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Ward S, Childs A, Staley C, Waugh C, Watts JA, Kotowska AM, Bhosale R, Borkar AN. Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution. Nat Commun 2024; 15:4367. [PMID: 38777820 PMCID: PMC11111741 DOI: 10.1038/s41467-024-48694-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
The 3D architecture of RNAs governs their molecular interactions, chemical reactions, and biological functions. However, a large number of RNAs and their protein complexes remain poorly understood due to the limitations of conventional structural biology techniques in deciphering their complex structures and dynamic interactions. To address this limitation, we have benchmarked an integrated approach that combines cryogenic OrbiSIMS, a state-of-the-art solid-state mass spectrometry technique, with computational methods for modelling RNA structures at atomic resolution with enhanced precision. Furthermore, using 7SK RNP as a test case, we have successfully determined the full 3D structure of a native RNA in its apo, native and disease-remodelled states, which offers insights into the structural interactions and plasticity of the 7SK complex within these states. Overall, our study establishes cryo-OrbiSIMS as a valuable tool in the field of RNA structural biology as it enables the study of challenging, native RNA systems.
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Affiliation(s)
- Shannon Ward
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Alex Childs
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Ceri Staley
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Christopher Waugh
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, LE12 5RD, UK
- RHy-X Limited, London, WC2A 2JR, UK
| | - Julie A Watts
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Anna M Kotowska
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Rahul Bhosale
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Aditi N Borkar
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK.
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, LE12 5RD, UK.
- RHy-X Limited, London, WC2A 2JR, UK.
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2
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Graham DJ, Gamble LJ. Back to the basics of time-of-flight secondary ion mass spectrometry of bio-related samples. I. Instrumentation and data collection. Biointerphases 2023; 18:021201. [PMID: 36990800 PMCID: PMC10063322 DOI: 10.1116/6.0002477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/30/2023] Open
Abstract
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is used widely throughout industrial and academic research due to the high information content of the chemically specific data it produces. Modern ToF-SIMS instruments can generate high mass resolution data that can be displayed as spectra and images (2D and 3D). This enables determining the distribution of molecules across and into a surface and provides access to information not obtainable from other methods. With this detailed chemical information comes a steep learning curve in how to properly acquire and interpret the data. This Tutorial is aimed at helping ToF-SIMS users to plan for and collect ToF-SIMS data. The second Tutorial in this series will cover how to process, display, and interpret ToF-SIMS data.
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3
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Hogan KA, Zeidler JD, Beasley HK, Alsaadi AI, Alshaheeb AA, Chang YC, Tian H, Hinton AO, McReynolds MR. Using mass spectrometry imaging to visualize age-related subcellular disruption. Front Mol Biosci 2023; 10:906606. [PMID: 36968274 PMCID: PMC10032471 DOI: 10.3389/fmolb.2023.906606] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 01/24/2023] [Indexed: 03/10/2023] Open
Abstract
Metabolic homeostasis balances the production and consumption of energetic molecules to maintain active, healthy cells. Cellular stress, which disrupts metabolism and leads to the loss of cellular homeostasis, is important in age-related diseases. We focus here on the role of organelle dysfunction in age-related diseases, including the roles of energy deficiencies, mitochondrial dysfunction, endoplasmic reticulum (ER) stress, changes in metabolic flux in aging (e.g., Ca2+ and nicotinamide adenine dinucleotide), and alterations in the endoplasmic reticulum-mitochondria contact sites that regulate the trafficking of metabolites. Tools for single-cell resolution of metabolite pools and metabolic flux in animal models of aging and age-related diseases are urgently needed. High-resolution mass spectrometry imaging (MSI) provides a revolutionary approach for capturing the metabolic states of individual cells and cellular interactions without the dissociation of tissues. mass spectrometry imaging can be a powerful tool to elucidate the role of stress-induced cellular dysfunction in aging.
