Systems and methods for ion switch mass spectrometry

Abstract

Described herein are ion switches, mass spectrometers, and analytical methods for high-duty cycle mass spectrometry. An ion switch comprises an ion switch inlet, a first ion switch outlet, a second ion switch outlet, a first ion guide channel disposed along a path between the ion inlet and the first ion switch outlet, a second ion guide channel disposed along a path between the ion switch inlet and the second ion switch outlet, and at least two switching electrodes positioned along the first ion guide channel and the second ion guide channel such that ions entering the ion switch inlet are selectively directed along the first ion guide channel or the second ion guide channel by modulating a phase of a waveform applied to the switching electrodes.

Description

SYSTEMS AND METHODS FOR ION SWITCH MASS SPECTROMETRYCROSS-REFERENCE

[0001] This application claims the benefit of U.S. Provisional Application No. 63 / 614,462, filed December 22, 2023, which is incorporated by reference in its entirety.BACKGROUND

[0002] Over the past few decades, mass spectrometers and analysis methods based on mass spectrometry have seen substantial improvements in instrument sensitivity and resolution, which has expanded their application into nearly every branch of physical science. There are, however, problems in these fields that remain unaddressed. Tandem mass spectrometers (MS / MS), particularly those with high mass resolving powers, suffer from substantial losses of ion flux between MSI and MS2, caused by a mismatch in ion transmission efficiency due to coupling very fast isolation in MSI with very slow spectral scanning in MS2. Accordingly, improved mass spectrometers and mass spectrometry-based methods of analysis are needed to mitigate these losses.SUMMARY

[0003] In one aspect, described herein are ion switches, mass spectrometers comprising ion switches, and mass spectrometry-based analysis methods that allow for parallel analysis of a single ion flux by a plurality of mass analyzers.

