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Exertier F, Tegg L, Taylor A, Cairney JM, Fu J, Marceau RKW. Nanoscale Analysis of Frozen Water by Atom Probe Tomography Using Graphene Encapsulation and Cryo-Workflows. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024:ozae054. [PMID: 38905154 DOI: 10.1093/mam/ozae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/24/2024] [Accepted: 05/28/2024] [Indexed: 06/23/2024]
Abstract
There has been an increasing interest in atom probe tomography (APT) to characterize hydrated and biological materials. A major benefit of APT compared to microscopy techniques more commonly used in biology is its combination of outstanding three-dimensional (3D) spatial resolution and mass sensitivity. APT has already been successfully used to characterize biominerals, revealing key structural information at the atomic scale, however there are many challenges inherent to the analysis of soft hydrated materials. New preparation protocols, often involving specimen preparation and transfer at cryogenic temperature, enable APT analysis of hydrated materials and have the potential to enable 3D atomic scale characterization of biological materials in the near-native hydrated state. In this study, samples of pure water at the tips of tungsten needle specimens were prepared at room temperature by graphene encapsulation. A comparative study was conducted where specimens were transferred at either room temperature or cryo-temperature and analyzed by APT by varying the flight path and pulsing mode. The differences between the analysis workflows are presented along with recommendations for future studies, and the compatibility between graphene coating and cryogenic workflows is demonstrated.
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Affiliation(s)
- Florant Exertier
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - Levi Tegg
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, NSW 2006, Australia
| | - Adam Taylor
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - Julie M Cairney
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jing Fu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Ross K W Marceau
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
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2
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Woods EV, Kim SH, El-Zoka AA, Stephenson LT, Gault B. Scalable substrate development for aqueous sample preparation for atom probe tomography. J Microsc 2023. [PMID: 38115688 DOI: 10.1111/jmi.13255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/13/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
Reliable and consistent preparation of atom probe tomography (APT) specimens from aqueous and hydrated biological specimens remains a significant challenge. One particularly difficult process step is the use of a focused ion beam (FIB) instrument for preparing the required needle-shaped specimen, typically involving a 'lift-out' procedure of a small sample of material. Here, two alternative substrate designs are introduced that enable using FIB only for sharpening, along with example APT datasets. The first design is a laser-cut FIB-style half-grid close to those used for transmission electron microscopy (TEM) that can be used in a grid holder compatible with APT pucks. The second design is a larger, standalone self-supporting substrate called a 'crown', with several specimen positions, which self-aligns in APT pucks, prepared by electrical discharge machining (EDM). Both designs are made nanoporous, to provide strength to the liquid-substrate interface, using chemical and vacuum dealloying. Alpha brass, a simple, widely available, lower-cost alternative to previously proposed substrates, was selected for this work. The resulting designs and APT data are presented and suggestions are provided to help drive wider community adoption.
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Affiliation(s)
- Eric V Woods
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - Se-Ho Kim
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials Science and Engineering, Korea University, Seoul, Republic of Korea
| | - Ayman A El-Zoka
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, London, UK
| | - L T Stephenson
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, New South Wales, Australia
| | - B Gault
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, London, UK
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3
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Schwarz TM, Ott J, Solodenko H, Schmitz G, Stender P. Nanoscale analysis of frozen honey by atom probe tomography. Sci Rep 2022; 12:17786. [PMID: 36273026 PMCID: PMC9587987 DOI: 10.1038/s41598-022-22717-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/18/2022] [Indexed: 01/19/2023] Open
Abstract
Three-dimensional reconstruction of the analysed volume is one of the main goals of atom probe tomography (APT) and can deliver nearly atomic resolution (~ 0.2 nm spatial resolution) and chemical information with a mass sensitivity down to the ppm range. Extending this technique to frozen biological systems would have an enormous impact on the structural analysis of biomolecules. In previous works, we have shown that it is possible to measure frozen liquids with APT. In this paper, we demonstrate the ability of APT to trace nanoscale precipitation in frozen natural honey. While the mass signals of the common sugar fragments CxHy and CxOyHz overlap with (H2O)nH from water, we achieved correct stoichiometric values via different interpretation approaches for the peaks and thus determined the water content reliably. Next, we use honey to investigate the spatial resolution capabilities as a step toward the measurement of biological molecules in solution in 3D with sub-nanometer resolution. This may take analytical techniques to a new level, since methods of chemical characterization for cryogenic samples, especially biological samples, are still limited.