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Affiliation(s)
- Kelly A. Hogan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Julianna D. Zeidler
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heather K. Beasley
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, United States
| | - Abrar I. Alsaadi
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States
| | - Abdulkareem A. Alshaheeb
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States
| | - Yi-Chin Chang
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
| | - Hua Tian
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
- *Correspondence: Hua Tian, ; Antentor O. Hinton Jr, ; Melanie R. McReynolds,
| | - Antentor O. Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, United States
- *Correspondence: Hua Tian, ; Antentor O. Hinton Jr, ; Melanie R. McReynolds,
| | - Melanie R. McReynolds
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
- *Correspondence: Hua Tian, ; Antentor O. Hinton Jr, ; Melanie R. McReynolds,
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4
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Noun M, Akoumeh R, Abbas I. Cell and Tissue Imaging by TOF-SIMS and MALDI-TOF: An Overview for Biological and Pharmaceutical Analysis. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-26. [PMID: 34809729 DOI: 10.1017/s1431927621013593] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The potential of mass spectrometry imaging (MSI) has been demonstrated in cell and tissue research since 1970. MSI can reveal the spatial distribution of a wide range of atomic and molecular ions detected from biological sample surfaces, it is a powerful and valuable technique used to monitor and detect diverse chemical and biological compounds, such as drugs, lipids, proteins, and DNA. MSI techniques, notably matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) and time of flight secondary ion mass spectrometry (TOF-SIMS), witnessed a dramatic upsurge in studying and investigating biological samples especially, cells and tissue sections. This advancement is attributed to the submicron lateral resolution, the high sensitivity, the good precision, and the accurate chemical specificity, which make these techniques suitable for decoding and understanding complex mechanisms of certain diseases, as well as monitoring the spatial distribution of specific elements, and compounds. While the application of both techniques for the analysis of cells and tissues is thoroughly discussed, a briefing of MALDI-TOF and TOF-SIMS basis and the adequate sampling before analysis are briefly covered. The importance of MALDI-TOF and TOF-SIMS as diagnostic tools and robust analytical techniques in the medicinal, pharmaceutical, and toxicology fields is highlighted through representative published studies.
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Affiliation(s)
- Manale Noun
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Rayane Akoumeh
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Imane Abbas
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
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5
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Weidner T, Castner DG. Developments and Ongoing Challenges for Analysis of Surface-Bound Proteins. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:389-412. [PMID: 33979545 PMCID: PMC8522203 DOI: 10.1146/annurev-anchem-091520-010206] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Proteins at surfaces and interfaces play important roles in the function and performance of materials in applications ranging from diagnostic assays to biomedical devices. To improve the performance of these materials, detailed molecular structure (conformation and orientation) along with the identity and concentrations of the surface-bound proteins on those materials must be determined. This article describes radiolabeling, surface plasmon resonance, quartz crystal microbalance with dissipation, X-ray photoelectron spectroscopy, secondary ion mass spectrometry, sum frequency generation spectroscopy, and computational techniques along with the information each technique provides for characterizing protein films. A multitechnique approach using both experimental and computation methods is required for these investigations. Although it is now possible to gain much insight into the structure of surface-bound proteins, it is still not possible to obtain the same level of structural detail about proteins on surfaces as can be obtained about proteins in crystals and solutions, especially for large, complex proteins. However, recent results have shown it is possible to obtain detailed structural information (e.g., backbone and side chain orientation) about small peptides (5-20 amino sequences) on surfaces. Current studies are extending these investigations to small proteins such as protein G B1 (∼6 kDa). Approaches for furthering the capabilities for characterizing the molecular structure of surface-bound proteins are proposed.
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Affiliation(s)
- Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark;
| | - David G Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, Departments of Bioengineering and Chemical Engineering, University of Washington, Seattle, Washington 98195, USA;
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6
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Tian H, Sheraz née Rabbani S, Vickerman JC, Winograd N. Multiomics Imaging Using High-Energy Water Gas Cluster Ion Beam Secondary Ion Mass Spectrometry [(H 2O) n-GCIB-SIMS] of Frozen-Hydrated Cells and Tissue. Anal Chem 2021; 93:7808-7814. [PMID: 34038090 PMCID: PMC8190772 DOI: 10.1021/acs.analchem.0c05210] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/05/2021] [Indexed: 11/29/2022]
Abstract
Integration of multiomics at the single-cell level allows the unambiguous dissecting of phenotypic heterogeneity at different states such as health, disease, and biomedical response. Imaging mass spectrometry holds the promise of being able to measure multiple types of biomolecules in parallel in the same cell. We have explored the possibility of using water gas cluster ion beam secondary ion mass spectrometry [(H2O)n-GCIB-SIMS] as an analytical tool for multiomics assay. (H2O)n-GCIB has been hailed as an ideal ionization source for biological sampling owing to the enhanced chemical sensitivity and reduced matrix effect. Taking advantage of 1 μm spatial resolution by using a high-energy beam system, we have clearly shown the enhancement of multiple intact biomolecules up to a few hundredfold in single cells. Coupled with the cryogenic sample preparation/measurement, the lipids and metabolites were imaged simultaneously within the cellular region, uncovering the pristine chemistry for integrated omics in the same sample. We have demonstrated that double-charged myelin protein fragments and single-charged multiple lipids and metabolites can be localized in the same cells/tissue with a single acquisition. Our exploration has also been extended to the capability of (H2O)n-GCIB in the generation of multiple charged peptides on protein standards. Frozen hydration combined with (H2O)n-GCIB provides the possibility of universal enhancement for the ionization of multiple bio-molecules, including peptides/proteins which has allowed "omics" to become feasible in the same sample using SIMS.