[0004] In one aspect, described herein, are multiplexed methods of acquiring tandem mass spectra of a sample. In some embodiments, the method comprises ionizing the sample using an ion source to produce gas-phase ions. In some embodiments, the method comprises introducing the gas-phase ions into a mass spectrometer. In some embodiments, the method comprises selecting a first mass isolation window of a first one of at least two mass analyzers corresponding to a first one of a plurality of ion switch outlets of the mass spectrometer. In some embodiments, the method comprises selecting a second mass isolation window of a second one of at least two mass analyzers corresponding to a second one of a plurality of ion switch outlets of the mass spectrometer. In some embodiments, the method comprises acquiring mass spectra of both the first and second mass isolation windows using the at least two mass analyzers. In some embodiments, the methods comprise selecting a third mass isolation window of a third one of the at least two mass analyzers corresponding to a third one of the plurality of ion switch outlets; and acquiring mass spectra of the first, second, and third mass isolation windows using the at least two mass analyzers. In some embodiments, the methods comprise selecting a fourth mass isolation window of a fourth one of the at least two mass analyzers corresponding to afourth one of the plurality of ion switch outlets; and acquiring mass spectra of the first, second, third, and fourth mass isolation windows using the at least two mass analyzers. In some embodiments, the methods comprise selecting a first upstream mass window of the first mass filter and / or a collision energy of the first collision cell. In some embodiments, the methods comprise selecting a second mass window of the second upstream mass filter and / or a collision energy of the second collision cell corresponding. In some embodiments, the methods comprise acquiring mass spectra of both the first and second mass windows and / or of the first and second collision energies using the at least one mass analyzer. In some embodiments, the methods further comprise selecting an ion injection timing sequence during which a plurality of outlets of the ion switch are to be selected using the ion switch selector. In some embodiments, the sample is a biological sample. In some embodiments, the sample is a proteomics sample. In some embodiments, the sample comprises at least 100 different proteins. In some embodiments, the sample is obtained from a chromatograph separation prior to analysis. In some embodiments, at least 1000 peptides (e.g., at least 5000, at least 10,000, or at least 20,000) are identified in the sample using the methods and / or mass spectrometers of this disclosure. In some embodiments, tandem mass spectra are acquired in DIA mode. In some embodiments, tandem mass spectra are acquired in DDA mode. In some embodiments, the tandem mass spectra are acquired in pseudo- DDA mode. In some embodiments, the MSI mass window is less than about 2 amu (e.g., 2, 1, or 0.5 amu). In some embodiments, the MSI mass window is less than about 10 amu. In some embodiments, the MSI mass window is less than about 5 amu. In some embodiments, the MSI mass window is less than about 4 amu. In some embodiments, the MS2 resolving power is at least 10,000 (e.g., at least 10,000, at least 30,000, at least 50,000, at least 300,000, or at least 1,000,000). In another aspect, described herein are tandem mass spectrometers. In some embodiments, the mass spectrometers comprise a vacuum system, an ion inlet, operably coupled to the vacuum system, and a first set of ion optics arranged within the vacuum system and configured to guide ions from the ion inlet toward an ion switch within the vacuum system. In some embodiments, the tandem mass spectrometers comprise a plurality of mass analyzers. In some embodiments, the tandem mass spectrometers comprise at least 3 mass analyzers. In some embodiments, the tandem mass spectrometers comprise at least 4 mass analyzers. In some embodiments, at least two mass analyzers are disposed in a single chamber of the vacuum system. In another aspect, described herein are ions switches for directing an ion flux to a plurality of mass analyzers. In some embodiments, the ion switches comprise an ion switch inlet and a plurality of ion switch outlets. In some embodiments, the ion switches comprise at least one ion outlet selector. In some embodiments, the at least one ion outlet selector is configurable to direct an ion flux entering through the ion switch inlet to one or more selected outlets of theplurality of ion switch outlets. In some embodiments, the ion outlet selector comprises at least one quadrupole disposed between the ion switch inlet and the plurality of ion switch outlets. In some embodiments, the at least one quadrupole is configurable to guide ions toward a selected one of the plurality of ion switch outlets. In some embodiments, the ion outlet selector comprises a plurality of RF and / or DC ion guide lenses. In some embodiments, ion switch directs the ion flux from the ion switch inlet, to two or more ion switch outlets simultaneously, or near simultaneously (e.g., within seconds or milliseconds). In some embodiments, ion optics comprise an ion funnel, a plurality of ion lenses, and one or more quadrupole ion guides. In some embodiments, the vacuum system comprises a plurality of vacuum chambers. In some embodiments, the at least two mass analyzers are disposed in separate chambers of the vacuum system. In some embodiments, the plurality of vacuum chambers are differentially pumped such that each chamber has a pressure different from the pressure in at least one of the other chambers. In some embodiments, a pressure in the ion switch during operation is less than about 10 p Torr. In some embodiments, the vacuum system comprises a plurality of vacuum chambers upstream of the ion switch inlet. In some embodiments, the plurality of ion switch outlets comprise two ion switch outlets. In some embodiments, the plurality of ion switch outlets comprise at least three (e.g., at least 3, 4, or 5) ion switch outlets. In some embodiments, the at least two mass analyzers comprise at least three (e.g., at least 3, 4, or 5) mass analyzers. In some embodiments, each of the at least two mass analyzers are operated at the same or substantially the same pressure. In some embodiments, substantially the same pressure denotes a pressure difference between vacuum chambers of each mass of no more than 30%, 20%, 10%, or 5%. In some embodiments, the at least two mass analyzers share common control electronics. In some embodiments, the common control electronics are used for control of ion manipulation, RF, and / or DC fields of the mass analyzers. In some embodiments, the at least one quadrupole disposed between the ion switch inlet and the plurality of ion switch outlets comprises a linear quadrupole. In some embodiments, the axis of the linear quadrupole is substantially orthogonal to the ion switch inlet axis. In some embodiments, each of the at least two mass analyzers is independently selected from a linear quadrupole ion trap mass analyzer, a three dimensional quadrupole ion trap mass analyzer, an electrostatic axially harmonic orbital trapping mass analyzer, a time-of-flight mass analyzer, a distance-of-flight mass analyzer, a magnetic sector mass analyzer, a Fourier-transform ion cyclotron residence (FT-ICR) mass analyzer, and a linear quadrupole mass analyzer. In some embodiments, each of the at least two mass analyzers are electrostatic axially harmonic orbital trapping, FT-ICR, or time-of-flight mass analyzers. In some embodiments, each of the at least two mass analyzers are electrostatic axially harmonic orbital trapping mass analyzers. In some embodiments, each of the at least two mass analyzersare FT-ICR mass analyzers. In some embodiments, each of the at least two mass analyzers are linear quadrupole ion trap mass analyzers. In some embodiments, each of the mass analyzers is configured to scan across an independently selected mass range during at least partially overlapping periods of time. In some embodiments, each of the mass analyzers is configured to scan across an independently selected mass range at essentially the same time. In some embodiments, the second set of ion optics comprises one or more collision activated dissociation cells each disposed between one or more of the ion switch outlets and one or more of the at least two mass analyzers. In some embodiments, the second set of ion optics comprises one or more quadrupole mass filters each disposed between one or more of the ion switch outlets and one or more of the at least two mass analyzers. In some embodiments, each of the plurality of ion switch outlets are gated using a set of stacked lenses corresponding to the individual ion switch outlet. In some embodiments, the ion switch and the at least two mass analyzers comprise at least a minimum number of ion switch outlets and a minimum number of mass analyzers required to minimize dead time when sequential ion injections are used to provide near simultaneous mass analysis of the different mass to charge isolation windows. In some embodiments, the ion source is an atmospheric pressure ion source. In some embodiments, the ion source is electrospray ionization (ESI). In some embodiments, the ion source is a nanoelectrospray emitter. In some embodiments, the mass spectra are acquired near simultaneously by sequentially injecting ions into the at least two mass analyzers through the plurality of ion switch outlets. In some embodiments, the dead time for near simultaneous acquisition by sequential ion injections is essentially zero. In some embodiments, methods of this disclosure comprise analyzing a biological sample comprising incubating a sensor element with a biological sample to form a biomolecule corona on the sensor element. In some embodiments, the methods comprise isolating biomolecules from the biomolecule corona. In some embodiments, analyzing the biomolecules using the mass spectrometry-based analysis methods disclosed herein. In some embodiments, the methods provided herein can comprise separating a biological sample over time (e.g., by liquid chromatography). In some embodiments, the methods comprise ionizing the biological sample as the biological sample is being separated. In some embodiments, the methods comprise introducing the gas-phase ions from the separated biological sample into a field asymmetric waveform ion mobility spectrometry device to selectively remove singly-charged ions, wherein the field asymmetric waveform ion mobility spectrometry device is maintained at a pressure below 100 torr. In some embodiments, the methods comprise introducing multiply-charged gas-phase ions from the field asymmetric waveform ion mobility spectrometry device to a travelling wave ion mobility device to separate the multiply-charged ions based on mobility. In some embodiments, the methods comprisesequentially introducing windows of ions having different ion mobilities from the travelling wave ion mobility spectrometry device into a collision cell and fragmenting the windows of ions. In some embodiments, the methods comprise sequentially analyzing the different windows of fragmented ions using a time-of-flight mass analyzer, wherein at least 100 different windows corresponding to different ion mobilities are analyzed each second. In some embodiments, the methods comprise filtering the windows of ions having different ion mobilities to remove ions outside of a window of 10 amu or less, wherein said filtering occurs before the introducing of ions into the collision cell. In some embodiments, the ions having different ion mobilities from the travelling wave ion mobility spectrometry device are not filtered based on m / z before introducing into the collision cell. In some embodiments, the time-of-flight mass analyzer is a sector time-of-flight mass analyzer. In some embodiments, the time-of-flight mass analyzer is an orthogonal acceleration time-of-flight mass analyzer. In some embodiments, sequentially analyzing the different windows of fragmented ions uses a plurality of time-of-flight mass analyzers. In some embodiments, the field asymmetric waveform ion mobility spectrometry device is maintained at a pressure below 100 torr. In another aspect described herein are systems comprising a liquid chromatography device configured to separate a biological sample over time. In some embodiments, the systems comprise an electrospray ionization device configured to ionize the biological sample while being separated by the liquid chromatography device. In some embodiments, the systems comprise a field asymmetric waveform ion mobility spectrometry device configured to selectively remove singly-charged gas-phase ions received from the electrospray ionization device. In some embodiments, the systems comprise a travelling wave ion mobility device configured to separate multiply-charged ions received from the field asymmetric waveform ion mobility spectrometry device based on mobility. In some embodiments, the systems comprise a collision cell configured to fragment ion-mobility-sorted, multiply charged ions received from the travelling wave ion mobility device. In some embodiments, the systems comprise a time-of-flight mass analyzer configured to analyze the fragmented ions from the collisional cell. In some embodiments, the systems comprise a mass filter configured to filter windows of ions having different ion mobilities from the travelling waive ion mobility device to remove ions outside of a window of 10 amu or less before introduction into the collision cell. In some embodiments, the systems do not include a mass filter to remove ions received from the travelling wave ion mobility device before introduction into the collision cell. In some embodiments, the time-of-flight mass analyzer is a sector time- of-flight mass analyzer. In some embodiments, the time-of-flight mass analyzer is an orthogonal acceleration time-of-flight mass analyzer. In some embodiments, the systems comprises a plurality of time-of-flight mass analyzers configured. In some embodiments, the fieldasymmetric waveform ion mobility spectrometry device is configured to remove singly-charged ions at a pressure below 100 torr. In some embodiments, the systems can be configured to perform any of the steps of any of the methods described herein. In one aspect, described herein are ion switches for guiding or switching an ion flux and / or ion current. In some embodiments, the ion switches comprise an ion switch inlet. In some embodiments, the ion switches comprise a first ion switch outlet. In some embodiments, the ion switches comprise a second ion switch outlet. In some embodiments, the ion switches comprise a first ion guide channel disposed along a path between the ion inlet and the first ion switch outlet, the first ion guide channel comprising at least one quadrupole ion guide. In some embodiments, the ion switches comprise a second ion guide channel disposed along a path between the ion switch inlet and the second ion switch outlet, the second ion guide channel comprising at least one quadrupole ion guide. In some embodiments, the ion switches comprise at least two switching electrodes positioned along the first ion guide channel and the second ion guide channel. In some embodiments, the ion switch is configured such that ions entering the ion switch inlet are selectively directed along the first ion guide channel or the second ion guide channel by modulating a phase of a waveform applied to the switching electrodes. In another aspect, described herein are tandem mass spectrometers. In some embodiments, the tandem mass spectrometers comprise two or more mass analyzers operably coupled by an ion switch, e.g., such as the ion switches described herein. In another aspect, described herein are methods of analyzing a sample by tandem mass spectrometry. In some embodiments, the methods comprise ionizing the sample using an ion source. In some embodiments, the methods comprise selectively directing ions from the ion source along an ion guide channel of an ion switch by modulating a phase of a waveform applied to one of more switching electrodes of the ion switch. In some embodiments, the methods comprise acquiring one or more mass spectra of the sample via at least two mass analyzers, each respectively coupled to an outlet of the ion switch. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a pressure inside the switch during operation is less than about 10 Torr (e.g., less than 5, 4, 3, 2, or 1 Torr). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a pressure inside the switch during operation about 10 mTorr to 3.5 Torr. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion switch further comprises one or more drag electrodes configured to apply a drag field. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the modulating the phase of the waveform applied to the switching electrodes comprises shifting the waveform by an offset value. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the offset value is about 45 degrees to about 180 degrees (e.g., about 45, about90, or about 180 degrees). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, an approximate cross-sectional inside diameter of the first and / or second ion guide channels is each independently about 1 mm to about 10 mm (e.g., about 1 mm, about 2 mm, about 3 mm, about 4 mm, about 5 mm, about 6 mm, about 7 mm, about 8 mm, about 9 mm, or about 10 mm). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion switch comprises a collisional cooling region which allows gas entering the ion switch to slow down prior to encountering the two or more switching electrodes. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a length of the collisional cooling region is about 10 mm to about 60 mm (e.g., about 10, 20, 30, 40, 50, or 60 mm). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the path of the first ion guide channel and / or the path of the second ion guide channel follows a straight line, a curvilinear arc, or a curve. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the first ion guide channel and / or the second ion guide channel each independently comprise one or more quadrupole ion guides. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion switch is constructed from printed circuit boards (PCBs). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion switch further comprises a third ion guide channel disposed between the ion switch inlet and a third ion switch outlet, and at least two additional switching electrodes, wherein the ion switch is configured such that ions entering the ion switch inlet are selectively directed to the first, second, or third ion switch outlets by modulating a phase of a waveform applied to the switching electrodes and / or the additional switching electrodes. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion switch further comprises a fourth ion guide channel disposed between the ion switch inlet and a fourth ion switch outlet, and a second set of at least two additional switching electrodes, wherein the ion switch is configured such that ions entering the ion switch inlet are selectively directed to the first, second, third, or fourth ion switch outlets by modulating a phase of a waveform applied to the switching electrodes, the additional switching electrodes, and / or the second set of additional switching electrodes. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion switch further comprises a fifth ion guide channel disposed between the ion switch inlet and a fifth ion switch outlet, and a third set of at least two additional switching electrodes, wherein the ion switch is configured such that ions entering the ion switch inlet are selectively directed to the first, second, third, fourth, or fifth ion switch outlets by modulating a phase of a waveform applied to the switching electrodes, the additional switching electrodes, the second set of additional switching electrodes, and / or thethird set of additional switching electrodes. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the waveform comprises a radio frequency (RF) (e.g., a sine-wave), and / or DC component. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion switch directs the ion flux from the ion switch inlet, to two or more ion switch outlets simultaneously, or near simultaneously. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, at least two mass analyzers comprise at least three (e.g., at least 3, 4, or 5) mass analyzers, each mass analyzer being coupled to a single ion source by the ion switch. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the at least two mass analyzers share common control electronics (e.g., for control of ion manipulation, RF, and / or DC fields of the mass analyzers). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, each of the at least two mass analyzers is independently selected from a linear quadrupole ion trap mass analyzer, a three dimensional quadrupole ion trap mass analyzer, an electrostatic axially harmonic orbital trapping mass analyzer, a time-of-flight mass analyzer, a distance-of-flight mass analyzer, a magnetic sector mass analyzer, a Fourier-transform ion cyclotron residence (FT-ICR) mass analyzer, and a linear quadrupole mass analyzer. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, each of the at least two mass analyzers are electrostatic axially harmonic orbital trapping, FT-ICR, or time-of-flight mass analyzers. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, each of the at least two mass analyzers are electrostatic axially harmonic orbital trapping mass analyzers. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, each of the at least two mass analyzers are FT-ICR mass analyzers. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, each of the at least two mass analyzers are linear quadrupole ion trap mass analyzers. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, each of the at least two mass analyzers are time-of-flight mass analyzers. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, wherein the time-of-flight mass analyzer is a sector time-of-flight mass analyzer or an orthogonal acceleration time-of-flight mass analyzer. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the time-of-flight mass analyzer is a sector time-of-flight mass analyzer. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the time-of-flight mass analyzer is an orthogonal acceleration time-of-flight mass analyzer. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, each of the mass analyzers isconfigured to scan across an independently selected mass range during at least partially overlapping periods of time. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, each of the mass analyzers is configured to scan across an independently selected mass range at essentially the same time. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion switch and the at least two mass analyzers comprise at least a minimum number of ion switch outlets and a minimum number of mass analyzers required to reduce dead time when sequential ion injections are used to provide near simultaneous mass analysis of the different mass to charge isolation windows. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion source is an atmospheric pressure ion source. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion source is electrospray ionization (ESI). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion source is a nano-electrospray emitter. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the methods further comprise: selecting a third mass isolation window of a third one of the at least two mass analyzers corresponding to a third one of the plurality of ion switch outlets; and acquiring mass spectra of the first, second, and third mass isolation windows using the at least two mass analyzers. In some embodiments of the methods described herein, the methods comprise selecting a fourth mass isolation window of a fourth one of the at least two mass analyzers corresponding to a fourth one of the plurality of ion switch outlets; and acquiring mass spectra of the first, second, third, and fourth mass isolation windows using the at least two mass analyzers. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the mass spectra are acquired near simultaneously by sequentially injecting ions into the at least two mass analyzers through the plurality of ion switch outlets. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the dead time for near simultaneous acquisition by sequential ion injections is essentially zero. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the methods further comprise, selecting an ion injection timing sequence during which a plurality of outlets of the ion switch are to be selected using the ion switch selector. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the sample is a biological sample. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the sample is a proteomics sample. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the sample comprises at least 100 different proteins. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the sample is obtained from a chromatographic separationprior to analysis. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, tandem mass spectra are acquired in DIA mode. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, tandem mass spectra are acquired in DDA mode. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the tandem mass spectra are acquired in pseudo-DDA mode. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the MSI mass window is less than about 2 amu (e.g., 2, 1, or 0.5 amu). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the MSI mass window is less than about 10 amu. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the MSI mass window is less than about 5 amu. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the MSI mass window is less than about 4 amu. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the MS2 resolving power is at least 10,000 (e.g., at least 10,000, at least 30,000, at least 50,000, at least 300,000, or at least 1,000,000). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the MS2 resolving power is less than 10,000,000 (e.g., less than 5,000,000, less than 1,000,000, less than 100,000, or less than 50,000). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, at least 1000 peptides (e.g., at least 5000, at least 10,000, or at least 20,000) are identified in the sample. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the ion switch comprises a first planar surface and a second planar surface, wherein the first ion guide channel and the second ion guide channel are disposed between the first planar surface and the second planar surface. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a first plurality of guide electrodes is disposed on the first planar surface, and wherein a second plurality of guide electrodes is disposed on the second planar surface. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the first plurality of guide electrodes and the second plurality of guide electrodes together define the first ion guide channel and the second ion guide channel. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a layout for the first plurality of guide electrodes on the first planar surface is a mirror image of a layout for the second plurality of guide electrodes on the second planar surface. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a first switching electrode is disposed on the first planar surface, and wherein a second switching electrode is disposed on the second planar surface. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, thefirst switching electrode and the second switching electrode have the same shape. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the first switching electrode and the second switching electrode are laterally aligned with respect to each other. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a shape of the first switching electrode is mirror image of a shape of the second switching electrode. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a shape of the first switching electrode is asymmetric. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a shape of the second switching electrode is asymmetric. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the first planar surface and the second planar surface are each printed circuit boards. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the first planar surface and the second planar surface are generally parallel. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the first planar surface and the second planar surface are at least about 2 mm apart (e.g., about 2 mm, about 4 mm, about 6 mm, or about 8 mm). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, the first planar surface and the second planar surface nor more than about 20 mm apart (e.g., about 20 mm, about 15 mm, about 12 mm, about 10 mm, or about 8 mm). In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a first plurality of drag electrodes are disposed on a side of the first planar surface opposite where the first plurality of guide electrodes are disposed. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a second plurality of drag electrodes are disposed on a side of the second planar surface opposite where the second plurality of guide electrodes are disposed. In some embodiments, of the methods, the mass spectrometers, or the ion switches described herein, a plurality of drag electrodes are disposed between the first planar surface and the second planar surface.INCORPORATION BY REFERENCE

