IP Library Granted Patent US 12,730,041
Granted Patent B2
US 12,730,041 · App. 18/661,104 · Granted Sep 8, 2026

Apparatus and methods for depositing ions onto a surface

Inventors: W. Henry Benner (Carmel, CA); Ben Aguilar (Monterey, CA)
Assignee: ION DX, INC.
G01N1/42
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Quick Facts
Patent No.
US 12,730,041
App. No.
18/661,104
Granted
Sep 8, 2026
Kind
B2
Abstract

Apparatus and methods are described for preparing samples for examination by cryo-electron microscopy. Molecules of interest, such as protein molecules in a solution, are electrosprayed and converted to singly-charged gas-phase ions. Particular conformation(s) of the protein ions are selected by using an ion mobility filter and deposited onto a cryo-EM grid at sub-eV kinetic energy for the purpose of preserving the molecule's higher order structure.

Claims (55)

1 . An apparatus for preparing samples for examination by cryo-EM, the apparatus comprising:

(a) an electrospray ion source;

(b) means to reduce the charge on electrospray droplets and ions;

(c) a mobility filter configured to select ions having a particular conformation out of a mixture of ions;

(d) a humidifier configured to control the dew point and temperature of ion-laden air;

(e) an ion focusing funnel;

(f) a holder for a cryo-EM grid;

(g) a cooled pedestal configured to preserve the conformation of deposited ions;

(h) a chamber for protecting deposited ions; and

(i) means to transfer deposited ions or particles into liquid nitrogen.

2 . The apparatus of claim 1 , wherein said means to reduce the charge on electrospray droplets and ions comprises a source of 210 Polonium, wherein alpha particles are released from the 210 Polonium into the electrospray droplets and ions.

3 . The apparatus of claim 1 , wherein said means to reduce the charge on electrospray droplets and ions comprises a source of electrons having an energy of less than about 20 eV, wherein said electrons are released into the electrospray droplets and ions.

4 . The apparatus of claim 1 , wherein the means to transfer deposited ions or particles into liquid nitrogen comprises tweezers.

5 . An apparatus for depositing samples onto a surface for subsequent analysis, the apparatus comprising:

(a) an electrospray ion source;

(b) means to reduce charge on electrospray droplets, ions and particles;

(c) a mobility filter configured to select ions and charged particles having a particular conformation or size out of a mixture of ions and particles;

(d) means to control dew point and temperature of ion-laden or particle-laden gas;

(e) means to control hydration of ions and charged-particles;

(f) an ion- and charged-particle focusing device;

(g) means to control kinetic energy of ions and charged-particles;

(h) a holder for substrates onto which ions or charged-particles are deposited;

(i) means to deposit ions and charged-particles onto a substrate;

(j) means to control temperature of the collection surface;

(k) a chamber configured to protect deposited ions or charged-particles;

(l) means for transferring deposited ions or charged-particles into ancillary analytical devices; and

(m) means to preserve deposited ions or charged particles with a cryo-protectant.

6 . The apparatus of claim 5 , wherein said means to reduce charge on electrospray droplets, ions and particles comprises a source of 210 Polonium, wherein alpha particles are released from the 210 Polonium into the electrospray droplets, ions and particles.

7 . The apparatus of claim 5 , wherein said means to reduce charge on electrospray droplets, ions and particles comprises a source of electrons having an energy of less than about 20 eV, wherein said electrons are released into the electrospray droplets, ions and particles.

8 . The apparatus of claim 5 , wherein said means to control dew point of ion-laden or particle-laden gas comprises a dew point controller configured to add or remove water vapor based on heating or cooling a supply of water vapor.

9 . The apparatus of claim 5 , wherein said means to control temperature of ion-laden or particle-laden gas comprises a temperature controller configured to sense temperature of gas flow.

10 . The apparatus of claim 5 , wherein said means to control hydration of ions and charged-particles comprises a humidifier configured to hydrate ions or particles based on condensing water vapor onto ions and charged-particles.