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Affiliation(s)
- Hua Tian
- Department
of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | | | - John C. Vickerman
- Manchester
Institute of Biotechnology, University of
Manchester, Manchester M1 7DN, U.K.
| | - Nicholas Winograd
- Department
of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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7
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Baio JE, Graham DJ, Castner DG. Surface analysis tools for characterizing biological materials. Chem Soc Rev 2020; 49:3278-3296. [PMID: 32390029 PMCID: PMC7337324 DOI: 10.1039/d0cs00181c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Surfaces represent a unique state of matter that typically have significantly different compositions and structures from the bulk of a material. Since surfaces are the interface between a material and its environment, they play an important role in how a material interacts with its environment. Thus, it is essential to characterize, in as much detail as possible, the surface structure and composition of a material. However, this can be challenging since the surface region typically is only minute portion of the entire material, requiring specialized techniques to selectively probe the surface region. This tutorial will provide a brief review of several techniques used to characterize the surface and interface regions of biological materials. For each technique we provide a description of the key underlying physics and chemistry principles, the information provided, strengths and weaknesses, the types of samples that can be analyzed, and an example application. Given the surface analysis challenges for biological materials, typically there is never just one technique that can provide a complete surface characterization. Thus, a multi-technique approach to biological surface analysis is always required.
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Affiliation(s)
- Joe E Baio
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Daniel J Graham
- National ESCA and Surface Analysis Center for Biomedical Problems, Box 351653, University of Washington, Seattle, WA 98195, USA. and Department of Bioengineering, Box 351653, University of Washington, Seattle, WA 98195, USA
| | - David G Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, Box 351653, University of Washington, Seattle, WA 98195, USA. and Department of Bioengineering, Box 351653, University of Washington, Seattle, WA 98195, USA and Department of Chemical Engineering, Box 351653, University of Washington, Seattle, WA 98195, USA
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8
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Gulin AA, Nadtochenko VA, Pogorelova VN, Melnikov MY, Pogorelov AG. Sample Preparation of Biological Tissues and Cells for the Time-of-Flight Secondary Ion Mass Spectrometry. JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1134/s106193482006009x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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A novel approach for 3D reconstruction of mice full-grown oocytes by time-of-flight secondary ion mass spectrometry. Anal Bioanal Chem 2019; 412:311-319. [DOI: 10.1007/s00216-019-02237-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/10/2019] [Accepted: 10/24/2019] [Indexed: 01/23/2023]
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10
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Improved ion imaging of slowly dried neurons and skin cells by graphene cover in time-of-flight secondary ion mass spectrometry. Biointerphases 2019; 14:051001. [PMID: 31529971 DOI: 10.1116/1.5118259] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful tool to obtain both chemical information and spatial distribution of specific molecules of interest on a specimen surface. However, since the focused ion beam requires ultrahigh vacuum conditions for desorption and ionization of analytes, proper specimen preparation, such as drying, freeze-drying, and frozen dehydration, is required for ToF-SIMS analysis. In particular, biological specimens with high moisture content generally have a problem of specimen deformation during the normal drying process for a vacuum environment. In this study, the authors propose a cellular specimen preparation method to improve the ion imaging of cells by reducing the deformation of specimens in ToF-SIMS analysis. When the cells on the slide substrate are completely covered with single-layer graphene, the ToF-SIMS imaging is improved by reduced cell deformation due to slow drying. In addition, the graphene encapsulation also induces a reduction in the yield of secondary ions, thereby suppressing the background ion spectra generated by the unwanted organic residues on the substrate, resulting in the improvement of ToF-SIMS imaging. The authors also found that adding plasma treatment to this sample preparation can further improve ion imaging of cells. After cell dehydration is completed, the covered graphene layer can be peeled off by air-plasma treatment and the unwanted organic residues on the substrate can be removed due to plasma cleaning, thereby much improving ion imaging of cells.