[0005] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and / or take precedence over any such contradictory material.BRIEF DESCRIPTION OF THE DRAWINGS

[0006] The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which:

[0007] FIG. 1A illustrates an example of a linear arrangement of ion guide electrodes useful in constructing an ion switch such as those described herein.

[0008] FIG. IB illustrates an example of a curved arrangements of ion guide electrodes useful in constructing an ion switch such as those described herein.

[0009] FIG. 1C illustrates an example arrangement of ion guide electrodes incorporating both curved and linear ion guide paths, useful as an ion switch as described herein.

[0010] FIG. 2 illustrates a first view of an example two-outlet ion switch utilizing an electrode geometry similar to that shown in FIG. 1C, which can be implemented, for example, using a printed circuit board (PCB) to house the guide electrodes.

[0011] FIG. 3 illustrates an alternate view of an example two-outlet ion switch utilizing an electrode geometry similar to that shown in FIG. 1C, which can be implemented, for example, using a printed circuit board (PCB) to house the guide electrodes.

[0012] FIG. 4 illustrates a second alternate view of an example two-outlet ion switch utilizing an electrode geometry similar to that shown in FIG. 1C, wherein the view shows an exposed non-conductive surface of a PCB which houses the electrode material illustrated in FIGs. 2 and 3.

[0013] FIG. 5 illustrates a computational multiphysics simulation of a potential well for the straight and curved paths of the example two-outlet ion switch illustrated in FIGs. 2-4, showing a 3D and a 2D voltage profile indicating a voltage applied to the diamond shaped electrode can create an ion confining electric field in the direction (z) of the curved path.