11 . The apparatus of claim 5 , wherein said means to control kinetic energy of ions and charged-particles comprises a mass flow controller or a pressure controller or an electric field generator, or any combination thereof.

12 . The apparatus of claim 11 , wherein said means to control kinetic energy uses physical distances, gas density, and gas velocity to produce ions and charged particles having low kinetic energy, wherein separation between electrically powered electrodes affects ion energy, wherein higher gas density reduces ion velocity and thus ion energy, and wherein velocity of ion- and particle-laden gas directly influences ion kinetic energy.

13 . The apparatus of claim 5 , wherein said means to deposit ions and charged-particles onto a substrate comprises an ion funnel.

14 . The apparatus of claim 5 , wherein said means to control temperature of the collection surface comprises a temperature controller.

15 . The apparatus of claim 5 , wherein said means for transferring deposited ions or charged-particles into ancillary analytical devices, comprises tweezers.

16 . The apparatus of claim 5 , wherein said means to preserve deposited ions or charged particles with a cryo-protectant comprises a refrigeration source.

17 . The apparatus of claim 5 , wherein said mobility filter comprises a nano-differential mobility analyzer.

18 . An apparatus for depositing samples onto a surface for subsequent analysis, the apparatus comprising:

(a) an electrospray source;

(b) a source of 210 Polonium, wherein alpha particles are released from the 210 Polonium into electrospray droplets, ions and particles, or a source of electrons having an energy of less than about 20 eV, wherein said electrons are released into the electrospray droplets, ions and particles;

(c) a mobility filter comprising a nano differential mobility analyzer;

(d) a temperature controller and dew point controller configured to control temperature and dew point of ion and particle flow streams wherein temperature control is based sensing gas flow temperature and wherein dew point control is provided by adding or removing water vapor based on heating or cooling a supply of water vapor;

(e) a humidifier configured to hydrate ions or particles based on condensing water vapor onto ions and charged particles;

(f) an ion funnel configured to increase flux of ions and charged particles so as to minimize time needed to deposit a predetermined number of ions or particles;

(g) a mass flow controller or a pressure controller or an electric field generator, or any combination thereof, configured to control kinetic energy using physical distances, gas density, and gas velocity to produce ions and charged particles having low kinetic energy, wherein separation between electrically powered electrodes affects ion energy, wherein higher gas density reduces ion velocity and thus ion energy, and wherein velocity of ion- and particle-laden gas directly influences ion kinetic energy;

(h) a holder configured to support a collection surface;

(i) an ion deposition device configured to use and control of electric fields, gas density and gas velocity for guiding ions and charged particles to strike the collection surface;

(j) an optional temperature controller configured to control temperature of the collection surface and collected ions and particles during the time they are collected;

(k) an optional temperature controller configured to control temperature of collected ions and particles after they are collected;

(l) a transfer stage or instrument for moving the collected particles out of the holder and into an ancillary analytical instrument of storage container;

(m) an optional temperature controller configured to control temperature of the collected ions and particles while the collected particles are transferred to alternative analytical devices; and

(o) a transfer stage or instrument for transferring the collected particles into a long-term storage container, such as a liquid-nitrogen dewar during the time they are collected.

19 . A method comprising preparing samples for examination by cryo-EM using the apparatus of any of claims 1 through 18 .