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11
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Lim H, Lee SY, Moon DW, Kim JY. Preparation of cellular samples using graphene cover and air-plasma treatment for time-of-flight secondary ion mass spectrometry imaging. RSC Adv 2019; 9:28432-28438. [PMID: 35529615 PMCID: PMC9071169 DOI: 10.1039/c9ra05205d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/06/2019] [Indexed: 11/21/2022] Open
Abstract
We report on sample preparation methods based on plasma treatment for an improvement of multiple molecular ion images of cellular membranes in the ToF-SIMS method. The air-plasma treatment of fixed cellular samples efficiently removed the organic residues of any solutions used during sample preparation and improved the quality of ToF-SIMS images due to the resulting clean surface. We also studied cell preparation methods that combine single-layer graphene covering with air-plasma treatment to achieve a synergistic effect that eliminates background spectra by organic impurities while minimizing morphological cell deformation in a vacuum environmental analysis. When the cellular sample on the glass substrate is completely covered with the single-layer graphene, the cells trapped between the graphene and the substrate can effectively reduce morphological deformation by slow-dehydration. After slow-dehydration of cells is completed inside the graphene-cover, the covered graphene layer can be peeled off by air-plasma treatment, and the unwanted organic residues on the surface of cells and substrate can also be removed by plasma cleaning, thereby much improving ion imaging of cells with the ToF-SIMS method. It is confirmed that the cell samples in which the graphene-cover was removed by air-plasma treatment maintained their morphology well in comparison with the rapid air-dried cells in atomic force microscopy (AFM) and ToF-SIMS images. Cell preparation methods that combine a single-layer graphene cover with air-plasma treatment for improvement of ToF-SIMS imaging.![]()
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Affiliation(s)
- Heejin Lim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST) 333 Techno Jungang Daero, Hyeonpung-Eup, Dalseong-Gun Daegu 42988 Republic of Korea
| | - Sun Young Lee
- Division of Technology Business, National Institute for Nanomaterials Technology (NINT), Pohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang Gyeongbuk 37673 Republic of Korea
| | - Dae Won Moon
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST) 333 Techno Jungang Daero, Hyeonpung-Eup, Dalseong-Gun Daegu 42988 Republic of Korea
| | - Jae Young Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST) 333 Techno Jungang Daero, Hyeonpung-Eup, Dalseong-Gun Daegu 42988 Republic of Korea .,Department of Robotics Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST) 333 Techno Jungang Daero, Hyeonpung-Eup, Dalseong-Gun Daegu 42988 Republic of Korea
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12
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Graham DJ, Gamble LJ. Dealing with image shifting in 3D ToF-SIMS depth profiles. Biointerphases 2018; 13:06E402. [PMID: 30185054 PMCID: PMC6125139 DOI: 10.1116/1.5041740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/01/2018] [Accepted: 08/07/2018] [Indexed: 11/17/2022] Open
Abstract
The high sputter efficiency and low damage of gas cluster ion beams have enabled depth profiling to greater depths within organic samples using time-of-flight secondary ion mass spectrometry (ToF-SIMS). Due to the typically fixed geometry of the ion sources used in ToF-SIMS, as one digs into a surface, the position sampled by ion beams shifts laterally. This causes a lateral shift in the resulting images that can become quite significant when profiling down more than one micron. Here, three methods to compensate for this image shifting are presented in order to more accurately stack the images to present a 3D representation. These methods include (1) using software to correct the image shifts post-acquisition, (2) correcting the sample height during acquisition, and (3) adjusting the beam position during acquisition. The advantages and disadvantages of these methods are discussed. It was found that all three methods were successful in compensating for image shifting in ToF-SIMS depth profiles resulting in a more accurate display of the 3D data. Features from spherical objects that were ellipsoidal prior to shifting were seen to be spherical after correction. Software shifting is convenient as it can be applied after data acquisition. However, when using software shifting, one must take into account the scan size and the size of the features of interest as image shifts can be significant and can result in cropping of features of interest. For depth profiles deeper than a few microns, hardware methods should be used as they preserve features of interest within the field of view regardless of the profile depth. Software shifting can also be used to correct for small shifts not accounted for by hardware methods. A combination of hardware and software shift correction can enable correction for a wide range of samples and profiling depths. The scripts required for the software shifting demonstrated herein are provided along with tutorials in the supplementary material.
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Affiliation(s)
- Daniel J Graham
- NESAC/BIO, Department of Bioengineering, University of Washington, Seattle, Washington 98195
| | - Lara J Gamble
- NESAC/BIO, Department of Bioengineering, University of Washington, Seattle, Washington 98195
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13
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Pogorelov AG, Gulin AA, Pogorelova VN, Panait AI, Pogorelova MA, Nadtochenko VA. The Use of ToF-SIMS for Analysis of Bioorganic Samples. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918020197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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14
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Court M, Barnes JP, Millet A. Identifying exposition to low oxygen environment in human macrophages using secondary ion mass spectrometry and multivariate analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1623-1632. [PMID: 28755479 DOI: 10.1002/rcm.7946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Macrophages are innate immune cells presenting a strong phenotypic plasticity and deeply involved in tissue homeostasis. Oxygen environmental tension is a physical parameter that could influence their polarizations. In this study we use time-of-flight secondary ion mass spectrometry (TOF-SIMS) to describe how various polarizations are modified by a low oxygen exposure. METHODS TOF-SIMS experiments were performed using an IONTOF ToF-SIMS 5-100 (ION-TOF GmbH, Munster, Germany). Analysis was performed using a pulsed 25 keV Bi3+ beam, sputtering was performed using a 250 eV Cs beam. Cells were fixed by paraformaldehyde before TOF-SIMS analysis. RESULTS Multivariate analysis of the TOF-SIMS spectra provided ion species associated with the exposure of macrophages to low oxygen concentration. We were able to obtain some species, specific of a particular polarization, advocating for the use of macrophages as reporter cells of oxygen tension in tissues. CONCLUSIONS Our study demonstrates that macrophage molecular signature to low oxygen environment is dependent on their polarization. TOF-SIMS shows the clear capability to produce species revealing this exposition. This result opens the way to the use of TOF-SIMS as a tool to explore hypoxia in human tissues.
