ion guide in a mass spectrometer) from an asymmetric operational state to a symmetric operational state together with application of a DC voltage between the ion guide and a downstream component (e.g., a downstream electrode) can be utilized for causing mass selective extraction of ions from the ion guide. Such a process can be utilized in a variety of ion guides. By way of example and without limitation, in the following discussion, the mass selective extraction of ions using various embodiments of the present teachings is described in connection with extraction of ions from an ion dissociation device.

[0195] By way of example, with reference to the flow chart of FIG. 4, in an embodiment of a method of performing mass spectrometry, a first RF voltage can be applied to a first pair of a first plurality of rods arranged in a multipole configuration and extending from a proximal end providing an inlet for receiving ions into a volume between the rods to a distal end providing an outlet through which ions can exit the multipole rod set, and a second RF voltage can be applied to a second pair of the first plurality of rods, where the second RF voltage has substantially the same frequency as the first RF voltage. A DC electric potential difference is established between at least one of the first and the second plurality of rods and at least one electrode that is axially separated from the distal end of the first and / or second plurality of rods. A difference between at least one of amplitudes and phases of the first RF voltage and the second RF voltage is adjusted so as to maintain radial confinement of the ions while transitioning the rod set from an asymmetric operational mode, e.g., established via providing a difference in the amplitude of RF voltages applied to different rod pairs and / or selecting an appropriate phase difference between the RF voltages, to a symmetric operational mode.

[0196] For example, in the asymmetric operational mode, an axial RF field can be established in a space between the distal end of the plurality of rods and the at least one electrode so as to generate a pseudopotential for trapping the ions within the rod set. As the rod set is transitioned from the asymmetric operational mode to the symmetric operational mode, the height of the pseudopotential barrier decreases, and ions, under the influence of the DC potential, can overcome the pseudopotential barrier to exit the rod set in a mass selective manner. It should be understood that the sequence of various steps of the method is not limited to that described above but can be modified. For example, the application of the first and the second RF voltage can be done in any order, or concurrently.

[0197] Such a method of performing mass selective ion extraction can be utilized in a variety of different mass spectrometric devices.

[0198] By way of example, FIG. 5 schematically depicts an ion dissociation device 400 in the form of an electron reaction device according to an embodiment, which includes a rod set assembly similar to that shown in FIGS. 1C and ID. More specifically, the ion dissociation device 400 includes two sets of L-shaped rods 402a / 402b (the rod set 402a and 402b are also herein referred to, respectively, as the input branch and output branch), that are positioned with an axial offset relative to one another to provide an ion trapping region 404 therebetween. In this example, each rod set includes four rods that are arranged relative to one another in a quadrupole configuration. The combination of the two sets of quadrupole rods provides an axial passageway 405 and a transverse passageway 407, where precursor ions can be introduced into the ion trapping region 404 via an inlet 404a of the axial passageway and product ions generated via electron capture dissociation of the precursor ions or any other electron-induced fragmentation process, such as EIEIO (electron impact excitation of ions from organics), EID (electron induced dissociation), and any remaining precursor ions can exit the ion reaction device via an outlet 404b of the axial passageway.

[0199] An electron beam 408 can be introduced into the ion trapping region 404 via an inlet 404c of the transverse passageway to interact with ions trapped in the ion trapping region 404, where the interaction of the electrons with the trapped ions can cause dissociation of the precursor ions, e.g., via electron capture dissociation. The electron beam can exit the ion reaction device via an outlet 404d of the transverse passageway.

[0200] A pair of gate electrodes 410a / 410b are positioned, respectively, in proximity of the inlet and the outlet of the axial passageway. Application of voltages to the gate electrodes 410a and 410b allow controlling the entry of ions into the ion dissociation device and the exit of the ions from the ion dissociation device, respectively. Another pair of gate electrodes 412a / 412b (also referred to herein as pole electrodes) are positioned, respectively, in proximity of the inlet and the outlet of the transverse passageway. The electrodes 412a / 412b can be biased via application of DC voltages thereto so as to inhibit the leakage of the product and precursor ions out of the ion dissociation device through the inlet and / or outlet of the transverse passageway.

[0201] In this embodiment, a DC voltage source 414, operating under the control of a controller 418, applies a DC voltage to the gate electrode 410b to generate a DC potential barrier that inhibits the ions from exiting the ion dissociation device. Other DC voltage sources (not shown) can be utilized to apply DC voltages to the other gate electrodes to inhibit the leakage of ions from the ion dissociation device.

[0202] Two RF voltage sources 420a and 420b, also operating under the control of the controller 418, apply RF voltages to rod set 402a and 402b, respectively, at the same RF frequency so as to generate an electromagnetic field within the ion dissociation device to cause radial confinement of the product and the residual precursor ions, if any. By way of example, the RF voltages can have a frequency in a range of about 100 kHz to about 10 MHz and an amplitude in a range of about 50 to about 10000 volts.

[0203] In use, prior to the introduction of precursor ions, the controller 418 can send control signals to the RF voltage sources 420a and 420b so that the amplitudes and the phases of the applied RF voltages are such that both rod sets 402a and 402b operate in a symmetric operational state. In such a symmetric operational state, the axial RF field vanishes (some axial fringing field in proximity of the inlet and outlet may be present) and hence facilitates the loading of a plurality of precursor ions into the dissociation device.

[0204] Subsequent to loading of the ions, the amplitude of the RF voltages applied to the rod sets 402a and 402b and / or their relative phases can be adjusted to transition the rod set into an asymmetric operational state in which a pseudopotential generated in the asymmetric operational state can help trap the ions within the trapping region 400 so that the ions can undergo interactions with an electron beam.

[0205] More specifically, an electron beam 421 can be introduced into the ion dissociation device via an inlet of the transverse passageway to interact with the precursor ions and generate product ions. In some cases, the application of a DC potential between the rods of the two rod sets 402a and 402b, e.g., via a DC voltage source 415, can push the generated product ions and any remaining precursor ions from the ion trapping region into the downstream branch.

[0206] In order to extract ions (e.g., the product ions and potentially any remaining precursor ions) from the ion dissociation device, the controller 418 can send control signals to the RF voltages source 420 to change the amplitude and / or the phase of the RF voltages applied to the rods of the rod set 402b so as to cause a transition of the rod set 402b from the asymmetric operational state into a symmetric operational state. As the amplitude of the axial RF field diminishes, the DC voltage difference between the gate electrode 410b and the rods of the rod set 402b can cause mass selective axial ejection of the ions from the rod set. For example, the control signals transmitted to the RF voltage source can cause the reduction of the amplitude of the RF voltages applied to one pole of the rod set and increase the amplitude of the RF voltages applied to the other pole of the rod set, e.g., in a manner shown in FIGS. 2 A and 2B, as discussed above.

[0207] As noted above, the transition of the rod set from the asymmetric to the symmetric operational state to cause mass selective extraction of ions from the rod set can be achieved by adjusting the amplitudes of the RF voltages applied to the A and B poles so that they are substantially equal while ensuring that the phase difference between those voltages is 180 degrees.