[0014] FIG. 6 illustrates a computational multiphysics simulation of a potential well for the straight and curved paths of the example two-outlet ion switch illustrated in FIGs. 2-4, showing a 3D and a 2D voltage profile when the diamond shaped electrode is applied with a voltage that create an ion confining electric field in the direction (z) of the straight path. By switching the polarity of the diamond shaped region, the ion confining region of the ion switch can be diverted from the straight path (FIG. 6) to the curved path (FIG. 5) of the example ion switch.

[0015] FIG. 7 illustrates a computational Multiphysics simulation of the example ion switch of FIGs. 2-6, showing ion trajectories for changing direction upon a change in polarity for ions of m / z 600, z=2+, collision cross section = 600 angstrom2, released at t=0 in steps of 2.5e-8 (s)until 2.5e-7 (s). Each release included 5 particles totaling up to 50 particles. Time step was adjusted to le-8 (s). Pressure inside the ion switch was simulated at 10 mTorr. Particles remained confined in the potential well and travel along the straight or curved path without wall loss.

[0016] FIG. 8 illustrates model parameters used for the simulation of the example ion switch detailed in FIG. 7.

[0017] FIG. 9 illustrates an example ion manifold with a DC Electric field or drag field for high pressure applications. In this embodiment the ion switch is equipped with a resistor chain that allows for a DC gradient or drag field along the ion path. The drag field may propel ions particularly when the switch is operated at elevated pressures (e.g., > 10 mTorr).

[0018] FIG. 10 illustrates an example assembly of the ion switch apparatus in 3D inside a vacuum chamber. In this embodiment the ion switch can be extended or daisy chained to create multiple ion outlets that can be connected to the inlet of the mass analyzer to operate a plurality of mass analyzer feeding off a single ion source. The ion switch is equipped with a resistor chain that allows for a DC gradient or drag field along the ion path.

[0019] FIG. 11 illustrates an alternate configuration of the modular ion switch design of FIG.10, which can accommodate switching between many outlets by combining modules. This embodiment shows the flexibility of orienting ion outlets allowed by the simplicity of the PCB based design.

[0020] FIG. 12 illustrates an example DIA scheme with ion parallel mass analyzer. Assuming most tryptic peptides register between m / z 400-900, DIA isolation of 1 amu, and a sampling rate of about 500 DIA windows / s (500Hz), two time-of-flight mass analyzers can be allotted the DIA windows to 250 DIA window / s per TOF. One additional TOF can be dedicated to produce MSI scan such that every DIA window will produce a pair of MSI and its associated MS2.Alternatively, all TOFs can be assigned to produce MS2 only.

[0021] FIG. 13 illustrates a schematic diagram of an example control switch for changing the direction of ion flow through ion switches described herein utilizing a field effect transistor (FET).

[0022] FIG. 14 shows a computer system that is programmed or otherwise configured to implement methods provided herein.

[0023] FIG. 15 illustrates an example implementation of a control circuit according to FIG. 13.

[0024] FIG. 16 illustrates an example of a detailed circuit diagram of the control circuit of FIG.14

[0025] FIG. 17 illustrates an example of a cross section of optional drag electrodes which can be implemented on any of the ion switches described herein. Cross section view showing topand bottom PCBs and drag field electrodes. Drag electrodes can be segments on the Z axis or angled to create the field. Planer QUAD electrodes could be segmented are also possible utilizing an on-board coupling network. Presence of a drag field in switch region increases complexity of the electric field used for switching, but can provide improved selection between outlets.

[0026] FIG. 18 illustrates a computational Multiphysics simulation of an example ion switch comprising an optional drag voltage, applied at optional drag electrodes.

[0027] FIG. 19 illustrates the potential well of the example ion switch of FIG. 17.

[0028] FIG. 20 illustrates an example simulated switching between two outlets of a high- pressure ion switch constructed using printed circuit boards.

[0029] FIG. 21 illustrates a simulation of the transit time for an ion to traverse the curved path of the example ion switch detailed in FIG. 20, which averaged to about 3 ms.

[0030] FIG. 22 illustrates an alternate view of the simulation of FIG. 21.

[0031] FIG. 23 illustrates parameters used for the Multiphysics simulations of FIGs. 21-22, as well as an additional alternate view of the simulation.

[0032] FIG. 24 illustrates a simulation of the same model as FIGs. 21-23, when the switching voltage is set for the straight path..

[0033] FIG. 25 illustrates a graph of transmission probability through an example ion switch described herein.

[0034] FIG. 26 illustrates a further view of simulated ion trajectories through a curved path of an example ion switch described herein.

[0035] FIG. 27 illustrates a simulation of switch voltage in conditions producing 1-3 eV range ion energy, in an example ion switch implementing optional drag electrodes. Collisional cooling can be applied by controlling ion-gas collision frequency.DETAILED DESCRIPTION

[0036] While various embodiments of the disclosure have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions can occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the disclosure described herein can be employed. The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.Definitions

[0037] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this disclosure belongs. All patents and publications referred to herein are incorporated by reference.

[0038] As used herein, “near simultaneous” generally refers to events which occur at nearly, but not exactly the same time. Near simultaneous can refer to parallel events which begin at different times (e.g., with start points within seconds or milliseconds of each other) or can refer to sequential events which occur in rapid succession (e.g., where the end of a first event occurs no more than milliseconds or hundreds of milliseconds before the start of a subsequent event).

[0039] As used herein, “dead time” and “dead-time” are used interchangeably and generally refer to a period of time during the operation of a mass spectrometer where one or more mass analyzers are not available to accept ions (such as when scanning an ion trap). Such dead time often causes ions to be diverted to waste.

[0040] As used herein, “quadrupole” generally refers to any device or method step relying on a combination of radiofrequency (or near radiofrequency AC) and DC fields to guide or select ions from an ion flux traversing the AC and / or DC fields. Quadrupoles can take a diverse variety of forms, including but not limited to linear true quadrupoles (i.e. with four straight, parallel, guide rods to which the RF and DC are applied), bent or twisted quadrupoles, hexapoles, octopoles, flatapoles, and the like. Quadrupoles can generally be operated as mass to charge ratio filters or selectors, or as broadband ion guides (e.g., in RF only mode). Ion transmission and / or filtering through a quadrupole can generally be described using a Matthieu stability diagram or calculation.

[0041] As used herein, “ion guide channel” generally refers to a configuration of electric fields which substantially confine ions to movement within a defined region of space. For example, a quadrupole ion guide can be used to create an ion guide channel within the region of space where ions are stabilized. As used herein, wherever the term quadrupole is used, it shall be generally understood that a quadrupole is associated with an ion guide channel.

[0042] As used herein, “ion optic” generally refers to any device or combination of devices that are capable of directing the path of an ion flux in a controlled manner. Non limiting examples include AC or DC lenses, quadrupoles, collision cells and the like.

[0043] As used herein, “mass analyzer” generally refers to a device which is capable of determining a mass to charge ratio and an intensity or a number of counts per second of one or more ions arriving at a detector comprised within the analyzer.

[0044] Whenever the term “at least,” “greater than,” or “greater than or equal to” precedes the first numerical value in a series of two or more numerical values, the term “at least,” “greaterthan” or “greater than or equal to” applies to each of the numerical values in that series of numerical values. For example, greater than or equal to 1, 2, or 3 is equivalent to greater than or equal to 1, greater than or equal to 2, or greater than or equal to 3.

[0045] Whenever the term “no more than,” “less than,” or “less than or equal to” precedes the first numerical value in a series of two or more numerical values, the term “no more than,” “less than,” or “less than or equal to” applies to each of the numerical values in that series of numerical values. For example, less than or equal to 3, 2, or 1 is equivalent to less than or equal to 3, less than or equal to 2, or less than or equal to 1.

[0046] As used herein, a “feature” identified by mass spectrometry includes a signal at a specific combination of retention time and m / z (mass-to-charge ratio), where each feature has an associated intensity. Some features are further fragmented in a second mass spectrometry analysis (MS2) for identification.