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Affiliation(s)
- Tim M. Schwarz
- grid.5719.a0000 0004 1936 9713Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany
| | - Jonas Ott
- grid.5719.a0000 0004 1936 9713Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany
| | - Helena Solodenko
- grid.5719.a0000 0004 1936 9713Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany
| | - Guido Schmitz
- grid.5719.a0000 0004 1936 9713Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany
| | - Patrick Stender
- grid.5719.a0000 0004 1936 9713Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany
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4
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Grandfield K, Micheletti C, Deering J, Arcuri G, Tang T, Langelier B. Atom Probe Tomography for Biomaterials and Biomineralization. Acta Biomater 2022; 148:44-60. [DOI: 10.1016/j.actbio.2022.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/18/2022] [Accepted: 06/06/2022] [Indexed: 01/27/2023]
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5
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Simulations of Cross-Amyloid Aggregation of Amyloid-β and Islet Amyloid Polypeptide Fragments. Biophys J 2022; 121:2002-2013. [PMID: 35538665 DOI: 10.1016/j.bpj.2022.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 11/21/2022] Open
Abstract
Amyloid-beta (Aβ) and islet amyloid polypeptide (IAPP) are small peptides, classified as amyloids, that have the potential to self-assemble and form cytotoxic species, such as small soluble oligomers and large insoluble fibrils. The formation of Aβ aggregates facilitates the progression of Alzheimer's disease (AD), while IAPP aggregates induce pancreatic β-cell apoptosis, leading to exacerbation of Type 2 diabetes (T2D). Cross-amyloid interactions between Aβ and IAPP have been described both in vivo and in vitro, implying the role of Aβ or IAPP as modulators of cytotoxic self-aggregation of each species, and suggesting that Aβ-IAPP interactions are a potential molecular link between AD and T2D. Using molecular dynamics simulations, "hot spot" regions of the two peptides were studied to understand the formation of hexamers in a heterogenous and homogenous peptide-containing environment. Systems of only Aβ(16-22) peptides formed antiparallel, β-barrel-like structures, while systems of only IAPP(20-29) peptides formed stacked, parallel beta sheets and had relatively unstable aggregation structures after 2 μs of simulation time. Systems containing both Aβ and IAPP (1:1 ratio) hexamers showed antiparallel, β-barrel-like structures, with an interdigitated arrangement of Aβ(16-22) and IAPP(20-29). These β-barrel structures have features of cytotoxic amyloid species identified in previous literature. Ultimately, this work seeks to provide atomistic insight into both the mechanism behind cross-amyloid interactions and structural morphologies of these toxic amyloid species.
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Stender P, Gault B, Schwarz TM, Woods EV, Kim SH, Ott J, Stephenson LT, Schmitz G, Freysoldt C, Kästner J, El-Zoka AA. Status and Direction of Atom Probe Analysis of Frozen Liquids. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-18. [PMID: 35039105 DOI: 10.1017/s1431927621013994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Imaging of liquids and cryogenic biological materials by electron microscopy has been recently enabled by innovative approaches for specimen preparation and the fast development of optimized instruments for cryo-enabled electron microscopy (cryo-EM). Yet, cryo-EM typically lacks advanced analytical capabilities, in particular for light elements. With the development of protocols for frozen wet specimen preparation, atom probe tomography (APT) could advantageously complement insights gained by cryo-EM. Here, we report on different approaches that have been recently proposed to enable the analysis of relatively large volumes of frozen liquids from either a flat substrate or the fractured surface of a wire. Both allowed for analyzing water ice layers which are several micrometers thick consisting of pure water, pure heavy water, and aqueous solutions. We discuss the merits of both approaches and prospects for further developments in this area. Preliminary results raise numerous questions, in part concerning the physics underpinning field evaporation. We discuss these aspects and lay out some of the challenges regarding the APT analysis of frozen liquids.