[0208] Again, in various embodiments, the adjustment of the RF voltages applied to the A and B poles can be utilized to transition the rod set from an asymmetric operational state into a symmetric operational state, which in combination with a DC potential established between the rod set and an external electrode axially separated from the outlet of the rod set, can cause mass selective axial ejection of the ions from the rod set.

[0209] II. Ion-ion reaction devices

[0210] In one aspect, ion-ion reaction devices are disclosed, which employ various embodiments of the present teachings for trapping ions within the ion-ion reaction device and can further optionally utilize various embodiments of the present teachings for causing mass selective extraction of the product ions from the ion-ion reaction device. With reference to the flow chart of FIG. 6A, in an embodiment of a method for mutual trapping of ions with opposite charge polarities within an ion-ion reaction device having a plurality of rods arranged in a multipole configuration, a first RF voltage is applied to a first pair of the plurality rods, and a second RF voltage having the same frequency as that of the first RF voltage is applied to a second pair of rods of the plurality of rods. Further, at least one of an amplitude difference and a phase difference between the first and the second RF voltage is selected so as to operate the rod set in an asymmetric operational state in order to cause mutual trapping of the positive and negative ions in the rod set.

[0211] By way of example, with reference to FIGS. 6B, 6C, and 6D, such an ion-ion reaction device 600 can include a rod assembly 602 formed by two sets of L-shaped rods 604 / 606 that are axially offset from one another to provide a trapping region 608 therebetween. Similar to the ion trap 200 discussed above, a plurality of gate electrodes 610, 612, 614, and 616 are positioned, respectively, at the inlet and the outlet of an axial channel of the rod assembly and at the openings of the transverse channel of the rod assembly, where application of appropriate voltages to these gate electrodes can facilitate the retention of the ions trapped within the ion-ion reaction device.

[0212] In use, an electron transfer dissociation (ETD) reagent (e.g., azulene, fluoranthene and azobenzene) or a proton transfer reaction (PTR) reagent (e.g., perfluoro- 1,3- dimethylcyclohexane) can be introduced into the ion-ion dissociation device 600 while the rod assembly 602 is being operated in a symmetric mode.

[0213] ETD and PTR reactive reagents are chemicals that are typically present in solid or liquid state at room temperature. With reference to FIG. 7, in various embodiments, a low pressure can be applied to a reservoir 700 containing such a reactive reagent to convert it into a gas phase. Further, a flow of a neutral gas, such as N2, can be employed as a carrier gas to introduce the reactive reagent into the ion-ion reaction device as neutral molecules.

[0214] Referring again to FIG. 6B, an electron beam 618 at a high kinetic energy (e.g., a kinetic energy greater than 20 eV, and preferably as high as 70 eV) can be introduced into the ion-ion reaction device via its transverse channel to ionize the reactive reagent within the ion trap, thereby generating a plurality of negatively-charged reactive reagents. To retain such negatively- charged reactive reagents within the ion trap, the gate electrodes can be maintained at negative DC potentials.

[0215] With reference to FIG. 6C, following the ionization of the reactive reagent, the operational state of the rod assembly can be switched into an asymmetric operational state and a plurality of positively charged precursor ions 620 is introduced into the ion-ion reaction device. The asymmetric operational state facilitates mutual trapping of the negatively charged reactive reagent ions and the positively charged precursor ions within the ion-ion reaction device via the generation of an axial pseudopotential via an inhomogeneous RF field. In particular, the operation of the rod assembly in an asymmetric operational state results in the generation of an inhomogeneous RF field not only along the longitudinal axis of the rod assembly but also along its transverse axis, thus providing mutual trapping of both the positive and the negative ions along both directions. In various embodiments, such mutual trapping of the positive and the negative ions can substantially confine the ions within the trapping region of the rod assembly.

[0216] At this stage, neutral bias can be applied to the gate electrodes and the axial RF field generated via transition of the operational state of the ion-ion reaction device into the asymmetric state is employed for trapping of both the positive and the negative ions.

[0217] The reaction of the positively charged precursor ions with the negatively charged reactive reagent ions can lead to dissociation or other physical-chemical transformations, such as for example charge reduction of at least a portion of the positively charged precursor ions, thereby generating a plurality of positively-charged product ions.

[0218] As shown in FIG. 6D, in this embodiment, the ion-ion reaction device is transitioned into a symmetric operational mode and the DC voltages applied to the gate electrodes are adjusted to drive all positively charged product ions out of the ion-ion reaction device. More specifically, as shown in FIG. 6C, the gate electrodes 610, 612 and 614 are positively biased and the gate electrode 616 remains neutral, thereby opening the outlet of the ion-ion reaction device to all of the positively charged product ions, thereby allowing the positively-charged product ions to exit the ion-ion reaction device.

[0219] The product ions exiting the ion-ion reaction device can be analyzed by a downstream mass analyzer (not shown in these figures), e.g., as discussed further below. In another embodiment, similar to the previous embodiment, a reactive reagent is introduced into the ion-ion dissociation device and is ionized while the ion-ion dissociation device is operating in a symmetric operational mode to generate a negatively charged reactive reagent. Subsequently, the ion-ion dissociation device is transitioned into an asymmetric operational mode, again similar to the previous embodiment, and the positively charged precursor ions are introduced into the ion-ion dissociation device to interact with the negatively charged reactive reagent ions and generate product ions.

[0220] Unlike the previous embodiment, in this embodiment, following the dissociation of the positively charged precursor ions into a plurality of product ions, the ion-ion reaction device remains in the asymmetric operational mode and mass selective ion extraction of the product ions from the ion-ion reaction device is achieved via mass selective ion extraction in accordance with various embodiments discussed herein. More specifically, as discussed in detail above, the transition of the ion-ion reaction device from an asymmetric operational mode to a symmetric operational mode, in combination with a DC potential established between the ion-ion reaction device and a downstream electrode positioned in proximity of the outlet of the ion-ion reaction device can cause mass selective extraction of the product ions from the ion-ion reaction device for introduction into a downstream mass analyzer.

[0221] In an alternative embodiment, the device during reaction is kept in an asymmetric state and the RF and DC voltages and phases are configured in such a way that product ions above certain m / z can overcome the axial pseudopotential barrier. In this case the mass selective ion extraction occurs in parallel with the reaction and can be used to eject product ions preventing them from an unwanted subsequent ion reaction (Fig 8A-8C).

[0222] Charge reduction devices

[0223] In another aspect, the present disclosure discloses charge reduction devices that can be employed in mass spectrometric systems. By way of example, with reference to FIGS. 8A, 8B, and 8C, such a charge reduction device 800 includes a rod assembly 801 having two sets of L- shaped rods 802 / 804 that are axially offset relative to one another to generate an ion trapping region therebetween. Similar to the previous embodiment, a plurality of gate electrodes 805a, 805b, 805c, and 805d (herein collectively referred to as gate electrodes 805), are positioned in proximity of the inlets and the outlets of the axial and the transverse channels of the rod assembly.