[0047] As used herein, the terms “amu”, “atomic mass units”, “m / z”, or “mass-to-charge ratio”, when used as a unit of measurement, are used interchangeably and generally refer to a mass-to- charge ratio in Thompsons (Th).Mass Spectrometry

[0048] Proteins comprise a large number of amino acids and are typically of significant molecular weight. Thus, accurate identification and quantitation of the protein by direct mass spectrometric measurement is challenging and may require using tandem mass spectrometry.

[0049] Most tandem mass spectrometers exhibit poor ion transmission efficiency due to a mismatch in the fast rate of MSI isolation and the slow speed of MS2 scan. Each window can contain 300-500 precursors for a highly complex sample. Such a population of precursors typically requires a high resolution from the mass analyzer, which can be delivered using high- resolution mass analyzers at the cost of scan speed. A slow scan speed can keep the analyzer occupied for extended periods, making it unavailable to accept ions from a second isolation window. Ions from the second isolation window or subsequent windows may be lost until a mass analyzer is freed up to accept ions, reducing the number of points that can be collected across a chromatographic peak. This constraint is common among present-generation mass spectrometers and can be referred to as a low-duty cycle problem.

[0050] An ion trap mass analyzer is unique in its ability to trap a population of ions and sequentially isolate all precursor ions with no loss of ions in the trap. Such a high-duty cycle process converts a significantly higher fraction of precursor ions in an MSI scan into MS2 fragments for peptide sequencing. One way of addressing the low duty-cycle issue is to use an array of ion trap like ion storage cells to buffer ions to compensate for slow scan speed bystoring ions from a peak of interest, where ions are stored in cells until the mass analyzer is available to accept the ions. However, these cells have a limited storage capacity, which may be insufficient alone for high-throughput proteomic analysis. For example, fast gradients such as 30 mins or less deliver significant counts of peptides per isolation window that convert to high ion counts. The high ion current flux and temporal proximity of chromatographic peaks can overwhelm the capacity of a storage cell. Ion switches of this disclosure may eliminate the need for storage cells and / or enhances their use by removing the need to "buffer" the ion flux.

[0051] Analysis of samples by tandem mass spectrometry can generally be classified as data independent analysis / acquisition (DIA) and data dependent analy si s / acqui sition (DDA) methods. DIA can be useful to determine what is present in a sample of potentially unknown identity. To determine the molecular structure of sample molecules, a mass spectrometer is typically first used to mass analyze all sample ions (precursor ions) within a selected window of mass to charge ratio (m / z). Such a scan is often denoted as an MSI scan. The selected sample ions are then fragmented and the resulting fragments are subsequently mass analyzed across the selected m / z range. The scan of the fragmented ions is often denoted as an MS2 scan.

[0052] DDA is typically useful to confirm that one or more species is / are present in a given sample. Methods of DDA identify a fixed number of precursor ion species, and select and analyze those via mass spectrometry by providing a more comprehensive mapping of fragments to individual parent ions. The determination of which precursor ion species are of interest in DDA may be based upon intensity ranking (for example, the top ten most abundant species as observed by peaks in a MSI spectrum), or by defining an “inclusion list” of precursor mass spectral peaks (for example by user selection), from which MS2 spectra are always acquired regardless of the intensity ranking of the peak in the MSI mass spectrum. Still otherwise, an “exclusion list” of peaks in MSI can be defined, for example by a user, based e.g., on prior knowledge of the expected sample contents.

[0053] DIA avoids the decisions typically necessary in DDA, by simply dividing the mass range of interest (typically user defined) into segments and obtaining MS2 spectra for each segment. With DIA, the acquisition of an MSI precursor spectrum may be omitted, since the parameters of the selection window for the sample ions carries information about the range of possible sample ions within that window.

[0054] One significant advantage of the ion switches described herein are that use of multiple mass analyzers in parallel may allow for near-zero dead time in MS / MS analysis. Accordingly, mass spectrometers comprising a plurality of mass analyzers and an ion switch as described herein can allow for scanning in a “pseudo-DDA” mode, wherein DIA is operated using very small mass windows, which results in a 1 : 1 or near 1 : 1 mapping of parent ions to MS2 spectra.For example, a method of DIA analysis using a mass window of less than 5 amu (e.g., less than 4, 3, 2, 1, or 0.5 amu) for each MS2 scan is discussed above. This relatively narrow mass window is similar to targeted mass windows used in a typical DDA approach. By using relatively narrow mass windows for each of the MS2 scans, the resulting MS2 spectra may be analyzed using DDA type databases and can provide a similar level of insight, rather than requiring subsequent experiments with full DIA scans.

[0055] The ion switches described herein may address one problem with using such a narrow mass window for each of the MS2 scans, which is that the number of scans required to build up a full range of MS2 scans for the mass range of interest increases. As a result, the time taken to perform a complete DIA analysis can become overly long, for example much longer than the duration of a chromatographic peak. If the DIA analysis is not completed within the duration of the chromatographic peak, the analysis may not provide meaningful data, as some parts of the analysis will not measure the sample peak.

[0056] Another problem that may be solved by the methods and ion switches described herein, is that the relatively narrow mass windows for each MS2 scan result in relatively few, if any, fragmenting ions reaching the detector at a given time. Thus, reducing the mass selection window for each MS2 scan results in a reduction in the mass accuracy and / or the sensitivity of the MS2 mass analyzer. This problem is exacerbated when attempting to perform a large number of MS2 scans at a sufficient frequency to fit all MS2 scans within the duration of a chromatographic peak.

[0057] Utilizing multiple mass analyzers coupled to an ion switch with a plurality of ion outlets can overcome one or more of these problems by eliminating or reducing analytical dead time and increasing ion transmission from an ion source to a detector through a tandem MS.

[0058] For pseudo-DDA analysis, narrow window DIA is repeated a number of times over the duration of a chromatographic peak. Accordingly, the cycle time of the DIA measurement may be adapted to be performed a plurality of times over the duration of a chromatographic peak. By performing DIA a number of times over the duration of the chromatographic peak, the peak may be sampled a number of times, allowing a complete picture of the peak to be established. The DIA methodology can be performed at least: 3, 4, 5, 7, 9 or preferably at least 10 times over the duration of a chromatographic peak.

[0059] As a solution, ion switches of this disclosure, in some embodiments, allow for continuous processing of ions using an array of mass analyzers without needing to store ions for a significant period of time. For example, while a mass analyzer processes precursor ions in the first window, ions from the second DIA window are sent to a second mass analyzer, which scans in parallel, increasing duty cycle by reducing (or even eliminating) dead-time. This can beaccomplished, for example, using a mass spectrometer with two or more mass analyzers. In some instances the duty cycle is increased, 5, 10, 15, 20, 25, 50, 75, 100, 150, 200, 300, or even 500 percent using the ion switch methods described herein. In some instances the dead time is decreased, 5, 10, 15, 20, 25, 50, 75, 100, 150, 200, 300, or even 500 percent using the ion switch methods described herein.Ion switches

[0060] Ion switches described herein are devices which can direct an ion flux entering through an inlet to a plurality of outlets in a configurable manner, either by selecting a particular outlet or by dividing the flux between selected outlets. Ion switches can comprise a series of electrodes in various geometries. Ion switches can comprise quadrupoles or other ion optics useful in guiding ions from the switch inlet to the selected switch outlet. In some embodiments, an ion switch disclosed herein comprises one or more of: an ion switch inlet; a first ion switch outlet; a second ion switch outlet; a first ion guide channel disposed along a path between the ion inlet and the first ion switch outlet, the first ion guide channel comprising at least one quadrupole ion guide; a second ion guide channel disposed along a path between the ion switch inlet and the second ion switch outlet, the second ion guide channel comprising at least one quadrupole ion guide; and at least two switching electrodes positioned along the first ion guide channel and the second ion guide channel. In some embodiments, the ion switch is configured such that ions entering the ion switch inlet are selectively directed along the first ion guide channel or the second ion guide channel by modulating a phase of a waveform applied to the switching electrodes.

[0061] Provided herein are methods of analyzing samples using tandem mass spectrometry. In some instances, methods comprise one or more steps of A method of analyzing a sample by tandem mass spectrometry, the method comprising: ionizing the sample using an ion source; selectively directing ions from the ion source along an ion guide channel of an ion switch by modulating a phase of a waveform applied to one of more switching electrodes of the ion switch; and acquiring one or more mass spectra of the sample via at least two mass analyzers, each respectively coupled to an outlet of the ion switch.