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Affiliation(s)
- Patrick Stender
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | - Baptiste Gault
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, London, UK
| | - Tim M Schwarz
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | - Eric V Woods
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - Se-Ho Kim
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - Jonas Ott
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | | | - Guido Schmitz
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | | | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569Stuttgart, Germany
| | - Ayman A El-Zoka
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
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7
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Schwarz TM, Dietrich CA, Ott J, Weikum EM, Lawitzki R, Solodenko H, Hadjixenophontos E, Gault B, Kästner J, Schmitz G, Stender P. 3D sub-nanometer analysis of glucose in an aqueous solution by cryo-atom probe tomography. Sci Rep 2021; 11:11607. [PMID: 34078953 PMCID: PMC8172843 DOI: 10.1038/s41598-021-90862-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/18/2021] [Indexed: 11/23/2022] Open
Abstract
Atom Probe Tomography (APT) is currently a well-established technique to analyse the composition of solid materials including metals, semiconductors and ceramics with up to near-atomic resolution. Using an aqueous glucose solution, we now extended the technique to frozen solutions. While the mass signals of the common glucose fragments CxHy and CxOyHz overlap with (H2O)nH from water, we achieved stoichiometrically correct values via signal deconvolution. Density functional theory (DFT) calculations were performed to investigate the stability of the detected pyranose fragments. This paper demonstrates APT’s capabilities to achieve sub-nanometre resolution in tracing whole glucose molecules in a frozen solution by using cryogenic workflows. We use a solution of defined concentration to investigate the chemical resolution capabilities as a step toward the measurement of biological molecules. Due to the evaporation of nearly intact glucose molecules, their position within the measured 3D volume of the solution can be determined with sub-nanometre resolution. Our analyses take analytical techniques to a new level, since chemical characterization methods for cryogenically-frozen solutions or biological materials are limited.
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Affiliation(s)
- T M Schwarz
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - C A Dietrich
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - J Ott
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - E M Weikum
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - R Lawitzki
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - H Solodenko
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - E Hadjixenophontos
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - B Gault
- Max-Planck-Institut Für Eisenforschung, Max-Planck-Str. 1, 40237, Düsseldorf, Germany.,Department of Materials, Royal School of Mines, Imperial College, Prince Consort Road, London, SW7 2BP, UK
| | - J Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - G Schmitz
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - P Stender
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany.
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8
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Wei Y, Varanasi RS, Schwarz T, Gomell L, Zhao H, Larson DJ, Sun B, Liu G, Chen H, Raabe D, Gault B. Machine-learning-enhanced time-of-flight mass spectrometry analysis. PATTERNS 2021; 2:100192. [PMID: 33659909 PMCID: PMC7892357 DOI: 10.1016/j.patter.2020.100192] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/13/2020] [Accepted: 12/17/2020] [Indexed: 01/06/2023]
Abstract
Mass spectrometry is a widespread approach used to work out what the constituents of a material are. Atoms and molecules are removed from the material and collected, and subsequently, a critical step is to infer their correct identities based on patterns formed in their mass-to-charge ratios and relative isotopic abundances. However, this identification step still mainly relies on individual users' expertise, making its standardization challenging, and hindering efficient data processing. Here, we introduce an approach that leverages modern machine learning technique to identify peak patterns in time-of-flight mass spectra within microseconds, outperforming human users without loss of accuracy. Our approach is cross-validated on mass spectra generated from different time-of-flight mass spectrometry (ToF-MS) techniques, offering the ToF-MS community an open-source, intelligent mass spectra analysis. A machine-learning method provides reliable atomic/molecular labels for ToF-MS No human labeling or prior information required The training dataset is artificially generated based on isotopic abundances Method validated on a variety of materials and two ToF-MS-based techniques
Time-of-flight mass spectrometry (ToF-MS) is a mainstream analytical technique widely used in biology, chemistry, and materials science. ToF-MS provides quantitative compositional analysis with high sensitivity across a wide dynamic range of mass-to-charge ratios. A critical step in ToF-MS is to infer the identity of the detected ions. Here, we introduce a machine-learning-enhanced algorithm to provide a user-independent approach to performing this identification using patterns from the natural isotopic abundances of individual atomic and molecular ions, without human labeling or prior knowledge of composition. Results from several materials and techniques are compared with those obtained by field experts. Our open-source, easy-to-implement, reliable analytic method accelerates this identification process. A wide range of ToF-MS-based applications can benefit from our approach, e.g., hunting for patterns of biomarkers or for contamination on solid surfaces in high-throughput data.