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Affiliation(s)
- Magali Court
- Inserm U1205, Grenoble, France
- University of Grenoble-Alpes, Grenoble, France
| | - Jean-Paul Barnes
- University Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Arnaud Millet
- Inserm U1205, Grenoble, France
- University of Grenoble-Alpes, Grenoble, France
- Team ATIP/Avenir Mechanobiology, Immunity and Cancer, Grenoble, France
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15
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Castner DG. Biomedical surface analysis: Evolution and future directions (Review). Biointerphases 2017; 12:02C301. [PMID: 28438024 PMCID: PMC5403738 DOI: 10.1116/1.4982169] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/03/2017] [Accepted: 04/10/2017] [Indexed: 01/22/2023] Open
Abstract
This review describes some of the major advances made in biomedical surface analysis over the past 30-40 years. Starting from a single technique analysis of homogeneous surfaces, it has been developed into a complementary, multitechnique approach for obtaining detailed, comprehensive information about a wide range of surfaces and interfaces of interest to the biomedical community. Significant advances have been made in each surface analysis technique, as well as how the techniques are combined to provide detailed information about biological surfaces and interfaces. The driving force for these advances has been that the surface of a biomaterial is the interface between the biological environment and the biomaterial, and so, the state-of-the-art in instrumentation, experimental protocols, and data analysis methods need to be developed so that the detailed surface structure and composition of biomedical devices can be determined and related to their biological performance. Examples of these advances, as well as areas for future developments, are described for immobilized proteins, complex biomedical surfaces, nanoparticles, and 2D/3D imaging of biological materials.
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Affiliation(s)
- David G Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, Molecular Engineering and Sciences Institute, Departments of Bioengineering and Chemical Engineering, University of Washington, Box 351653, Seattle, Washington 98195-1653
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16
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Lovrić J, Malmberg P, Johansson BR, Fletcher JS, Ewing AG. Multimodal Imaging of Chemically Fixed Cells in Preparation for NanoSIMS. Anal Chem 2016; 88:8841-8. [PMID: 27462909 DOI: 10.1021/acs.analchem.6b02408] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In this work, we have employed time-of-flight secondary ion mass spectrometry (ToF-SIMS) to image chemically fixed adrenal cells prepared for transmission electron microscopy (TEM) and subsequent high-spatial-resolution NanoSIMS imaging. The sample fixation methodology preserves cell morphology, allows analysis in the ultrahigh vacuum environment, and reduces topographic artifacts, thus making these samples particularly favorable for ToF-SIMS analysis. ToF-SIMS imaging enables us to determine the chemistry and preservation capabilities of the chemical fixation as well as to locate specific ion species from OsO4. The OsO4 species have been localized in lysosomes of cortical cells, a type of adrenal cell present in the culture. NanoSIMS imaging of the (190)Os(16)O(-) ion species in cortical cells reveals the same localization as a wide range of OsO4 ions shown with ToF-SIMS. Even though we did not use during NanoSIMS imaging the exact OsxOy(-) ion species discovered with ToF-SIMS, ToF-SIMS allowed us to define the specific subcellular features in a high spatial resolution imaging mode. This study demonstrates the possibility for application of ToF-SIMS as a screening tool to optimize high-resolution imaging with NanoSIMS, which could replace TEM for localization in ultrahigh resolution imaging analyses.