[0062] Example ion switches which can select between two or more outlets are shown in FIGs. 2-12, 18-24, 26, and 27. An ion beam directed by ion optics enters an ion switch, which can selectively direct the ion beam to one of two or more mass analyzers. Separate ion optics may be positioned before each mass analyzer. In some embodiments, the ion switch includes electrodes extending in a direction oblique or substantially perpendicular to the ion beam to selectively direct ions towards a mass analyzer.

[0063] In some embodiments, a network of electrodes may be used to selectively direct incoming ions towards a particular mass analyzer. In some cases, a pair of parallel surfaces, each with a network of electrodes, may be used to selectively direct incoming ions toward a particular mass analyzer. As a non-limiting example, the parallel surfaces may be printed circuit boards (PCBs) designed to selectively control ion movement towards a plurality mass analyzers.

[0064] In some cases, Ion switches of this disclosure can utilize a linear quadrupole to keep ions contained within one or more guide channels. Switch inlets and switch outlets for a linear quadrupole-based ion switch can comprise an aperture formed into one or more of the quadrupole electrodes. The ion beam can be selectively directed through the aperture towards a first mass analyzer or directed past the aperture towards a second mass analyzer. A linear quadrupole based switch can be rotated such that its axis is orthogonal to a beam of ions entering the quadrupole through an ion switch inlet, or can be set at an angle.

[0065] In some cases, the quadrupole creates a curved path for the ion beam, and apertures are located along this path and operably coupled to separate mass analyzers. In some cases, the quadrupole may have a serpentine path. The skilled person, guided by the teachings in the present application, will appreciate other configurations for the quadrupole.

[0066] Ions can be guided through an ion switch utilizing a quadrupole by applying the appropriate RF and / or DC fields to guide the ion flux from the inlet of the switch to one or more selected outlets.

[0067] In some embodiment, the ion switch may further include one or more drag electrodes. The drag electrodes may be configured to generate an electric field to move ions along first ion guide channel or the second ion guide channel. In some embodiments, the drag electrodes can have progressively increasing or decreasing voltages along the first ion guide channel or the second ion guide channel. In some embodiments, a travelling wave may be applied to the drag electrodes to move ions the first ion guide channel or the second ion guide channel.

[0068] The location of the drag electrodes is not particularly limited, and may be positioned in any manner to move ions along a desired path. In some embodiments, the drag electrodes may be positioned between guide electrodes. For example, the drag electrodes may be positioned as depicted in FIG. 17. In some embodiments, the drag electrodes are disposed within one or more substrates (e.g., PCB) having the guide electrodes disposed thereon. In some embodiments, the drag electrodes are disposed on one or more substrates, wherein guide electrodes are disposed on an opposite side of the substrate.

[0069] The skilled person, guided by the teaching of the present application, will appreciate that various suitable pressures may be used when operating the ion switch of the present disclosure. In some embodiments, the ion switch may be operated at a pressure of less than 10 Torr.

[0070] The ion switch of the present disclosure may, for example, be used in the methods and devices disclosed in International Application No. PCT / US2023 / 078724, filed on November 3, 2023, and U.S. Application No. 63 / 486,905, filed on February 24, 2023, which are hereby incorporated by reference in their entirety. For example, the ion switch may be used as part of the ion manifolds to selectively direct ions to a plurality of mass analyzers.Computer systems

[0071] The present disclosure provides computer systems that are programmed to implement methods of the disclosure. FIG. 14 shows a computer system 1501 that is programmed or otherwise configured to implement the methods and systems described herein. The computer system 1501 can be an electronic device of a user or a computer system that is remotely located with respect to the electronic device. The electronic device can be a mobile electronic device.

[0072] The computer system 1501 includes a central processing unit (CPU, also “processor” and “computer processor” herein) 1505, which can be a single core or multi core processor, or a plurality of processors for parallel processing. The computer system 1501 also includes memory or memory location 1510 (e.g., random-access memory, read-only memory, flash memory), electronic storage unit 1515 (e.g., hard disk), communication interface 1520 (e.g., network adapter) for communicating with one or more other systems, and peripheral devices 1525, such as cache, other memory, data storage and / or electronic display adapters. The memory 1510, storage unit 1515, interface 1520 and peripheral devices 1525 are in communication with the CPU 1505 through a communication bus (solid lines), such as a motherboard. The storage unit 1515 can be a data storage unit (or data repository) for storing data. The computer system 1501 can be operatively coupled to a computer network (“network”) 1530 with the aid of the communication interface 1520. The network 1530 can be the Internet, an internet and / or extranet, or an intranet and / or extranet that is in communication with the Internet. The network 1530 in some cases is a telecommunication and / or data network. The network 1530 can include one or more computer servers, which can enable distributed computing, such as cloud computing. The network 1530, in some cases with the aid of the computer system 1501, can implement a peer-to-peer network, which may enable devices coupled to the computer system 1501 to behave as a client or a server.

[0073] The CPU 1505 can execute a sequence of machine-readable instructions, which can be embodied in a program or software. The instructions may be stored in a memory location, such as the memory 1510. The instructions can be directed to the CPU 1505, which can subsequently program or otherwise configure the CPU 1505 to implement methods of the present disclosure. Examples of operations performed by the CPU 1505 can include fetch, decode, execute, and writeback.

[0074] The CPU 1505 can be part of a circuit, such as an integrated circuit. One or more other components of the system 1501 can be included in the circuit. In some cases, the circuit is an application specific integrated circuit (ASIC).

[0075] The storage unit 1515 can store files, such as drivers, libraries and saved programs. The storage unit 1515 can store user data, e.g., user preferences and user programs. The computer system 1501 in some cases can include one or more additional data storage units that are external to the computer system 1501, such as located on a remote server that is in communication with the computer system 1501 through an intranet or the Internet.

[0076] The computer system 1501 can communicate with one or more remote computer systems through the network 1530. For instance, the computer system 1501 can communicate with a remote computer system of a user. Examples of remote computer systems include personal computers (e.g., portable PC), slate or tablet PC’s (e.g., Apple® iPad, Samsung® Galaxy Tab), telephones, Smart phones (e.g., Apple® iPhone, Android-enabled device, Blackberry®), or personal digital assistants. The user can access the computer system 1501 via the network 1530.

[0077] Methods as described herein can be implemented by way of machine (e.g., computer processor) executable code stored on an electronic storage location of the computer system 1501, such as, for example, on the memory 1510 or electronic storage unit 1515. The machine executable or machine readable code can be provided in the form of software. During use, the code can be executed by the processor 1505. In some cases, the code can be retrieved from the storage unit 1515 and stored on the memory 1510 for ready access by the processor 1505. In some situations, the electronic storage unit 1515 can be precluded, and machine-executable instructions are stored on memory 1510.

[0078] The code can be pre-compiled and configured for use with a machine having a processer adapted to execute the code, or can be compiled during runtime. The code can be supplied in a programming language that can be selected to enable the code to execute in a pre-compiled or as-compiled fashion.

[0079] Aspects of the systems and methods provided herein, such as the computer system 1501, can be embodied in programming. Various aspects of the technology may be thought of as “products” or “articles of manufacture” typically in the form of machine (or processor) executable code and / or associated data that is carried on or embodied in a type of machine readable medium. Machine-executable code can be stored on an electronic storage unit, such as memory (e.g., read-only memory, random-access memory, flash memory) or a hard disk. “Storage” type media can include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memories, tape drives, disk drives and the like, which may provide non-transitory storage at any time for the softwareprogramming. All or portions of the software may at times be communicated through the Internet or various other telecommunication networks. Such communications, for example, may enable loading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server. Thus, another type of media that may bear the software elements includes optical, electrical and electromagnetic waves, such as used across physical interfaces between local devices, through wired and optical landline networks and over various air-links. The physical elements that carry such waves, such as wired or wireless links, optical links or the like, also may be considered as media bearing the software. As used herein, unless restricted to non-transitory, tangible “storage” media, terms such as computer or machine “readable medium” refer to any medium that participates in providing instructions to a processor for execution.

[0080] Hence, a machine readable medium, such as computer-executable code, may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non-volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computer(s) or the like, such as may be used to implement the databases, etc. shown in the drawings. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and / or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution.