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Affiliation(s)
- Ye Wei
- Max-Planck-Institut für Eisenforschung, Max-Planck-Strasse 1, 40237 Düsseldorf, Germany
| | | | - Torsten Schwarz
- Max-Planck-Institut für Eisenforschung, Max-Planck-Strasse 1, 40237 Düsseldorf, Germany
| | - Leonie Gomell
- Max-Planck-Institut für Eisenforschung, Max-Planck-Strasse 1, 40237 Düsseldorf, Germany
| | - Huan Zhao
- Max-Planck-Institut für Eisenforschung, Max-Planck-Strasse 1, 40237 Düsseldorf, Germany
| | - David J Larson
- CAMECA Instruments, 5470 Nobel Drive, Madison, WI 53711, USA
| | - Binhan Sun
- Max-Planck-Institut für Eisenforschung, Max-Planck-Strasse 1, 40237 Düsseldorf, Germany
| | - Geng Liu
- Key Laboratory for Advanced Materials of Ministry of Education, School of Materials Science and Engineering, Tsinghua University, Beijing 100084, China
| | - Hao Chen
- Key Laboratory for Advanced Materials of Ministry of Education, School of Materials Science and Engineering, Tsinghua University, Beijing 100084, China
| | - Dierk Raabe
- Max-Planck-Institut für Eisenforschung, Max-Planck-Strasse 1, 40237 Düsseldorf, Germany
| | - Baptiste Gault
- Max-Planck-Institut für Eisenforschung, Max-Planck-Strasse 1, 40237 Düsseldorf, Germany.,Department of Materials, Royal School of Mines, Imperial College, London SW7 2AZ, UK
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9
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Gault B, Chiaramonti A, Cojocaru-Mirédin O, Stender P, Dubosq R, Freysoldt C, Makineni SK, Li T, Moody M, Cairney JM. Atom probe tomography. NATURE REVIEWS. METHODS PRIMERS 2021; 1:10.1038/s43586-021-00047-w. [PMID: 37719173 PMCID: PMC10502706 DOI: 10.1038/s43586-021-00047-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/01/2021] [Indexed: 09/19/2023]
Abstract
Atom probe tomography (APT) provides three-dimensional compositional mapping with sub-nanometre resolution. The sensitivity of APT is in the range of parts per million for all elements, including light elements such as hydrogen, carbon or lithium, enabling unique insights into the composition of performance-enhancing or lifetime-limiting microstructural features and making APT ideally suited to complement electron-based or X-ray-based microscopies and spectroscopies. Here, we provide an introductory overview of APT ranging from its inception as an evolution of field ion microscopy to the most recent developments in specimen preparation, including for nanomaterials. We touch on data reconstruction, analysis and various applications, including in the geosciences and the burgeoning biological sciences. We review the underpinnings of APT performance and discuss both strengths and limitations of APT, including how the community can improve on current shortcomings. Finally, we look forwards to true atomic-scale tomography with the ability to measure the isotopic identity and spatial coordinates of every atom in an ever wider range of materials through new specimen preparation routes, novel laser pulsing and detector technologies, and full interoperability with complementary microscopy techniques.
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Affiliation(s)
- Baptiste Gault
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College, London, UK
| | - Ann Chiaramonti
- National Institute of Standards and Technology, Applied Chemicals and Materials Division, Boulder, CO, USA
| | | | - Patrick Stender
- Institute of Materials Science, University of Stuttgart, Stuttgart, Germany
| | - Renelle Dubosq
- Department of Earth and Environmental Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | - Tong Li
- Institute for Materials, Ruhr-Universität Bochum, Bochum, Germany
| | - Michael Moody
- Department of Materials, University of Oxford, Oxford, UK
| | - Julie M. Cairney
- Australian Centre for Microscopy and Microanalysis, University of Sydney, Sydney, New South Wales, Australia
- School of Aerospace, Mechanical and Mechatronic Engineering, University of Sydney, Sydney, New South Wales, Australia
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10
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El-Zoka AA, Kim SH, Deville S, Newman RC, Stephenson LT, Gault B. Enabling near-atomic-scale analysis of frozen water. SCIENCE ADVANCES 2020; 6:6/49/eabd6324. [PMID: 33277259 PMCID: PMC7821902 DOI: 10.1126/sciadv.abd6324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/21/2020] [Indexed: 05/04/2023]
Abstract
Transmission electron microscopy went through a revolution enabling routine cryo-imaging of biological and (bio)chemical systems, in liquid form. Yet, these approaches typically lack advanced analytical capabilities. Here, we used atom probe tomography to analyze frozen liquids in three dimensions with subnanometer resolution. We introduce a specimen preparation strategy using nanoporous gold. We report data on 2- to 3-μm-thick layers of ice formed from both high-purity deuterated water and a solution of 50 mM NaCl in high-purity deuterated water. The analysis of the gold-ice interface reveals a substantial increase in the solute concentrations across the interface. We explore a range of experimental parameters to show that atom probe analyses of bulk aqueous specimens come with their own challenges and discuss physical processes that produce the observed phenomena. Our study demonstrates the viability of using frozen water as a carrier for near-atomic-scale analysis of objects in solution by atom probe tomography.