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 10, 2024
From: BENNER, W. HENRY; AGUILAR, BEN
To: ION DX, INC.
Reel/Frame 067668/0908 →
Continuity (4)
Continuation PCTUS2022081328 · Dec 10, 2022
Provisional Application 63291441 · Dec 19, 2021
Provisional Application 63288478 · Dec 10, 2021
Related Publication 20240319054A1 · Sep 26, 2024
References Cited (67)
US 5076097A · Zarrin · 1991 [cited by applicant]
US 9666423B2 · Benner · 2017 [cited by applicant]
US 10204774B2 · Benner · 2019 [cited by applicant]
US 10876202B2 · Verbeck, IV · 2020 [cited by applicant]
US 11037777B2 · Cooks · 2021 [cited by applicant]
US 11092523B2 · Coon · 2021 [cited by applicant]
US 11217425B2 · Straw · 2022 [cited by applicant]
US 11333629B2 · Benner · 2022 [cited by applicant]
US 11796505B2 · Benner · 2023 [cited by applicant]
US 20010035494A1 · Scalf · 2001 [cited by applicant]
US 20150200083A1 · Brown · 2015 [cited by examiner]
US 20150340221A1 · Benner · 2015 [cited by applicant]
US 20170263427A1 · Benner · 2017 [cited by applicant]
US 20180002806A1 · Verbeck, IV · 2018 [cited by applicant]
US 20190086423A1 · Jarrold · 2019 [cited by applicant]
US 20200158607A1 · Coon · 2020 [cited by applicant]
US 20210278369A1 · Benner · 2021 [cited by applicant]
US 20220276201A1 · Benner · 2022 [cited by applicant]
EP 0746751 · 1996 [cited by applicant]
EP 1380045 · 2004 [cited by applicant]
GB 2441200A · 2008 [cited by applicant]
WO 2022155306A1 · 2022 [cited by applicant]
WO 2023108163A1 · 2023 [cited by applicant]
Badu-Tawiah, Abraham K., et al., “Ambient lon Soft Landing”, Analytical Chemistry, ACS Publishing, 2011, pp. 2648-2654. [cited by applicant]
Deng, Zhitao, et al., “A Close Look at Proteins: Submolecular Resolution of Two-and-Three-Dimensionally Folded Cytochrome c at Surfaces”, Nano Letters, ACS Publications, 2012, pp. 2452-2458. [cited by applicant]
Esser, Tim K,, et al., “Mass-selective and ice-free cryo-EM protein sample preparation via native electrospray ion-beam deposition”, https://www.biorxiv.org/content/10.1101/2021.10.18.464782v1, Oct. 19, 2021, pp. 1-29. [cited by applicant]
Esser, Tim K,, et al., “Mass-selective and ice-free cryo-EM protein sample preparation via native electrospray ion- beam deposition”, https://www.biorxiv.org/content/10.1101/2021.10.18.464782v1, Oct. 19, 2021, pp. 1-9. [cited by applicant]
Franchetti, V., et al., “Soft Landing of IONS as a Means of Surface Modification”, International Journal of Mass Spectrometry and Ion Physics, vol. 23, 1977, pp. 29-35. [cited by applicant]
Hoffman, William, et al., “Toward a Reusable Surface-Enhanced Raman Spectroscopy (SERS) Substrate by Soft-Landing Ion Mobility”, Applied Spectroscopy, vol. 67, No. 6, 2013, pp. 656-660. [cited by applicant]
Johnson, Grant E., et al., “Soft-and Reactive Landings of IONS Onto Surfaces: Concepts and Applications”, Mass Spectroscopy Reviews, vol. 35, 2016, pp. 439-479. [cited by applicant]
Li, Chengjue, et al., “Determining Ultrafine Particle Collection Efficiency in a Nanometer Aerosol Sampler”, Aerosol Science and Technology, vol. 44, 2010, pp. 1027-1041. [cited by applicant]
Longchamp, Jean-Nicolas, et al., “Imaging proteins at the single-molecule level”, www.pnas.org/cgi/doi/10.1073/pnas.1614519114, Dec. 13, 2026, pp. 1-6. [cited by applicant]
Mikhailov, Victor A., et al., “Mass-Selective Soft Landing of Protein Assemblies with Controlled Landing Energies”, Analytical Chemistry, ACS Publications, 2014, pp. 8321-8328. [cited by applicant]