[0081] The computer system 1501 can include or be in communication with an electronic display 1535 that comprises a user interface (UI) 1540 for providing, for example, selection of ion switch injection parameters. Examples of UI’s include, without limitation, a graphical user interface (GUI) and web-based user interface.

[0082] Methods and systems of the present disclosure can be implemented by way of one or more algorithms. An algorithm can be implemented by way of software upon execution by the central processing unit 1505.EXAMPLES

[0083] The following examples are provided to further illustrate some embodiments of the present disclosure, but are not intended to limit the scope of the disclosure; it will be understood by their exemplary nature that other procedures, methodologies, or techniques known to those skilled in the art may alternatively be used.Example 1: Multi-port Ion Switch for Parallel Scanning of Numerous Mass Analyzers

[0084] FIGs. 9-12 show example geometry for ion switches with an array of switch outlets used to accomplish deflection of ions from a single ion source between multiple mass analyzers (e.g., as shown in FIG. 12). The ion switch can utilize micro-electrodes printed on a PCB substrate (e.g., as shown in FIGs. 2-4) and can be scaled to an arbitrary number of switch outlets / mass analyzers. Each electrode can apply a DC and RF voltage to route ions into a network of mass analyzers, allowing for significant reductions in dead time, and / or multiplexed MS2 analysis.Example 2: Proteomic Measurements using Zero Dead-Time Tandem Mass Spectrometry using a Multiport Ion Switch

[0085] A timing sequence for injecting and analyzing ions such that the parallel utility of a mass spectrometer comprising multiple mass analyzers can be leveraged to improve the tandem mass spec duty cycle. The mass range, which contains peptides, is divided into small windows in a DIA mode where each window is 10 amu wide; ions in each window are injected into each ion trap for analysis. The ion switch can convert the ions in each isolation window to the number of elementary charges. The number of elementary charges injected into each ion trap mass analyzer can be regulated to avoid space charge repulsion and optimize transmission of the total ion flux into a plurality of ion trap mass analyzers.

[0086] Even with a small DIA isolation window of 10 amu the ion flux in the isolation window can be high enough to breach the upper limit of one million charges. Overfilling of the ion trap is avoided by implementing an Automated Gain Control (AGC) which regulates the ion injection time (IT) to control the total number of charges deposited into the ion trap. In a first scheme (Scheme 1) the IT is shorter than the time required for an ion trap mass analyzer to scan the range m / z 400 to m / z 900. Once ion injection in trap-1 is complete or when trap-1 starts a scan, the ion beam is deflected to build an AGC target for injecting ions into trap-2. However, when trap-2 starts a scan, the ion trap-1 is still scanning, and the ion beam is deflected to waste.This period is called dead time when the mass analyzer is "blind" to the incoming ion beam. Peptide ions arriving in the dead period are not recorded in an MSI or MS2 and are never sequenced. Scheme 1 clarifies that more than two ion traps are needed to improve the duty cycle such that the dead time is negligible. The latter scenario is addressed in second scheme (Scheme 2), where four ion trap mass analyzers are networked to use the ion beam continuously. At the end of each MSI scan, the ion beam is deflected into the injection device of the next available ion trap. In this example, ion trap 1 is available for analysis at the end of ion trap four, thus eliminating the need for a fifth ion trap mass analyzer.Example 3: Computational Multiphysics Simulations of Example Ion Switch Configurations

[0087] A commercial computational multiphysics simulation package was used to construct example geometries of ion switches to demonstrate the feasibility of directing an ion flux to a selected outlet. Geometries tested and results are depicted in FIGs. 5-8 and 18-27.

[0088] While preferred embodiments of the present disclosure have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the present disclosure may be employed in practicing the present disclosure. It is intended that the following claims define the scope of the present disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby. The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.

Claims

CLAIMSWhat is claimed is:

1. An ion switch comprising: an ion switch inlet; a first ion switch outlet; a second ion switch outlet; a first ion guide channel disposed along a path between the ion inlet and the first ion switch outlet, the first ion guide channel comprising at least one quadrupole ion guide; a second ion guide channel disposed along a path between the ion switch inlet and the second ion switch outlet, the second ion guide channel comprising at least one quadrupole ion guide; and at least two switching electrodes positioned along the first ion guide channel and the second ion guide channel; wherein the ion switch is configured such that ions entering the ion switch inlet are selectively directed along the first ion guide channel or the second ion guide channel by modulating a phase of a waveform applied to the switching electrodes.

2. A mass spectrometer comprising: two or more mass analyzers operably coupled by the ion switch of claim 1.

3. A method of analyzing a sample by tandem mass spectrometry, the method comprising: ionizing the sample using an ion source; selectively directing ions from the ion source along an ion guide channel of an ion switch of claim 1 by modulating a phase of a waveform applied to one of more switching electrodes of the ion switch; and acquiring one or more mass spectra of the sample via at least two mass analyzers, each respectively coupled to an outlet of the ion switch.

4. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein a pressure inside the switch during operation is less than about 10 Torr (e.g., less than 5, 4, 3, 2, or 1 Torr).

5. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein a pressure inside the switch during operation about 10 mTorr to 3.5 Torr.

6. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein the ion switch further comprises one or more drag electrodes configured to apply a drag field.

7. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein the modulating the phase of the waveform applied to the switching electrodes comprises shifting the waveform by an offset value.

8. The method, the mass spectrometer, or the ion switch of claim 7, wherein the offset value is about 45 degrees to about 180 degrees (e.g., about 45, about 90, or about 180 degrees).

9. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein an approximate cross-sectional inside diameter of the first and / or second ion guide channels is each independently about 1 mm to about 10 mm (e.g., about 1 mm, about 2 mm, about 3 mm, about 4 mm, about 5 mm, about 6 mm, about 7 mm, about 8 mm, about 9 mm, or about 10 mm).

10. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein the ion switch comprises a collisional cooling region which allows gas entering the ion switch to slow down prior to encountering the two or more switching electrodes.

11. The method, the mass spectrometer, or the ion switch of claim 10, wherein a length of the collisional cooling region is about 10 mm to about 60 mm (e.g., about 10, 20, 30, 40, 50, or 60 mm).

12. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein the path of the first ion guide channel and / or the path of the second ion guide channel follows a straight line, a curvilinear arc, or a curve.

13. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein the first ion guide channel and / or the second ion guide channel each independently comprise one or more quadrupole ion guides.

14. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein the ion switch is constructed from printed circuit boards (PCBs).

15. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein the ion switch further comprises a third ion guide channel disposed between the ion switch inlet and a third ion switch outlet, and at least two additional switching electrodes, wherein the ion switch is configured such that ions entering the ion switchinlet are selectively directed to the first, second, or third ion switch outlets by modulating a phase of a waveform applied to the switching electrodes and / or the additional switching electrodes.

16. The method, the mass spectrometer, or the ion switch of claim 15, wherein the ion switch further comprises a fourth ion guide channel disposed between the ion switch inlet and a fourth ion switch outlet, and a second set of at least two additional switching electrodes, wherein the ion switch is configured such that ions entering the ion switch inlet are selectively directed to the first, second, third, or fourth ion switch outlets by modulating a phase of a waveform applied to the switching electrodes, the additional switching electrodes, and / or the second set of additional switching electrodes.

17. The method, the mass spectrometer, or the ion switch of claim 16, wherein the ion switch further comprises a fifth ion guide channel disposed between the ion switch inlet and a fifth ion switch outlet, and a third set of at least two additional switching electrodes, wherein the ion switch is configured such that ions entering the ion switch inlet are selectively directed to the first, second, third, fourth, or fifth ion switch outlets by modulating a phase of a waveform applied to the switching electrodes, the additional switching electrodes, the second set of additional switching electrodes, and / or the third set of additional switching electrodes.

18. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein the waveform comprises a radio frequency (RF) (e.g., a sine-wave), and / or DC component.

19. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein the ion switch directs the ion flux from the ion switch inlet, to two or more ion switch outlets simultaneously, or near simultaneously.

20. The method or the mass spectrometer of any of the preceding claims, wherein the at least two mass analyzers comprise at least three (e.g., at least 3, 4, or 5) mass analyzers, each mass analyzer being coupled to a single ion source by the ion switch.

21. The method or the mass spectrometer of any of the preceding claims, wherein the at least two mass analyzers share common control electronics (e.g., for control of ion manipulation, RF, and / or DC fields of the mass analyzers).