[0224] Initially, as shown in FIG. 8A, the charge reduction device 800 is operated in a symmetric operational mode while the reactive reagent is introduced into the charge reduction device and undergoes ionization via exposure to an electron beam to form negatively charged reactive reagent ions. During this stage, the gate electrodes are negatively biased to ensure that the negatively charged reactive reagent ions remain trapped within the charge reduction ion device.

[0225] Subsequently, as shown in FIG. 8B, the ion charge reduction device 800 is transitioned into an asymmetric operational mode, the gate electrodes are transitioned into neutral bias and positively charged precursor ions are introduced into the charge reduction device. As noted above, the transition of the charge reduction device into the asymmetric operational mode results in the generation of a pseudopotential, via an axial RF field, that facilitates the mutual trapping of the negatively charged reactive reagent ions and the positively charged precursor ions in the charge reduction device. In this embodiment, the interaction of the negatively charged reactive reagent ions with the positively charged precursor ions can result in a reduction in the electric charge state of the positive precursor ions, thereby generating charge reduced species.

[0226] In this embodiment, the charge reduced species generated via the interaction of the positively charged precursor ions with the negatively charged reactive reagent ions are mass selectively extracted from the charge reduction device. More specifically, as shown in FIG. 8C, the charge reduction device can be transitioned from the asymmetric operational state into a symmetric operational state while a negative bias voltage applied to the gate electrode 805c causes mass selective extraction of ions from the charge reduction device (as the pseudopotential barrier is reduced, ions, under the influence of the electric field generated by the negative bias voltage, can overcome the pseudopotential barrier in a mass selective manner to exit the charge reduction device).

[0227] III. Multiplexing applications As noted above, the systems and methods for generating a pseudopotential barrier, via axial RF fields, according to the present teachings can be employed in a variety of mass spectrometric applications. In some applications, a plurality of different ion populations with different m / z ratios can be stored in a mass selective ion extraction device, where the ions associated with these populations can be extracted from the mass selective ion extraction device on a mass selective basis and processed. In other words, in such embodiments, multiplexed processing of different populations of ions can be achieved.

[0228] In one such multiplexing application, a high-resolution mass filter is employed to introduce distinctly separated m / z ion packets into a mass selective ion extraction device such that ion populations with different m / z ratios are accumulated in the mass selective ion extraction device before their mass selective extraction and introduction into an ion dissociation device.

[0229] With reference to the flow chart of FIG. 9A, in an embodiment of such a method, a plurality of precursor ions having ion populations with different m / z ratios are introduced into a mass filter, where the mass filter is configured such that at least two populations of the precursor ions are within its transmission window such that those populations of the precursor ions pass through the mass filter to be introduced into a mass selective ion extraction device at least for a portion of time. Each precursor ion population may be introduced concurrently or sequentially with the mass filter configured appropriately. During the loading of the mass selective ion extraction device, the device can be operated in a symmetric operational mode to facilitate the introduction of the precursor ions into the ion extraction device. The device can then be transitioned into an asymmetric operational mode to facilitate trapping the loaded precursor ions therein. The precursor ions can then be mass selectively extracted from the mass selective ion extraction device by transitioning the mass selective ion extraction device from the asymmetric operational mode to a symmetric operational mode in combination with application of a DC electric potential between the device and an external electrode. The extracted precursor ions can be fragmented and mass analyzed.

[0230] As discussed in more detail below, in some cases different ion groups can be extracted as temporally disjoint ion clouds while in other cases two or more ion groups may be substantially co-extracted as a plurality of ion clouds, where two or more of the ion clouds may have a partial temporal overlap. By way of example, FIG. 9B schematically depicts a mass spectrometer 900 according to an embodiment in which a high-resolution mass filter is used to transmit ion packets separated based on their m / z ratios into a downstream mass selective ion extraction device in which the ions are separated in time and then transmitted to a downstream ion dissociation device.

[0231] More specifically, the mass spectrometer 900 includes an ion source 901 that can receive a sample, e.g., from an LC column or via other mechanisms, such as an ultrasound sample ejection system, and can ionize one or more analytes in the sample to generate a plurality of ions. A variety of ion sources can be employed. By way of example, and without limitation, the ion source can be an electrospray ionization device, a nebulizer assisted electrospray device, a chemical ionization device, a nebulizer assisted atomization device, a chemical ionization device, a matrix-assisted laser desorption / ionization (MALDI) ion source, a photoionization device, a laser ionization device, a thermospray ionization device, an inductively coupled plasma (ICP) ion source, a sonic spray ionization device, a glow discharge ion source, and an electron impact ion source, among others.

[0232] The mass spectrometer 900 further includes a mass filter 904 that is configured as a notch filter, which receives the plurality of ions from the ion source 901 and allows the passage of ions having m / z ratios within its transmission windows. By way of illustration, FIG. 9C shows a hypothetical example of a plurality of precursor ions, labeled as ions A, B, C, D, E, and F, generated by the ion source 901. FIG. 9D shows a hypothetical example of m / z transmission windows 906, 907, and 908 of the mass filter 904, which allows passage of the precursor ions A, D, and F while blocking the transmission of the precursor ions B, D, and E.

[0233] Referring again to FIG. 9B, a mass selective ion extraction device 902 receives the ions transmitted through the mass filter 904. The transfer of ions from the mass filter 904 into the ion extraction device 902 is such that the precursor ion populations A, C, and F are accumulated within the mass selective ion extraction device 902 prior to initiating their mass selective extraction, as depicted in FIG. 9E.

[0234] In various embodiments, the mass resolution of the mass filter can be at least equal to, and preferably greater than, a mass resolution associated with the mass selective ion extraction device 902. In other words, in this example, the mass selective ion extraction device can be utilized to extract each of the ion populations A, C, and F independent of the other two ion populations. By way of example, and without limitation, the m / z resolution of the mass selective ion extraction device can be in a range of about 5 to about 500 and the m / z separation between successive ion transmission windows can be in a range of about 10 to about 1000. Alternatively, two or more of the ion populations may be extracted with some temporal overlap between their extracted ions.

[0235] The mass selective extraction of the ions accumulated in the mass selective ion extraction device can be achieved via transitioning the mass selective ion extraction device from an asymmetric operational state to a symmetric operational state together with application of a DC potential at the outlet of the device, e.g., in a manner discussed above. For example, the mass selective ion extraction device can include a plurality of rods arranged in a quadrupole configuration and the amplitudes and / or the phases of the RF voltages applied to the A and B poles of the quadrupole rods can be selected in a manner discussed herein to cause, in combination with a DC potential established between the rods and a downstream component (e.g., a gate electrode), the mass selective extraction of the accumulated ions. In this example, such a mass selective extraction of the ion populations A, D and F will result in the extraction of the ion populations in the following order: F followed by D and then followed by A. By way of illustration, FIG. 9F shows the mass dependent transmission profile of the mass selective ion extraction device between an initial m / z ratio setting and a final m / z ratio setting.