Nasibulin, Albert G., et al., “TEM imaging of mass-selected polymer molecules”, Journal of Nanoparticle Research, vol. 4, 2002, pp. 449-453. [cited by applicant]
Ochner, Hannah, et al., “Low-energy holography imaging of conformational variability of single-antibody molecules from elecrospray ion beam deposition”, PNAS, vol. 118, No. 51, 2021, pp. 1-8. [cited by applicant]
Rawat, Vivek K., et al., “Modeling vapor uptake induced mobility shifts in peptide ions observed with transversal modulation ion mobility spectrometry-mass spectrometry”, Royal Society of Chemistry, Analyst, vol. 140, 2… [cited by applicant]
Tata, Alessandra, et al., “From vacuum to atmospheric pressure: A review of ambient ion soft landing”, International Journal of Mass Spectrometry, vol. 450, 2020, pp. 1-11. [cited by applicant]
Volnay, Michael, et al., “Preparative Soft and Reactive Landing of Multiply Charged Protein Ions on a Plasma-Treated Metal Suface”, Analytical Chemistry, vol. 77, No. 15, 2005, pp. 4890-4896. [cited by applicant]
Walton, Barbara, L., et al., “Sub-eV ion deposition utilizing soft-landing ion mobility for controlled ion, ion cluster, and charged nanoparticle deposition”, International Journal of Mass Spectrometry, vol. 370, 2014, … [cited by applicant]
Walz, Andreas, et al., “Navigate flying molecular elephants safely to the ground: mass-selective soft landing up to the Mega-Dalton range by Electrospray Controlled lon-Beam Deposition”, Beilstein Journal of Nanotechnol… [cited by applicant]
Westphall, Michael S., et al., “Three-dimensional structure determination of protein complexes using matrix-landing mass spectrometry”, Nature Communications, https://doi.org/10.1038/s41467-022-29964-4, vol. 13, Apr. 27… [cited by applicant]
Xiang, Maiqi, et al., “Airborne nanoparticle collection efficiency of a TEM grid-equipped sampling system”, Aerosol Science and Technology, Jan. 22, 2021, pp. 1-14. [cited by applicant]
Frederik, Peter M., et al., “Controlled Vitrification”, Handbook of Cyro-Preparation Methods for Electron Microscopy, Chapter 4, Jan. 2009, pp. 1-12. [cited by applicant]
ISA/US, United States Patent and Trademark Office (USPTO), International Search Report and Written Opinion issued Mar. 15, 2023, related PCT international application No. PCT/US2022/081328, pp. 1-10, with claims searche… [cited by applicant]
Wyttenbach, Thomas, et al., “Design of a new electrospray ion mobility mass spectrometer”, International Journal of Mass Spectromtry, vol. 212, 2001, pp. 13-23. [cited by applicant]
Wang, Peng, et al., “Helical Peptide Arrays on Self-Assembled Monolayer Surfaces Through Soft and Reactive Landing of Mass-Selected lons”, OSTI.gov, A Journal of the German Chemical Society, Aug. 11, 2008,. [cited by applicant]
Rinke, G., S Rauschenbach, L Harnau, A Albarghash, M Peuly and K Kern, Nano Letters DOI 10.1021/nl502122j, 2014. [cited by applicant]
Page, Jason S., et al., Journal of American Society Mass Spectromtry, vol. 17, No. 4, 2006, pp. 586-592. [cited by applicant]
Ouyang, Zheng, et al., “Preparing Protein Microarrays by Soft-Landing of Mass-Selected lons”, Science, vol. 301, Sep. 5, 2003, pp. 1351-1354. [cited by applicant]
Tang, Keql, et al., “High-Sensitivity Ion Mobility Spectrometry/Mass Spectrometry Using Electrodynamic lon Funnel Interfaces”, Analytical Chemistry, vol. 77, No. 10, 2005, pp. 3330-3339. [cited by applicant]