22. The method or the mass spectrometer of any of the preceding claims wherein each of the at least two mass analyzers is independently selected from a linear quadrupole ion trap mass analyzer, a three dimensional quadrupole ion trap mass analyzer, an electrostaticaxially harmonic orbital trapping mass analyzer, a time-of-flight mass analyzer, a distance-of-flight mass analyzer, a magnetic sector mass analyzer, a Fourier-transform ion cyclotron residence (FT-ICR) mass analyzer, and a linear quadrupole mass analyzer.

23. The method or the mass spectrometer of claim 22, wherein each of the at least two mass analyzers are electrostatic axially harmonic orbital trapping, FT-ICR, or time-of-flight mass analyzers.

24. The method or the mass spectrometer of claim 22, wherein each of the at least two mass analyzers are electrostatic axially harmonic orbital trapping mass analyzers.

25. The method or the mass spectrometer of claim 22, wherein each of the at least two mass analyzers are FT-ICR mass analyzers.

26. The method or the mass spectrometer of claim 22, wherein each of the at least two mass analyzers are linear quadrupole ion trap mass analyzers.

27. The method or the mass spectrometer of claim 22, wherein each of the at least two mass analyzers are time-of-flight mass analyzers.

28. The method or the mass spectrometer of any of the preceding claims, wherein the time- of-flight mass analyzer is a sector time-of-flight mass analyzer or an orthogonal acceleration time-of-flight mass analyzer.

29. The method or the mass spectrometer of claim 28, wherein the time-of-flight mass analyzer is a sector time-of-flight mass analyzer.

30. The method or the mass spectrometer of claim 28, wherein the time-of-flight mass analyzer is an orthogonal acceleration time-of-flight mass analyzer.

31. The method or the mass spectrometer of any of the preceding claims, wherein each of the mass analyzers is configured to scan across an independently selected mass range during at least partially overlapping periods of time.

32. The method or the mass spectrometer of any of the preceding claims, wherein each of the mass analyzers is configured to scan across an independently selected mass range at essentially the same time.

33. The method or the mass spectrometer of any of the preceding claims, wherein the ion switch and the at least two mass analyzers comprise at least a minimum number of ion switch outlets and a minimum number of mass analyzers required to reduce dead time when sequential ion injections are used to provide near simultaneous mass analysis of the different mass to charge isolation windows.

34. The method of any of the preceding claims, wherein the ion source is an atmospheric pressure ion source.

35. The method of claim 34, wherein the ion source is electrospray ionization (ESI).

36. The method of claim 35, wherein the ion source is a nano-electrospray emitter.

37. The method of any of the preceding claims, further comprising: selecting a third mass isolation window of a third one of the at least two mass analyzers corresponding to a third one of the plurality of ion switch outlets; and acquiring mass spectra of the first, second, and third mass isolation windows using the at least two mass analyzers.

38. The method of any of the preceding claims, further comprising: selecting a fourth mass isolation window of a fourth one of the at least two mass analyzers corresponding to a fourth one of the plurality of ion switch outlets; and acquiring mass spectra of the first, second, third, and fourth mass isolation windows using the at least two mass analyzers.

39. The method of any of the preceding claims, wherein the mass spectra are acquired near simultaneously by sequentially injecting ions into the at least two mass analyzers through the plurality of ion switch outlets.

40. The method of claim 39, wherein the dead time for near simultaneous acquisition by sequential ion injections is essentially zero.

41. The method of any of the preceding claims further comprising, selecting an ion injection timing sequence during which a plurality of outlets of the ion switch are to be selected using the ion switch selector.

42. The method of any of the preceding claims, wherein the sample is a biological sample.

43. The method of any of the preceding claims, wherein the sample is a proteomics sample.

44. The method of any of the preceding claims, wherein the sample comprises at least 100 different proteins.

45. The method of any of the preceding claims, wherein the sample is obtained from a chromatographic separation prior to analysis.

46. The method of any of the preceding claims, wherein tandem mass spectra are acquired in DI A mode.

47. The method of any of the preceding claims, wherein tandem mass spectra are acquired in DDA mode.

48. The method of any of the preceding claims, wherein the tandem mass spectra are acquired in pseudo-DDA mode.

49. The method of any of the preceding claims, wherein the MSI mass window is less than about 2 amu (e.g., 2, 1, or 0.5 amu).

50. The method of any of the preceding claims, wherein the MSI mass window is less than about 10 amu.

51. The method of any of the preceding claims, wherein the MS 1 mass window is less than about 5 amu.

52. The method of any of the preceding claims, wherein the MSI mass window is less than about 4 amu.

53. The method of any of the preceding claims wherein the MS2 resolving power is at least 10,000 (e.g., at least 10,000, at least 30,000, at least 50,000, at least 300,000, or at least 1,000,000).

54. The method of any of the preceding claims wherein the MS2 resolving power is less than 10,000,000 (e.g., less than 5,000,000, less than 1,000,000, less than 100,000, or less than 50,000).

55. The method of any of the preceding claims wherein at least 1000 peptides (e.g., at least 5000, at least 10,000, or at least 20,000) are identified in the sample.

56. The method, the mass spectrometer, or the ion switch of any of the preceding claims, wherein the ion switch comprises a first planar surface and a second planar surface, wherein the first ion guide channel and the second ion guide channel are disposed between the first planar surface and the second planar surface.

57. The method, the mass spectrometer, or the ion switch of claim 56, wherein a first plurality of guide electrodes is disposed on the first planar surface, and wherein a second plurality of guide electrodes is disposed on the second planar surface.

58. The method, the mass spectrometer, or the ion switch of claim 57, wherein the first plurality of guide electrodes and the second plurality of guide electrodes together define the first ion guide channel and the second ion guide channel.

59. The method, the mass spectrometer, or the ion switch of any one of claims 57-58, wherein a layout for the first plurality of guide electrodes on the first planar surface is a mirror image of a layout for the second plurality of guide electrodes on the second planar surface.

60. The method, the mass spectrometer, or the ion switch of any one of claims 56-59, wherein a first switching electrode is disposed on the first planar surface, and wherein a second switching electrode is disposed on the second planar surface.

61. The method, the mass spectrometer, or the ion switch of claim 60, wherein the first switching electrode and the second switching electrode have the same shape.

62. The method, the mass spectrometer, or the ion switch of any one of claims 58-61, wherein the first switching electrode and the second switching electrode are laterally aligned with respect to each other.

63. The method, the mass spectrometer, or the ion switch of any one of claims 58-62, wherein a shape of the first switching electrode is mirror image of a shape of the second switching electrode.

64. The method, the mass spectrometer, or the ion switch of any one of claims 58-63, wherein a shape of the first switching electrode is asymmetric.

65. The method, the mass spectrometer, or the ion switch of any one of claims 58-64, wherein a shape of the second switching electrode is asymmetric.

66. The method, the mass spectrometer, or the ion switch of any one of claims 58-65, wherein the first planar surface and the second planar surface are each printed circuit boards.

67. The method, the mass spectrometer, or the ion switch of any one of claims 56-66, wherein the first planar surface and the second planar surface are generally parallel.

68. The method, the mass spectrometer, or the ion switch of any one of claims 56-67, wherein the first planar surface and the second planar surface are at least about 2 mm apart (e.g., about 2 mm, about 4 mm, about 6 mm, or about 8 mm).

69. The method, the mass spectrometer, or the ion switch of any one of claims 56-68, wherein the first planar surface and the second planar surface nor more than about 20 mm apart (e.g., about 20 mm, about 15 mm, about 12 mm, about 10 mm, or about 8 mm).

70. The method, the mass spectrometer, or the ion switch of any one of claims 57-69, wherein a first plurality of drag electrodes are disposed on a side of the first planar surface opposite where the first plurality of guide electrodes are disposed.

71. The method, the mass spectrometer, or the ion switch of any one of claims 57-70, wherein a second plurality of drag electrodes are disposed on a side of the second planar surface opposite where the second plurality of guide electrodes are disposed.

72. The method, the mass spectrometer, or the ion switch of any one of claims 56-70, wherein a plurality of drag electrodes are disposed between the first planar surface and the second planar surface.

73. The method or mass spectrometer of any of the preceding claims, wherein the mass spectrometer is a tandem mass spectrometer.

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