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Affiliation(s)
- Jelena Lovrić
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96, Gothenburg, Sweden.,National Center for Imaging Mass Spectrometry, Chalmers University of Technology and Gothenburg University , SE-412 96, Gothenburg, Sweden
| | - Per Malmberg
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96, Gothenburg, Sweden.,National Center for Imaging Mass Spectrometry, Chalmers University of Technology and Gothenburg University , SE-412 96, Gothenburg, Sweden
| | - Bengt R Johansson
- Electron Microscopy Unit, Institute of Biomedicine, University of Gothenburg , SE-405 30, Gothenburg, Sweden
| | - John S Fletcher
- National Center for Imaging Mass Spectrometry, Chalmers University of Technology and Gothenburg University , SE-412 96, Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg , SE-412 96, Gothenburg, Sweden
| | - Andrew G Ewing
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96, Gothenburg, Sweden.,National Center for Imaging Mass Spectrometry, Chalmers University of Technology and Gothenburg University , SE-412 96, Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg , SE-412 96, Gothenburg, Sweden
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17
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Storage of cell samples for ToF-SIMS experiments-How to maintain sample integrity. Biointerphases 2016; 11:02A313. [PMID: 26810048 DOI: 10.1116/1.4940704] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In order to obtain comparable and reproducible results from time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis of biological cells, the influence of sample preparation and storage has to be carefully considered. It has been previously shown that the impact of the chosen preparation routine is crucial. In continuation of this work, the impact of storage needs to be addressed, as besides the fact that degradation will unavoidably take place, the effects of different storage procedures in combination with specific sample preparations remain largely unknown. Therefore, this work examines different wet (buffer, water, and alcohol) and dry (air-dried, freeze-dried, and critical-point-dried) storage procedures on human mesenchymal stem cell cultures. All cell samples were analyzed by ToF-SIMS immediately after preparation and after a storage period of 4 weeks. The obtained spectra were compared by principal component analysis with lipid- and amino acid-related signals known from the literature. In all dry storage procedures, notable degradation effects were observed, especially for lipid-, but also for amino acid-signal intensities. This leads to the conclusion that dried samples are to some extent easier to handle, yet the procedure is not the optimal storage solution. Degradation proceeds faster, which is possibly caused by oxidation reactions and cleaving enzymes that might still be active. Just as well, wet stored samples in alcohol struggle with decreased signal intensities from lipids and amino acids after storage. Compared to that, the wet stored samples in a buffered or pure aqueous environment revealed no degradation effects after 4 weeks. However, this storage bears a higher risk of fungi/bacterial contamination, as sterile conditions are typically not maintained. Thus, regular solution change is recommended for optimized storage conditions. Not directly exposing the samples to air, wet storage seems to minimize oxidation effects, and hence, buffer or water storage with regular renewal of the solution is recommended for short storage periods.
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18
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3D chemical characterization of frozen hydrated hydrogels using ToF-SIMS with argon cluster sputter depth profiling. Biointerphases 2016; 11:02A301. [DOI: 10.1116/1.4928209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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19
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Hua X, Szymanski C, Wang Z, Zhou Y, Ma X, Yu J, Evans J, Orr G, Liu S, Zhu Z, Yu XY. Chemical imaging of molecular changes in a hydrated single cell by dynamic secondary ion mass spectrometry and super-resolution microscopy. Integr Biol (Camb) 2016; 8:635-644. [DOI: 10.1039/c5ib00308c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Affiliation(s)
- Xin Hua
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu Province, 211189, China
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Craig Szymanski
- W. R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Zhaoying Wang
- W. R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Yufan Zhou
- W. R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Xiang Ma
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jiachao Yu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu Province, 211189, China
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - James Evans
- W. R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Galya Orr
- W. R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Songqin Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu Province, 211189, China
| | - Zihua Zhu
- W. R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Xiao-Ying Yu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
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20
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Robinson MA, Graham DJ, Morrish F, Hockenbery D, Gamble LJ. Lipid analysis of eight human breast cancer cell lines with ToF-SIMS. Biointerphases 2015; 11:02A303. [PMID: 26319020 PMCID: PMC4552699 DOI: 10.1116/1.4929633] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/13/2015] [Accepted: 08/17/2015] [Indexed: 12/25/2022] Open
Abstract
In this work, four triple negative (TN) cell lines, three ER+ and PR+ receptor positive (RP) cell lines, and one ER+, PR+, and HER2+ cell line were chemically distinguished from one another using time-of-flight secondary ion mass spectrometry (ToF-SIMS) and principal component analysis (PCA). PCA scores separation was observed between the individual cell lines within a given classification (TN and RP) and there were distinctly different trends found in the fatty acid and lipid compositions of the two different classifications. These trends indicated that the RP cell lines separated out based on the carbon chain length of the lipids while the TN cell lines showed separation based on cholesterol-related peaks (in the positive ion data). Both cell types separated out by trends in fatty acid chain length and saturation in the negative ions. These chemical differences may be manifestations of unique metabolic processes within each of the different cell lines. Additionally, the HER2+ cell line was distinguished from three other RP cell types as having a unique distribution of fatty acids including anticorrelation to 18-carbon chain fatty acids. As these cell lines could not be grown in the same growth media, a combination of chemical fixation, rinsing, C60 (+) presputtering, and selection of cellular regions-of-interest is also presented as a successful method to acquire ToF-SIMS data from cell lines grown in different media.