[0236] Referring again to FIG. 9B, the ions extracted from the mass selective ion extraction device are introduced into an ion fragmentation device (herein also referred to as an ion dissociation device) 906 in which the precursor ions can undergo fragmentation to generate a plurality of product ions. A variety of ion fragmentation devices can be employed. By way of example, the ion fragmentation device can be an electron activated dissociation (EAD) device, such as that discussed above or alternatively collision activated dissociation (CAD) device often referred as collision induced dissociation (CID) device.

[0237] The mass spectrometer 900 further includes a mass analyzer 908 that is positioned downstream of the ion fragmentation device 906, which receives the product ions and generates mass data that can be utilized by an analysis module 910 to assign detected product ions to particular precursor ions. With reference to FIGS. 9G and 9H, in some embodiments, two consecutive clouds of precursor ions extracted from the mass selective ion extraction device, herein referred to as cloud 1 and cloud 2, may have a partial temporal overlap as they enter a downstream fragmentation device, assumed to be a collision cell in this example. Typically, precursor ions entering a collision cell travel through the cell without undergoing dissociation. As they undergo collisions with the background gas, they undergo dissociation close to the outlet of the collision cell to form product ions. Although different product ions can be generated from each of the individual precursor ions, the product ions associated with the same type of precursor ions may have a similar temporal profile, as shown schematically in FIG. 9H.

[0238] As shown in FIG. 91, the spectral lines in the mass spectrum of the product ions can be correlated to the ions originating from the same precursor or in some cases to their respective precursor ion. This can be achieved by comparing their respective temporal arrival profiles and grouping according to their similarity. In some embodiments, where the product ion can belong to multiple types of precursor ions, an additional step of signal decomposition may be performed using conventional linear algebra algorithms such as non-negative least squares (NNLS) algorithm among other known decomposition techniques.

[0239] With reference to the flow chart of FIG. 10, in another aspect, a method for performing mass spectrometry is disclosed in which a plurality of precursor ions is accumulated in a mass selective ion extraction device and then mass selectively extracted from the mass selective ion extraction device to be introduced into a downstream mass filter, which is adjusted in synchrony with the mass selective extraction of the ions. The ions passing through the mass filter are subjected to fragmentation to generate a plurality of product ions and mass analysis of the product ions is performed.

[0240] By way of illustration, FIG. 11A depicts schematically a mass spectrometric system 1000 that can perform the above methods. The mass spectrometric system 1000 includes an ion source 1002 that can receive a sample and generate a plurality of ions (herein referred to as precursor ions). A mass selective ion extraction device 1004 operating according to an embodiment of the present teachings is positioned downstream of the ion source (in some embodiments one or more ion guides may be also positioned between the ion source and the mass selective ion extraction device) to receive the precursor ions. The precursor ions can be loaded into the mass selective ion extraction device over a predefined ion loading period, e.g., an ion loading period in a range of about 5ms to about 100ms.

[0241] The mass selective ion extraction device 1004 is configured according to the present teachings to use a pseudopotential barrier generated via an axial RF field to retain the ions within the mass selective ion extraction device. The mass selective extraction of the ions over a temporal period can be achieved by reducing the height of the pseudopotential barrier together with the application of a DC potential between the ion extraction device and an electrode positioned in proximity of the outlet of the mass selective ion extraction device. By way of illustration, and without limitation, FIG. 11B schematically depicts an example of an ion transmission profile of the mass selective ion extraction device as a function of time, indicating that the precursor ions are extracted in a high m / z to low m / z order.

[0242] Referring again to FIG. 11 A, a mass filter 1006 positioned downstream of the mass selective ion extraction device 1004 receives the precursor ions as they are extracted from the mass selective ion extraction device. As the m / z ratio of the extracted ions increases during an ion extraction period, the mass filter is adjusted in synchrony with the change in the m / z ratios of the extracted ions such that the mass filter can allow the passage of at least a portion of the ions extracted at a given time from the mass selective ion extraction device. In various embodiments, the mass filter can be characterized by a bandpass (transmission window) centered at a particular m / z ratio. In some such embodiments, the adjustment of the mass filter can include scanning the transmission window of the mass filter in the m / z space while maintaining the width of the transmission window substantially constant. In other embodiments, the width of the transmission window may also be adjusted as the transmission window is scanned in the m / z space. In other embodiments, the mass filter can be stepped in synchrony with the mass selective device.

[0243] By way of further illustration, FIG. 11C schematically depicts an example of the transmission profile of a mass filter as a function of time in the m / z space. FIG. 11D in turn shows the synchrony between the change in the m / z ratio at the center of the ion transmission window of the mass filter and the change, as a function of time, in the m / z ratio of ions being extracted from the mass selective ion extraction device. In particular, FIG. 11D shows that the scanning of the m / z ratio at the center of the ion transmission window is performed such that at any given time, the m / z ratio is substantially equal to the m / z ratio of ions being extracted from the mass selective ion extraction device at that time.

[0244] In various embodiments, the mass filter exhibits a bandpass having an m / z transmission profile that is encompassed by the transmission profile of the mass selective ion extraction device. In other words, in some such embodiments, the mass selective ion extraction device can effectively operate as a low-resolution mass filter while the mass filter provides separation of the ions received from the mass selective ion extraction device at a higher resolution. By way of example, and without limitation, the mass resolution of the mass selective ion extraction device can be in a range of about 1 to about 500 and the mass resolution of the mass filter can be in a range of about 10 to about 10000.

[0245] In some embodiments, the m / z center of the bandpass of the mass filter at the initiation of the mass selective extraction of ions from the ion extraction device and its rate of change during mass selective extraction of ions from the mass selective ion extraction device can be selected based on previously-obtained temporal profile of m / z ratios of ions extracted from the mass selective ion extraction device.

[0246] Further, in various embodiments, the number of ions introduced into the mass selective ion extraction device can be controlled so as to reduce, and preferably eliminate, the potential effects of space charge within the mass selective ion extraction device on the extraction of the ions. For example, the space charge may effectively lower the trapping potential leading to premature ion release. In addition, it can further lower the resolution of the mass selective ion extraction device owing to co-release of ions with different m / z ratios. According to some embodiments, one way to control space charge effects can be by adjusting the trap fill time. Such adjustment can be implemented either by shortening the trap fill time or by interleaving several segments which either allow the passage or blocking of ions. In some embodiments, the fill time may be controlled only for a subpopulation of the ions. For example, the mass filter 904, preceding the ion trap, can be configured for transmission of a first m / z range for a time interval ti and a second m / z range for time interval t2. Typically, ion trapping devices exhibit satisfactory performance when the ion load does not exceed a certain threshold, e.g., 1,000,000 elementary charges. In order to estimate the necessary fill time for the trap, it is desirable to know the ion current filling the trap. In some embodiments, this is achieved by measuring the mass spectra containing ions of interest and recording ion intensities and using them for estimation of fill time. In some embodiment, this is achieved by measuring the induced charge on the ion optic or any other characteristic indicative of the number of charges.

[0247] Referring again to FIG. 11 A, the precursor ions selected by the mass filter, i.e., the ions passing through the mass filter, are received by a downstream ion fragmentation device 1008 (which is herein also referred to as an ion dissociation device) in which the precursor ions (or at least a portion thereof) undergo fragmentation to generate a plurality of product ions. A mass analyzer 1010 positioned downstream of the ion fragmentation device 1008 receives the product ions and generates mass data that can be utilized by an analysis module 1012 for mass analysis, e.g., for correlating the product ions to specific precursor ions.