Kim, Taeman, et al., “Design and Implementation of a New Electrodynamic lon Funnel”, Analytical Chemistry, vol. 72, No. 10, 2000, pp. 2247-2255. [cited by applicant]
Kaufman, Stanley, L., et al., “Macromolecule Analysis Based on Electrophoretic Mobility in Air: Globular Proteins”, Analytical Chemistry, vol. 68, 1996, pp. 1895-1904. [cited by applicant]
Julian, Ryan R., et al., “lon Funnels for the Masses: Experiments and Simulations with a Simplified Ion Funnel”, American Society for Mass Spectrometry, 2005, pp. 1708-1712. [cited by applicant]
Hogan, Christopher J., “Charge Reduced Electrospray Size Spectrometry of Mega-and Gigadalton Complexes: Whole Viruses and Virus Fragments”, Analytical Chemistry, vol. 78, No. 3, 2006, pp. 844-852. [cited by applicant]
Golongan, B, et al., 2006 in Laskin J and C Lifshitz C, Eds., Principles of mass spectrometry applied to biomolecules, John Wiley& Sons., Inc., Hoboken, NJ. [cited by applicant]
Fernandez de la Mora, Juan, et al., “The potential differential mobility analysis coupled to MS for the study of very large singly and multiply charged proteins and protein complexes in the gas phase”, Biotechnology Jou… [cited by applicant]
Clowers, Brian H., et al., “Enhanced lon Utilization Efficiency Using an Electrodynamic Ion Funnel Trap as an Injection Mechanism for Ion Mobility Spectrometry”, Analytical Chemistry, vol. 80, 2008, pp. 612-623. [cited by applicant]
Chaudhary, A., et al., “A novel planar ion funnel design for miniature ion optics”, Review of Scientific Instruments, vol. 85, No. 10, 2014, pp. 1-6. [cited by applicant]
Blake, Thomas A., et al., “Preparative Linear Ion Trap Mass Spectrometer for Separation and Collection of Purified Proteins and Peptides in Arrays Using lon Soft Landing”, Analytical Chemistry, vol. 76, 2004, pp. 6293-6… [cited by applicant]
Simmons, Justin L.P., et al., “Separating and visualising protein assemblies by means of preparative mass spectrometry and microscopy”, Journal of Structural Biology, vol. 172, 2010, pp. 161-168. [cited by applicant]
Belov, Mikhail, E., et al., “Dynamically Multiplexed Ion Mobility Time-of-Flight Mass Spectrometry”, Analytical Chemistry, vol. 80, No. 15, 2008, pp. 5873-5883. [cited by applicant]
Baker, Erin Shammel, et al., “Ion Mobility Spectrometry-Mass Spectrometry Performance Using Electrodynamic Ion Funnels and Elevated Drift Gas Pressures”, Journal of American Society of Mass Spectrom, vol. 18, 2007, pp. … [cited by applicant]
European Patent Office (EPO), Communication (Extended European Search Report) issued Dec. 8, 2025, related European patent application No. 22905443.2, pp. 1-26, with claims searched, pp. 27-31. [cited by applicant]
Cavalier, Annie, et al., “Cryo-Preparation Methods for Electron Microscopy”, Methods in Visualization Series, CRC Press, 2009, pp. 1-31. [cited by applicant]
IPEA/US, United States Patent and Trademark Office, International Preliminary Report on Patentability issued Jun. 5, 2024, related PCT international application No. PCT/US2022/081328, pp. 1-8, with claims examined, pp. … [cited by applicant]
Ayodeji, Ifeoluwa, “Differential Mobility Spectrometry-Mass spectrometry (DMS-MS) for Forensic and Nuclear-Forensic applications” (2020), USF Tampa Graduate Theses and Dissertations. https://digitalcommons.usf.edu/etd/8… [cited by applicant]
Badu-Tawiah, Abraham et al., “Ambient lon Soft Landing”, Anal. Chem. 2011, 83, 2648-2654, published Mar. 16, 2011. [cited by applicant]