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Affiliation(s)
- Michael A Robinson
- National ESCA and Surface Analysis Center for Biomedical Problems, Department of Chemical Engineering, University of Washington, Seattle, Washington 98195
| | - Daniel J Graham
- National ESCA and Surface Analysis Center for Biomedical Problems, Department of Bioengineering, University of Washington, Seattle, Washington 98195
| | - Fionnuala Morrish
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - David Hockenbery
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Lara J Gamble
- National ESCA and Surface Analysis Center for Biomedical Problems, Department of Bioengineering, University of Washington, Seattle, Washington 98195
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21
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Assessment of different sample preparation routes for mass spectrometric monitoring and imaging of lipids in bone cells via ToF-SIMS. Biointerphases 2015; 10:019016. [PMID: 25791294 DOI: 10.1116/1.4915263] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In ToF-SIMS analysis, the experimental outcome from cell experiments is to a great extent influenced by the sample preparation routine. In order to better judge this critical influence in the case of lipid analysis, a detailed comparison of different sample preparation routines is performed-aiming at an optimized preparation routine for systematic lipid imaging of cell cultures. For this purpose, human mesenchymal stem cells were analyzed: (a) as chemically fixed, (b) freeze-dried, and (c) frozen-hydrated. For chemical fixation, different fixatives, i.e., glutaraldehyde, paraformaldehyde, and a mixture of both, were tested with different postfixative handling procedures like storage in phosphate buffered saline, water or critical point drying. Furthermore, secondary lipid fixation via osmium tetroxide was taken into account and the effect of an ascending alcohol series with and without this secondary lipid fixation was evaluated. Concerning freeze-drying, three different postprocessing possibilities were examined. One can be considered as a pure cryofixation technique while the other two routes were based on chemical fixation. Cryofixation methods known from literature, i.e., freeze-fracturing and simple frozen-hydrated preparation, were also evaluated to complete the comparison of sample preparation techniques. Subsequent data evaluation of SIMS spectra in both, positive and negative, ion mode was performed via principal component analysis by use of peak sets representative for lipids. For freeze-fracturing, these experiments revealed poor reproducibility making this preparation route unsuitable for systematic investigations and statistic data evaluation. Freeze-drying after cryofixation showed improved reproducibility and well preserved lipid contents while the other freeze-drying procedures showed drawbacks in one of these criteria. In comparison, chemical fixation techniques via glutar- and/or paraformaldehyde proved most suitable in terms of reproducibility and preserved lipid contents, while alcohol and osmium treatment led to the extraction of lipids and are therefore not recommended.
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22
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Gamble LJ, Graham DJ, Bluestein B, Whitehead NP, Hockenbery D, Morrish F, Porter P. ToF-SIMS of tissues: "lessons learned" from mice and women. Biointerphases 2015; 10:019008. [PMID: 25708638 PMCID: PMC4327923 DOI: 10.1116/1.4907860] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/23/2015] [Accepted: 01/29/2015] [Indexed: 11/17/2022] Open
Abstract
The ability to image cells and tissues with chemical and molecular specificity could greatly expand our understanding of biological processes. The subcellular resolution mass spectral imaging capability of time of flight secondary ion mass spectrometry (ToF-SIMS) has the potential to acquire chemically detailed images. However, the complexities of biological systems combined with the sensitivity of ToF-SIMS require careful planning of experimental methods. Tissue sample preparation methods of formalin fixation followed by paraffin embedding (FFPE) and OCT embedding are compared. Results show that the FFPE can potentially be used as a tissue sample preparation protocol for ToF-SIMS analysis if a cluster ion pre-sputter is used prior to analysis and if nonlipid related tissue features are the features of interest. In contrast, embedding tissue in OCT minimizes contamination and maintains lipid signals. Various data acquisition methodologies and analysis options are discussed and compared using mouse breast and diaphragm muscle tissue. Methodologies for acquiring ToF-SIMS 2D images are highlighted along with applications of multivariate analysis to better identify specific features in a tissue sections when compared to H&E images of serial sections. Identification of tissue features is necessary for researchers to visualize a molecular map that correlates with specific biological features or functions. Finally, lessons learned from sample preparation, data acquisition, and data analysis methods developed using mouse models are applied to a preliminary analysis of human breast tumor tissue sections.
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Affiliation(s)
- Lara J Gamble
- Department of Bioengineering, Molecular Engineering and Sciences Building, University of Washington, Box 351653, Seattle, Washington 98195-1653
| | - Daniel J Graham
- Department of Bioengineering, Molecular Engineering and Sciences Building, University of Washington, Box 351653, Seattle, Washington 98195-1653
| | - Blake Bluestein
- Department of Bioengineering, Molecular Engineering and Sciences Building, University of Washington, Box 351653, Seattle, Washington 98195-1653
| | - Nicholas P Whitehead
- Department of Physiology and Biophysics, University of Washington, Box 357290, Seattle, Washington 98195-1653
| | - David Hockenbery
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | | | - Peggy Porter
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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23
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Abstract
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a rapidly developing technique for the characterization of a wide range of materials. Recently, advances in instrumentation and sample preparation approaches have provided the ability to perform 3D molecular imaging experiments. Polyatomic ion beams, such as C60, and gas cluster ion beams, often Arn (n = 500-4000), substantially reduce the subsurface damage accumulation associated with continued bombardment of organic samples with atomic beams. In this review, the capabilities of the technique are discussed and examples of the 3D imaging approach for the analysis of model membrane systems, plant single cell, and tissue samples are presented. Ongoing challenges for 3D ToF-SIMS imaging are also discussed along with recent developments that might offer improved 3D imaging prospects in the near future.