[0248] The mass filter 1006 can include a plurality of rods that are arranged relative to one another in a multipole configuration (e.g., a quadrupole configuration) and to which RF and DC voltages are applied in a manner known in the art, and as informed by the present teachings, to achieve a desired transmission window.

[0249] In various embodiments, rather than scanning the ion transmission window of the mass filter substantially continuously, the transmission window can be stepped through the relevant m / z range to allow reducing the range of m / z ratios associated with packets of precursor ions received from the mass selective ion extraction device prior to their fragmentation. By way of example, and without limitation, the step size for changing the m / z ratio corresponding to the center of the bandpass of the mass filter can be in a range of about 0.1 Da to about 10000 Da.

[0250] IV. Tandem mass spectrometry with multiple steps of analysis

[0251] In another aspect, the present disclosure provides triple stage mass spectrometry

[0252] 2 (MS / MS / MS, also referred to as MS ) systems and methods in which multiple stages of ion fragmentation may be utilized, e.g., for structural analysis of a compound. As will be discussed in greater detail below, the MS framework includes an ion trap (also referred to as an m / z (or mass) selective extraction device) that receives a first set of ions (which may be product ions produced using an ion dissociation device) and transfers during different time intervals, different groups of the received ions, according to m / z ratios associated with the different groups, to a downstream ion dissociation (fragmentation) device. The fragmentation device dissociates at least a portion of the received groups of ions to produce a second set of product ions that are then analyzed by a mass analyzer.

[0253] More particularly, FIG. 12 schematically depicts an example of a mass spectrometer 1200 that can be utilized to implement the above MS / MS / MS framework. The mass spectrometer 1200 includes an ion source 1201 that can receive a sample and ionize the sample to generate a plurality of precursor ions. The ion source 1201 may be similar to the ion sources used by the various other frameworks discussed above in relation to, for example, FIG. 9B. Accordingly, by way of example, and without limitation, the ion source 1201 can include an electrospray ionization device, a nebulizer assisted electrospray device, a chemical ionization device, a nebulizer assisted atomization device, a chemical ionization device, a matrix-assisted laser desorption / ionization (MALDI) ion source, a photoionization device, a laser ionization device, a thermospray ionization device, an inductively coupled plasma (ICP) ion source, a sonic spray ionization device, a glow discharge ion source, and an electron impact ion source, among others.

[0254] With continued reference to FIG. 12, the ion source 1201 produces source ions that, in some embodiments, are delivered to, and received by, a mass filter 1202 that allows the passage of those ions having an m / z ratio within the mass filter’s bandpass. The bandpass characteristics of the mass filter 1202 may be controllably adjusted using, for example, RF and DC voltage sources (not shown in FIG. 12). For example, in various embodiments, the mass filter 1202 may be implemented using a multipole arrangement of rods, such as, for example, a four-rod quadrupole configuration. RF voltages as well as a DC resolving voltages can be applied to the electrode rods arrangement used in the mass filter to radially focus the ions and to select ions having a target m / z ratio (e.g., precursor ions) as they pass through the mass filter. The multipole rod set of the mass filter can be provided with RF / DC voltages controllably selected so that the mass filter establishes a transmission window of chosen m / z ratios, such that the selected ions can traverse the mass filter largely unperturbed. Ions having m / z ratios falling outside the window, however, do not attain stable ion trajectories within the multipole rods of the mass filter and can thus be prevented (inhibited) from traversing the mass filter to reach downstream sections of the mass spectrometer 1200. Precursor ions filtered from the incoming source ions through operation of the mass filter 1202 (in implementations of the mass spectrometer 1200 where the optional mass filter 1202 is used) are received by a first ion fragmentation device (also referred to as an ion dissociation device) 1204 that causes dissociation of at least a portion of the received precursor ions to generate a first set of a plurality of primary product ions (the first set of product ions) that may have ions with different m / z ratios (spanning an m / z range). The first ion fragmentation device 1204 may be implemented in a manner similar to the implementations discussed above in relation to the framework realized through the mass spectrometer 900. For example, the ion fragmentation device 1204 can be an electron activated dissociation (EAD) device, or alternatively collision activated dissociation (CAD) device often referred as collision induced dissociation (CID) device. An EAD fragmentation procedure can be implemented using, for example, the devices 400 or 600 depicted in FIGS. 5 and 6B, respectively, and discussed above. Under the EAD approach, an electron beam with high kinetic energy is directed at precursor ions (the electron beam may be perpendicular to the path followed by the precursor ions). The interaction of the electron beam and the precursor ions produces product ions (e.g., negatively charged ions). A CID-type fragmentation approach may be implemented by colliding selected accelerated ions with neutral molecules (such as nitrogen). Other types of ion fragmentation techniques, such as ultraviolet photodissociation (UVPD), infrared photodissociation (IRMPD), electron-induced dissociation (EID), electron capture dissociation (ECD), etc., may also be used to implement the fragmentation device.

[0255] As further illustrated in FIG. 12, a mass selective ion extraction device 1206 (also referred to as an ion trap extraction device (or just “ion trap”), or an m / z selective transfer device) is positioned downstream of the ion fragmentation device 1204 to receive the product ions generated in the fragmentation device. Subsequent to the loading of the first set of product ions into the extraction device 1206, the populations of the product ions having different m / z ratios are m / z selectively extracted based on their m / z ratios (e.g., in a high to low m / z order).

[0256] The m / z selective extraction device 1206 may be implemented in a manner similar to the extraction devices described herein in relation to the mass selective extraction device 902 of FIG. 9B. Thus, for example, the m / z (mass) selective extraction of the ions accumulated in the extraction device (or ion trap device) 1206 can be achieved by transitioning the device 1206 from an asymmetric operational state to a symmetric operational state together with application of a DC potential at the outlet of the device (as more particularly discussed above). For example, the mass selective ion extraction device can include a plurality of rods arranged in a multipole (e.g., quadrupole, hexapole, octupole, etc.) configuration, and the amplitudes and / or the phases of the RF voltages applied to pairs of those rods (designated, for example, as the A and B poles) can be selected in a manner discussed herein to cause, in combination with a DC potential established between the rods and a downstream component (e.g., a gate electrode), the m / z selective extraction of at least some of the groups of accumulated product ions in the device 1206. Using the example of FIGS. 9C-E, an m / z selective extraction of the ion populations A, D and F can result in the extraction of the ion populations in an order based on those ion populations’ m / z ratios (different extraction orders can also be implemented). Thus, the controlled extraction (transfer) of the groups of ions will transfer the ions (to a downstream section, such as a second fragmentation device) in the following order: F followed by D and then followed by A.