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Affiliation(s)
- A A El-Zoka
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany.
| | - S-H Kim
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - S Deville
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, 69622 Villeurbanne, France
| | - R C Newman
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Canada
| | - L T Stephenson
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - B Gault
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany.
- Department of Materials, Royal School of Mines, Imperial College London, London, UK
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11
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Schwarz TM, Weikum EM, Meng K, Hadjixenophontos E, Dietrich CA, Kästner J, Stender P, Schmitz G. Field evaporation and atom probe tomography of pure water tips. Sci Rep 2020; 10:20271. [PMID: 33219263 PMCID: PMC7680140 DOI: 10.1038/s41598-020-77130-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/05/2020] [Indexed: 01/12/2023] Open
Abstract
Measuring biological samples by atom probe tomography (APT) in their natural environment, i.e. aqueous solution, would take this analytical method, which is currently well established for metals, semi-conductive materials and non-metals, to a new level. It would give information about the 3D chemical structure of biological systems, which could enable unprecedented insights into biological systems and processes, such as virus protein interactions. For this future aim, we present as a first essential step the APT analysis of pure water (Milli-Q) which is the main component of biological systems. After Cryo-preparation, nanometric water tips are field evaporated with assistance by short laser pulses. The obtained data sets of several tens of millions of atoms reveal a complex evaporation behavior. Understanding the field evaporation process of water is fundamental for the measurement of more complex biological systems. For the identification of the individual signals in the mass spectrum, DFT calculations were performed to prove the stability of the detected molecules.
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Affiliation(s)
- T M Schwarz
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - E M Weikum
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - K Meng
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - E Hadjixenophontos
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - C A Dietrich
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - J Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - P Stender
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany.
| | - G Schmitz
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
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12
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Qiu S, Zheng C, Garg V, Chen Y, Gervinskas G, Li J, Dunstone MA, Marceau RKW, Fu J. Three-Dimensional Chemical Mapping of a Single Protein in the Hydrated State with Atom Probe Tomography. Anal Chem 2020; 92:5168-5177. [DOI: 10.1021/acs.analchem.9b05668] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shi Qiu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Changxi Zheng
- ARC Centre of Excellence for Future Low-Energy Electronics Technologies, Monash University, Clayton, VIC 3800, Australia
- School of Physics and Astronomy, Monash University, Clayton, VIC 3800, Australia
| | - Vivek Garg
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Yu Chen
- Monash Centre for Electron Microscopy, Monash University, Clayton, VIC 3800, Australia
| | - Gediminas Gervinskas
- Monash Ramaciotti Centre for Cryo Electron Microscopy, Monash University, Clayton, VIC 3800, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Michelle A. Dunstone
- Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Ross K. W. Marceau
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - Jing Fu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
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13
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Di Natale C, La Manna S, Avitabile C, Florio D, Morelli G, Netti PA, Marasco D. Engineered β-hairpin scaffolds from human prion protein regions: Structural and functional investigations of aggregates. Bioorg Chem 2020; 96:103594. [PMID: 31991323 DOI: 10.1016/j.bioorg.2020.103594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 12/16/2022]
Abstract
The investigation of conformational features of regions of amyloidogenic proteins are of great interest to deepen the structural changes and consequent self-aggregation mechanisms at the basis of many neurodegenerative diseases. Here we explore the effect of β-hairpin inducing motifs on regions of prion protein covering strands S1 and S2. In detail, we unveiled the structural and functional features of two model chimeric peptides in which natural sequences are covalently linked together by two dipeptides (l-Pro-Gly and d-Pro-Gly) that are known to differently enhance β-hairpin conformations but both containing N- and the C-terminal aromatic cap motifs to further improve interactions between natural strands. Spectroscopic investigations at solution state indicate that primary assemblies of the monomers of both constructs follow different aggregativemechanisms during the self-assembly: these distinctions, evidenced by CD and ThT emission spectroscopies, reflect into great morphological differences of nanostructures and suggest that rigid β-hairpin conformations greatly limit amyloid-like fibrillogenesis. Overall data confirm the important role exerted by the β-structure of regions S1 and S2 during the aggregation process and lead to speculate to its persistence even in unfolding conditions.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy; Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Sara La Manna
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Concetta Avitabile
- Institute of Biostructures and Bioimaging (IBB), National Research Council, Via Mezzocannone 16, 80134 Naples, Italy
| | - Daniele Florio
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy; Task force di Ateneo"METODOLOGIE ANALITICHE PER LA SALVAGUARDIA DEI BENI CULTURALI" MASBC, University of Naples "Federico II", Italy.