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24
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Lanni EJ, Dunham SJB, Nemes P, Rubakhin SS, Sweedler JV. Biomolecular imaging with a C60-SIMS/MALDI dual ion source hybrid mass spectrometer: instrumentation, matrix enhancement, and single cell analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1897-907. [PMID: 25183225 DOI: 10.1007/s13361-014-0978-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 05/09/2023]
Abstract
We describe a hybrid MALDI/C(60)-SIMS Q-TOF mass spectrometer and corresponding sample preparation protocols to image intact biomolecules and their fragments in mammalian spinal cord, individual invertebrate neurons, and cultured neuronal networks. A lateral spatial resolution of 10 μm was demonstrated, with further improvement feasible to 1 μm, sufficient to resolve cell outgrowth and interconnections in neuronal networks. The high mass resolution (>13,000 FWHM) and tandem mass spectrometry capability of this hybrid instrument enabled the confident identification of cellular metabolites. Sublimation of a suitable matrix, 2,5-dihydroxybenzoic acid, significantly enhanced the ion signal intensity for intact glycerophospholipid ions from mammalian nervous tissue, facilitating the acquisition of high-quality ion images for low-abundance biomolecules. These results illustrate that the combination of C60-SIMS and MALDI mass spectrometry offers particular benefits for studies that require the imaging of intact biomolecules with high spatial and mass resolution, such as investigations of single cells, subcellular organelles, and communities of cells.
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Affiliation(s)
- Eric J Lanni
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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25
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Carlred L, Gunnarsson A, Solé-Domènech S, Johansson B, Vukojević V, Terenius L, Codita A, Winblad B, Schalling M, Höök F, Sjövall P. Simultaneous Imaging of Amyloid-β and Lipids in Brain Tissue Using Antibody-Coupled Liposomes and Time-of-Flight Secondary Ion Mass Spectrometry. J Am Chem Soc 2014; 136:9973-81. [DOI: 10.1021/ja5019145] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Louise Carlred
- Chemistry,
Materials and Surfaces, SP Technical Research Institute of Sweden, P.O. Box 857, SE-501 15 Borås, Sweden
- Department
of Applied Physics, Division of Biological Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Anders Gunnarsson
- Department
of Applied Physics, Division of Biological Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Santiago Solé-Domènech
- Department
of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Björn Johansson
- Department
of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Vladana Vukojević
- Department
of Clinical Neuroscience, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Lars Terenius
- Department
of Clinical Neuroscience, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Alina Codita
- Department
of Neurobiology, Care Sciences and Society, KI Alzheimer Disease Research
Center, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - Bengt Winblad
- Department
of Neurobiology, Care Sciences and Society, KI Alzheimer Disease Research
Center, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - Martin Schalling
- Department
of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Fredrik Höök
- Department
of Applied Physics, Division of Biological Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Peter Sjövall
- Chemistry,
Materials and Surfaces, SP Technical Research Institute of Sweden, P.O. Box 857, SE-501 15 Borås, Sweden
- Department
of Applied Physics, Division of Biological Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
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26
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Brison J, Robinson MA, Benoit DS, Muramoto S, Stayton PS, Castner DG. TOF-SIMS 3D imaging of native and non-native species within HeLa cells. Anal Chem 2013; 85:10869-77. [PMID: 24131300 PMCID: PMC3889863 DOI: 10.1021/ac402288d] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this study, a non-native chemical species, bromodeoxyuridine (BrdU), was imaged within single HeLa cells using time-of-flight secondary ion mass spectrometry (TOF-SIMS). z-corrected 3D images were reconstructed that accurately portray the distribution of intracellular BrdU as well as other intracellular structures. The BrdU was localized to the nucleus of cells, whereas structures composed of CxHyOz(-) species were located in bundles on the periphery of cells. The CxHyOz(-) subcellular features had a spatial resolution at or slightly below a micrometer (900 nm), as defined by the distance between the 16% and 84% intensities in a line scan across the edge of the features. Additionally, important parameters influencing the quality of the HeLa cell 3D images were investigated. Atomic force microscopy measurements revealed that the HeLa cells were sputtered at a rate of approximately 4 nm per 10(13) C60(+) ions/cm(2) at 10 keV and a 45° incident angle. Optimal 3D images were acquired using a Bi3(+) liquid metal ion gun operating in the simultaneous high mass and spatial resolution mode.
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Affiliation(s)
- Jeremy Brison
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, WA 98195-1653
- Department of Bioengineering, University of Washington, Seattle, WA 98195-1653
| | - Michael A. Robinson
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, WA 98195-1653
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-1653
| | | | - Shin Muramoto
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, WA 98195-1653
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-1653
| | - Patrick S. Stayton
- Department of Bioengineering, University of Washington, Seattle, WA 98195-1653
| | - David G. Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, WA 98195-1653
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-1653
- Department of Bioengineering, University of Washington, Seattle, WA 98195-1653
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