[0257] Thus, in example embodiments, the ion trap (m / z selective extraction) device 1206 is configured to transfer different groups of the first set of product ions during different time intervals to a second ion dissociation device so as to cause dissociation of at least a portion of the first set of product ions to generate a second set of product ions, with at least some of the first set of the product ions in each of the different groups (of the ions accumulated in the device 1206) having one or more m / z ratios different than other one or more m / z ratios of at least some of the ions in other ones of the different groups. In various examples, the ion trap (extraction device) configured to transfer the first set of product ions is configured to m / z selectively extract the first set of the product ions from the ion trap.

[0258] In various examples of the ion trap used to extract groups of ions with different m / z ratios may include at least a first plurality of rods arranged in a multipole configuration and extending from a proximal end providing an inlet for receiving at least the first set of product ions, to a distal end providing an outlet through which resultant ions processed by the ion trap, at least one electrode positioned downstream of the ion trap and axially separated from a distal end of the plurality of rods, at least one RF voltage source to apply a first RF voltage to one pair of the plurality of rods and apply a second RF voltage to another pair thereof, at least one DC voltage source to establish a DC electric potential between said at least one electrode and said plurality of rods, and a controller in communication with the at least one RF voltage source and said at least one DC voltage source. The controller is configured to send control signals to said RF voltage source to adjust any of an amplitude and a phase difference between the first and the second RF voltages so as to cause, in combination with said DC electric potential, an ordered m / z selective extraction of the different groups of ions during the different time intervals, resulting from operations of the ion trap on the at least the first set of product ions, according to respective one or more different m / z ratios associated with the different groups of ions.

[0259] In some embodiments, the controller configured to send signals to adjust any of the amplitude and the phase difference between the first and the second RF voltages may be configured to controllably adjust any of the amplitude and the phase difference between the first and the second RF voltages to cause m / z selective extraction from high to low of the one or more different m / z ratios associated with the different groups of the first set of product ions. In some embodiments, the controller may be configured to send control signals to adjust the phase difference between the first and the second RF voltages while maintaining the amplitude difference to cause m / z selective extraction of said different groups of product ions, according to the respective different m / z values associated with the different groups of product ions, from the ion trap. In some embodiments, the controller may be configured to send control signals to adjust the amplitude difference between the first and the second RF voltages while maintaining the phase difference substantially constant so as to cause m / z selective extraction of said different groups of product ions. In some embodiments, the controller may be configured to send control signals to adjust any of the amplitude and the phase difference between the first and the second RF voltages to cause m / z selective extraction from high to low m / z ratios, during the different time intervals, for the different groups of ions.

[0260] In some embodiments, the ion trap implementations to selectively extract ions may be realized using a Zeno trap to sequentially release ions with the same ion energy from the trap to downstream sections (including the mass analyzer) of the mass spectrometer. Further details about such ion traps are provided in US 7,456,388, entitled “Ion guide for mass spectrometer,” the content of which is incorporated herein by reference in its entirety.

[0261] Another example of an ion trap arrangement that may be used in conjunction with the implementations described herein is one in which ions are trapped in a linear ion trap, (which may be at the end of the first fragmentation device) in a radial pseudopotential well created by a first dipolar RF voltage of a first frequency applied to each opposite pair of rods (of a quadrupole rod arrangement) and an axial pseudopotential well created at least in part by additional RF (AC) voltage of a second frequency is applied to all four rods (of a quadrupole rod arrangement) with the same amplitude and phase. The pseudopotential created by the second RF field is mass dependent, and by ramping down the second RF voltage, ions can be released from the trap sequentially from high m / z to low. Further details regarding this ion trapping approach are provided in “A Novel Ion Trap That Enables High Duty Cycle and Wide m / z Range on an Orthogonal Injection TOF Mass Spectrometer” by Alexander V. Loboda et al. (Journal of the American Society for Mass Spectrometry, Volume 20, Issue 7, July 2009, Pages 1342-1348), the content of which is incorporated herein by reference in its entirety.

[0262] Yet another example of an ion trap arrangement that may be used in conjunction with the implementations described herein is one in which ions are trapped in a linear ion trap (which may be at the end of the first fragmentation device) in in a radial pseudopotential well created by a first dipolar RF voltage of a first frequency applied to each opposite pair of rods (of a quadrupole rod arrangement) and axial pseudopotential well created at least in part by additional RF (AC) voltage of a second frequency applied to an exit electrode of the linear ion trap. The pseudopotential created by RF field is mass dependent, and by ramping down the RF voltage, ions can be released from the trap sequentially from high m / z to low. Further details regarding this ion trapping approach are provided in “A Novel Ion Trap That Enables High Duty Cycle and Wide m / z Range on an Orthogonal Injection TOF Mass Spectrometer” by Alexander V. Loboda et al. (Journal of the American Society for Mass Spectrometry, Volume 20, Issue 7, July 2009, Pages 1342-1348), the content of which is incorporated herein by reference in its entirety.

[0263] In yet another embodiment, instead of ramping down the second RF voltage with the second frequency in any of the embodiments wherein the axial potential well is formed at least in part by said second RF voltage the mass selective release of ions can be facilitated by ramping up the DC voltage difference between the exit lens electrode and the multipole rods forming the linear ion trap, such that trapped ions experience stronger pull towards said exit lens at each subsequent time during the mass selective extraction process. Yet another example of an ion trapping approach is one in which superposition of a repulsive potential applied to an exit lens of an ion trap, in combination with the diminishing quadrupole potential in the fringing region near the end of a quadrupole rod array, gives rise to an approximately conical surface on which the net axial force experienced by an ion, averaged over one RF cycle, is zero. This conical surface is referred to as the cone of reflection because it divides the regions of ion reflection and ion ejection. Once an ion penetrates this surface, it experiences a strong net positive axial force and is accelerated toward the exit lens. As a consequence of the strong dependence of the axial field on radial displacement, trapped thermalized ions can be ejected axially from a linear ion trap in a mass-selective way when their radial amplitude is increased through a resonant response to an auxiliary signal. Further details regarding this ion trapping and extraction approach are provided in “Mass selective axial ion ejection from a linear quadrupole ion trap” by F. A. Londry el al. (J Am Soc Mass Spectrom 2003 Oct; 14(10): 1130-47), the content of which is incorporated herein by reference in its entirety.

[0264] In the latter example the order of mass selective ion ejection can be either from high m / z to low m / z or from low m / z to high m / z.

[0265] Other ion trapping and extraction approaches can also be used in conjunction with implementations of the mass spectrometers and techniques described herein.

[0266] In some cases, the m / z ratio(s) of ions in consecutive populations of the first set of product ions exiting the ion trap may be distinct while in other cases, they may have some overlap. Further, while in some cases, the range of m / z ratios in each population of the ions can be narrow (e.g., 1 Da), in other cases, a larger range of m / z ratios, e.g., in a range of 5 - 10 Da, may be present in each population of the first set of the product ions exiting the ion trap.