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14
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Rivas NA, Babayigit A, Conings B, Schwarz T, Sturm A, Garzón Manjón A, Cojocaru-Mirédin O, Gault B, Renner FU. Cryo-focused ion beam preparation of perovskite based solar cells for atom probe tomography. PLoS One 2020; 15:e0227920. [PMID: 31945119 PMCID: PMC6964857 DOI: 10.1371/journal.pone.0227920] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/02/2020] [Indexed: 11/19/2022] Open
Abstract
Focused-ion beam lift-out and annular milling is the most common method used for obtaining site specific specimens for atom probe tomography (APT) experiments and transmission electron microscopy. However, one of the main limitations of this technique comes from the structural damage as well as chemical degradation caused by the beam of high-energy ions. These aspects are especially critical in highly-sensitive specimens. In this regard, ion beam milling under cryogenic conditions has been an established technique for damage mitigation. Here, we implement a cryo-focused ion beam approach to prepare specimens for APT measurements from a quadruple cation perovskite-based solar cell device with 19.7% efficiency. As opposed to room temperature FIB milling we found that cryo-milling considerably improved APT results in terms of yield and composition measurement, i.e. halide loss, both related to less defects within the APT specimen. Based on our approach we discuss the prospects of reliable atom probe measurements of perovskite based solar cell materials. An insight into the field evaporation behavior of the organic-inorganic molecules that compose the perovskite material is also given with the aim of expanding the applicability of APT experiments towards nano-characterization of complex organo-metal materials.
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Affiliation(s)
- Nicolás Alfonso Rivas
- Institute for Materials Research (IMO), Hasselt University, Diepenbeek, Limburg, Belgium
- IMEC vzw. Division IMOMEC, Diepenbeek, Limburg, Belgium
- Department of Microstructure physics and alloy design, Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf, North Rhein-Westfalia, Germany
- * E-mail:
| | - Aslihan Babayigit
- Institute for Materials Research (IMO), Hasselt University, Diepenbeek, Limburg, Belgium
- IMEC vzw. Division IMOMEC, Diepenbeek, Limburg, Belgium
| | - Bert Conings
- Institute for Materials Research (IMO), Hasselt University, Diepenbeek, Limburg, Belgium
- IMEC vzw. Division IMOMEC, Diepenbeek, Limburg, Belgium
| | - Torsten Schwarz
- Department of Microstructure physics and alloy design, Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf, North Rhein-Westfalia, Germany
| | - Andreas Sturm
- Department of Microstructure physics and alloy design, Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf, North Rhein-Westfalia, Germany
| | - Alba Garzón Manjón
- Department of Microstructure physics and alloy design, Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf, North Rhein-Westfalia, Germany
| | | | - Baptiste Gault
- Department of Microstructure physics and alloy design, Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf, North Rhein-Westfalia, Germany
- Department of Materials, Royal School of Mines, Imperial College, London, United Kingdom
| | - Frank Uwe Renner
- Institute for Materials Research (IMO), Hasselt University, Diepenbeek, Limburg, Belgium
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