[0267] With continued reference to FIG. 12, another (second in the example mass spectrometer 1200) ion fragmentation device 1208 is positioned downstream of the mass selective ion extraction device 1206 and receives the populations (groups) of the first set of ions as they exit the m / z selective ion extraction device 1206. The second fragmentation device 1208 may be implemented in a manner similar to the fragmentation device 1204 discussed above. Each population (group of ions) received by the second ion fragmentation device 1208 undergoes fragmentation to generate a secondary set of product ions. A mass analyzer 1210 positioned downstream of the second ion fragmentation device 1208 receives the secondary product ions and generates mass data, which can be analyzed by an analysis module 1212. Examples of mass analyzers that may be used with the system depicted in FIG. 12 include a time-of-flight mass analyzer, a quadrupole mass analyzer, an Orbitrap mass analyzer, an FTICR (Fourier transform ion cyclotron resonance) mass analyzer, etc.

[0268] By way of example, and without limitation, the mass analysis module can operate on the mass data generated by the mass analyzer 1210 to derive correspondence between the secondary product ions and the first set of product ions, as well as correspondence between the first set of product ions and the precursor ions. In other words, in various embodiments, for each of the groups of the second set of product ions (produced by the second fragmentation device 1208), the group of the first set of product ions giving rise to that group of secondary product ions, and the precursor ions giving rise to the group of the first set of product ion, can be determined. Thus, in various embodiments, the analysis module 1312 is configured to correlate at least some of the groups of the second set of product ions to one of the different groups of the first set of product ions. In some embodiments, the first fragmentation device and the mass selective extraction device can be the same device with two or more operation modes.

[0269] In various embodiments, a dual RF power supply with independent control of two RF channels (herein referred to for ease of description as RF A and RF B) can be employed for adjusting the amplitudes and / or phases of the RF signals. By way of example, such an RF power supply is disclosed in published international patent application WO 2023 / 026201 A2 titled “System and method of driving radio frequency for multipole ion processing device,” which is herein incorporated by reference in its entirety.

[0270] With reference to FIG. 13A, embodiments of the MS framework described herein also include methods in which a plurality of ions having a target m / z ratio can undergo dissociation to generate a plurality of primary product ions. A mass (m / z) selective ion extraction device can then be loaded with two or more populations of the primary product ions having different m / z ratios and the product ions can be m / z selectively extracted from the mass selective ion extraction device such that different populations of the first set of product ions are extracted in different time intervals. The extracted primary product ions are then introduced into a downstream ion fragmentation device to undergo fragmentation to generate a second set of product ions, which can be mass analyzed.

[0271] More particularly, with reference next to FIG. 13B, a flowchart of an example procedure 1300 to perform triple tandem mass spectrometry is provided. The procedure 1300 includes dissociating 1310 a plurality of precursor ions to generate a first set of product ions, where ions with approximately same m / z (e.g., same m / z’s, or m / z’s within a narrow range of ratios) being associated in a group, and with said first set of product ions containing at least two groups of ions with distinct m / z’s. The procedure 1300 further includes introducing 1320 the first set of product ions into an ion trap, and transferring 1330 different groups of the first set of product ions during different time intervals from the ion trap to an ion dissociation device so as to cause dissociation of at least a portion of the first set of product ions to generate a second set of product ions.

[0272] In some embodiment, the step of transferring the first set of product ions may include m / z selectively extracting the first set of product ions from the ion trap. In such embodiments, m / z selectively extracting the first set of product ions may include introducing the plurality of precursor ions into an upstream ion dissociation device to cause dissociation of at least a portion of the plurality of precursor ions so as to generate at least the first set product ions, directing said first set of product ions into the ion trap, with the ion trap including a plurality of rods arranged in a multipole configuration providing an inlet to receive the first set of product ions, and an outlet through which resultant ions processed by the ion trap exit. A first RF voltage may be applied to at least one pair of the plurality of rods and a second RF voltage may be applied to at least another pair of the plurality of rods. Such embodiments further include establishing a DC electric potential between at least one electrode positioned downstream of the plurality of rods and axially separated from a distal end thereof and said plurality of rods, and controllably adjusting any of an amplitude and a phase difference between the first and the second RF voltages so as to cause, in combination with said DC electric potential, an ordered m / z selective extraction of the different groups of the first set of product ions, during the different time intervals, according to respective different one or more m / z ratios associated with the each of the different groups of the first set of product ions. In some embodiments, controllably adjusting any of the amplitude and the phase difference between the first and the second RF voltages so as to cause the ordered m / z selective extraction of the different groups of the first set of product ions may include controllably adjusting any of the amplitude and the phase difference between the first and the second RF voltages to cause m / z selective extraction from high to low of the one or more m / z ratios associated with the different groups of the first set of product ions.

[0273] In some examples, the procedure may further include introducing input source ions into a mass filter located upstream of the upstream ion dissociation device, with the mass filter being configured to allow passage of precursor ions having an m / z ratio of interest, and with the precursor ions corresponding to the plurality of ions introduced to the upstream ion dissociation device. The upstream ion dissociation device and said ion trap may be implemented as a single device.

[0274] Turning back to FIG. 13, the procedure 1300 additionally includes acquiring 1340 a mass spectrum of the second set of product ions. In various examples, acquiring the mass spectrum of the secondary product ions may include utilizing any of a time-of-flight, a quadrupole, an Orbitrap, and an FTICR (Fourier transform ion cyclotron resonance) mass analyzer.

[0275] In some embodiments, the procedure 1300 may further include correlating each of the second set of product ions to one of said different groups of the first set of product ions. In various examples, the ion trap may exhibit a mass extraction resolution equal to or greater than an m / z separation of said first set of product ions and said second set of product ions.

[0276] Various controllers utilized in the practice of the present teachings, such as those discussed above, can be implemented using software, firmware, and hardware in a manner known in the art and as informed by the present teachings. By way of example, FIG. 14 schematically depicts an example of implementation of such a controller 1400 having a digital processing unit 1402 that can communicate via one or more communications buses 1403 with a random access memory (RAM) module 1404 and a permanent memory 1405. By way of example, various instructions for operating a device according to various embodiments, such as those discussed above, can be stored in the permanent memory and can be accessed during runtime via the digital processing unit 1402 to perform methods according to various embodiments. By way of example, such instruction can include the amplitudes and / or the phases of RF voltages generated by various RF voltage sources operating under the control of the controller and / or DC voltage generated by DC voltage sources.

[0277] Although some aspects have been described in the context of a system and / or an apparatus, it is clear that these aspects also represent a description of the corresponding method, where a block or device corresponds to a method step or a feature of a method step. Analogously, aspects described in the context of a method step also represent a description of a corresponding block or item or feature of a corresponding apparatus. Some or all of the method steps may be executed by (or using) a hardware apparatus, like for example, a processor, a microprocessor, a programmable computer or an electronic circuit. In some embodiments, some one or more of the most important method steps may be executed by such an apparatus.

[0278] Depending on certain implementation requirements, embodiments of the invention can be implemented in hardware and / or in software. The implementation can be performed using a non- transitory storage medium such as a digital storage medium, for example a floppy disc, a DVD, a Blu-Ray, a CD, a ROM, a PROM, and EPROM, an EEPROM or a FLASH memory, having electronically readable control signals stored thereon, which cooperate (or are capable of cooperating) with a programmable computer system such that the respective method is performed. Therefore, the digital storage medium may be computer readable.

[0279] Those having ordinary skill in the art will appreciate that various changes can be made to the above embodiments without departing from the scope of the present teachings.

Claims

What is claimed is:

1. A method of performing mass spectrometry, comprising: dissociating a plurality of precursor ions to generate a first set of product ions, wherein ions with approximately same m / z are associated in a group, and wherein said first set of product ions contains at least two groups of ions with distinct m / z’s; introducing the first set of product ions into an ion trap; transferring different groups of the first set of product ions during different time intervals from the ion trap to an ion dissociation device so as to cause dissociation of at least a portion of the first set of product ions to generate a second set of product ions, and acquiring a mass spectrum of the second set of product ions.

2. The method of Claim 1, further comprising correlating each of the second set of product ions to one of said different groups of the first set of product ions.

3. The method of Claim 1, wherein the step of transferring the first set of product ions comprises m / z selectively extracting the first set of product ions from the ion trap.

4. The method of Claim 3, wherein m / z selectively extracting the first set of product ions comprises: introducing the plurality of precursor ions into an upstream ion dissociation device to cause dissociation of at least a portion of the plurality of precursor ions so as to generate at least the first set of product ions; directing said first set of product ions into the ion trap, wherein the ion trap comprises a plurality of rods arranged in a multipole configuration providing an inlet to receive the first set of product ions, and an outlet through which resultant ions processed by the ion trap exit, wherein a first RF voltage is applied to at least onepair of the plurality of rods and a second RF voltage is applied to at least another pair of the plurality of rods; establishing a DC electric potential between at least one electrode positioned downstream of the plurality of rods and axially separated from a distal end thereof and said plurality of rods; and controllably adjusting any of an amplitude and a phase difference between the first and the second RF voltages so as to cause, in combination with said DC electric potential, an ordered m / z selective extraction of the different groups of the first set of product ions, during the different time intervals, according to respective different one or more m / z ratios associated with the each of the different groups of the first set of product ions.

5. The method of claim 4, wherein controllably adjusting any of the amplitude and the phase difference between the first and the second RF voltages so as to cause the ordered m / z selective extraction of the different groups of the first set of product ions comprises: controllably adjusting any of the amplitude and the phase difference between the first and the second RF voltages to cause m / z selective extraction from high to low of the one or more m / z ratios associated with the different groups of the first set of product ions.

6. The method of claim 4, further comprising: introducing input source ions into a mass filter located upstream of the upstream ion dissociation device, wherein the mass filter is configured to allow passage of precursor ions having an m / z ratio of interest, and wherein the precursor ions correspond to the plurality of ions introduced to the upstream ion dissociation device.

7. The method of Claim 6, wherein said upstream ion dissociation device and said ion trap are implemented as a single device.

8. The method of Claim 1, wherein said ion trap exhibits a mass extraction resolution equal to or greater than an m / z separation of a first group of product ions and a second group of product ions.

9. The method of Claim 1, wherein acquiring the mass spectrum of the secondary product ions comprises utilizing any of a time-of-flight, a quadrupole, an Orbitrap, and an FTICR (Fourier transform ion cyclotron resonance) mass analyzer.

10. A mass spectrometer, comprising: a first ion dissociation device for receiving a plurality of ions and causing dissociation of at least a portion thereof to generate a first set of product ions, wherein ions with approximately same m / z are associated in a group, and wherein said first set of product ions contains at least two groups of ions with distinct m / z’s; an ion trap to receive the first set of product ions and to transfer different groups of the first set of product ions during different time intervals to a second ion dissociation device so as to cause dissociation of at least a portion of the first set of product ions to generate a second set of product ions; and a mass analyzer to acquire a mass spectrum of the second set of product ions.

11. The mass spectrometer of Claim 10, further comprising: an analysis module to correlate each of the second set of product ions to one of said different groups of the first set of product ions.

12. The mass spectrometer of Claim 10, wherein the ion trap configured to transfer the first set of product ions is configured to m / z selectively extract the first set of product ions from the ion trap.

13. The mass spectrometer of Claim 12, wherein the ion trap configured to m / z selectively extract the first set of product ions comprises: at least a first plurality of rods arranged in a multipole configuration and extending from a proximal end providing an inlet for receiving at least the first set of product ions, to a distal end providing an outlet through which resultant ions processed by the ion trap; at least one electrode positioned downstream of said ion trap and axially separated from a distal end of said plurality of rods; at least one RF voltage source to apply a first RF voltage to one pair of the plurality of rods and apply a second RF voltage to another pair thereof; at least one DC voltage source to establish a DC electric potential between said at least one electrode and said plurality of rods; and a controller in communication with said at least one RF voltage source and said at least one DC voltage source, said controller being configured to send control signals to said RF voltage source for adjusting any of an amplitude and a phase difference between the first and the second RF voltages so as to cause, in combination with said DC electric potential, an ordered m / z selective extraction of the different groups of ions during the different time intervals, resulting from operations of the ion trap on the at least the first set of product ions, according to respective one or more different m / z ratios associated with the different groups of ions.

14. The mass spectrometer of Claim 13, wherein the controller configured to send signals to adjust any of the amplitude and the phase difference between the first and the second RF voltages so as to cause the ordered m / z selectiveextraction of the different groups of the first set of product ions is configured to: controllably adjust any of the amplitude and the phase difference between the first and the second RF voltages to cause m / z selective extraction from high to low of the one or more different m / z ratios associated with the different groups of the first set of product ions.

15. The mass spectrometer of Claim 13, wherein said controller is configured to send control signals to adjust the phase difference between the first and the second RF voltages while maintaining the amplitude difference to cause m / z selective extraction of said different groups of product ions, according to the respective different m / z values associated with the different groups of product ions, from the ion trap.

16. The mass spectrometer of Claim 13, wherein said controller is configured to send control signals to adjust the amplitude difference between the first and the second RF voltages while maintaining the phase difference substantially constant so as to cause m / z selective extraction of said different groups of product ions.

17. The mass spectrometer Claim 13, wherein the controller configured to send control signals to adjust any of the amplitude and the phase difference between the first and the second RF voltages so as to cause the ordered m / z selective extraction of different groups of ions is configured to: send control signals to adjust any of the amplitude and the phase difference between the first and the second RF voltages to cause m / z selective extraction from high to low m / z ratios, during the different time intervals, for the different groups of ions.

18. The mass spectrometer of claimlO, further comprising: a mass filter located upstream of the first ion dissociation device and configured to receive a plurality of precursor ions and to allow passage of a subset of the plurality of the precursor ions having an m / z ratio of interest through the mass filter, wherein the precursor ions correspond to the plurality of ions received by the first ion dissociation device.

19. The mass spectrometer Claim 10, wherein the mass analyzer comprises any of a time-of-flight mass analyzer, a quadrupole mass analyzer, an Orbitrap mass analyzer, and an FTICR (Fourier transform ion cyclotron resonance) mass analyzer.

20. The mass spectrometer Claim 10, wherein said ion trap exhibits a mass extraction resolution equal to or greater than an m / z separation of said first set of product ions and said second set of product ions.

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