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Grusky DS, Moss FR, Boxer SG. Recombination between 13C and 2H to Form Acetylide ( 13C 22H -) Probes Nanoscale Interactions in Lipid Bilayers via Dynamic Secondary Ion Mass Spectrometry: Cholesterol and GM 1 Clustering. Anal Chem 2022; 94:9750-9757. [PMID: 35759338 PMCID: PMC10075087 DOI: 10.1021/acs.analchem.2c01336] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although it is thought that there is lateral heterogeneity of lipid and protein components within biological membranes, probing this heterogeneity has proven challenging. The difficulty in such experiments is due to both the small length scale over which such heterogeneity can occur, and the significant perturbation resulting from fluorescent or spin labeling on the delicate interactions within bilayers. Atomic recombination during dynamic nanoscale secondary ion imaging mass spectrometry (NanoSIMS) is a non-perturbative method for examining nanoscale bilayer interactions. Atomic recombination is a variation on conventional NanoSIMS imaging, whereby an isotope on one molecule combines with a different isotope on another molecule during the ionization process, forming an isotopically enriched polyatomic ion in a distance-dependent manner. We show that the recombinant ion, 13C22H-, is formed in high yield from 13C- and 2H-labeled lipids. The low natural abundance of triply labeled acetylide also makes it an ideal ion to probe GM1 clusters in model membranes and the effects of cholesterol on lipid-lipid interactions. We find evidence supporting the cholesterol condensation effect as well as the presence of nanoscale GM1 clusters in model membranes.
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Affiliation(s)
- Dashiel S Grusky
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Frank R Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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2
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Abstract
High-resolution imaging with secondary ion mass spectrometry (nanoSIMS) has become a standard method in systems biology and environmental biogeochemistry and is broadly used to decipher ecophysiological traits of environmental microorganisms, metabolic processes in plant and animal tissues, and cross-kingdom symbioses. When combined with stable isotope-labeling-an approach we refer to as nanoSIP-nanoSIMS imaging offers a distinctive means to quantify net assimilation rates and stoichiometry of individual cell-sized particles in both low- and high-complexity environments. While the majority of nanoSIP studies in environmental and microbial biology have focused on nitrogen and carbon metabolism (using 15N and 13C tracers), multiple advances have pushed the capabilities of this approach in the past decade. The development of a high-brightness oxygen ion source has enabled high-resolution metal analyses that are easier to perform, allowing quantification of metal distribution in cells and environmental particles. New preparation methods, tools for automated data extraction from large data sets, and analytical approaches that push the limits of sensitivity and spatial resolution have allowed for more robust characterization of populations ranging from marine archaea to fungi and viruses. NanoSIMS studies continue to be enhanced by correlation with orthogonal imaging and 'omics approaches; when linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. Here we present an updated description of the primary materials, methods, and calculations used for nanoSIP, with an emphasis on recent advances in nanoSIMS applications, key methodological steps, and potential pitfalls.
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Affiliation(s)
- Jennifer Pett-Ridge
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
| | - Peter K Weber
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
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3
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Gyngard F, Steinhauser ML. Biological explorations with nanoscale secondary ion mass spectrometry. JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY 2019; 34:1534-1545. [PMID: 34054180 PMCID: PMC8158666 DOI: 10.1039/c9ja00171a] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Investigation of biological processes at the single cell or subcellular level is critical in order to better understand heterogenous cell populations. Nanoscale secondary ion mass spectrometry (NanoSIMS) enables multiplexed, quantitative imaging of the elemental composition of a sample surface at high resolution (< 50 nm). Through measurement of two different isotopic variants of any given element, NanoSIMS provides nanoscale isotope ratio measurements. When coupled with stable isotope tracer methods, the measurement of isotope ratios functionally illuminates biochemical pathways at suborganelle resolution. In this review, we describe the practical application of NanoSIMS to study biological processes in organisms ranging from microbes to humans, highlighting experimental applications that have provided insight that is largely unattainable by other methods.
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Affiliation(s)
- Frank Gyngard
- Center for NanoImaging, Division of Genetics, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Matthew L Steinhauser
- Center for NanoImaging, Division of Genetics, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
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4
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Rozas EE, Mendes MA, Custódio MR, Espinosa DCR, do Nascimento CAO. Self-assembly of supramolecular structure based on copper-lipopeptides isolated from e-waste bioleaching liquor. JOURNAL OF HAZARDOUS MATERIALS 2019; 368:63-71. [PMID: 30665109 DOI: 10.1016/j.jhazmat.2019.01.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/12/2019] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
Supramolecular structures were produced by auto-assembling CuCN blocks derived from copper-lipopeptides (CuLps) isolated from bioleaching liquor. Lipopeptides produced by B. subtilis Hyhel1 have been previously related as responsible by bioleaching and intracellular copper crystal production. However, there were no records relating CuLps to extracellular copper crystal production. To study this process, CuLps were isolated from bioleaching liquor and kept at 8 °C to facilitate the CuLps aggregation. After three months, blue spheres (BS) were observed in the CuLp fraction. These spheres were then analyzed by SEM-EDS, MALDI-TOF-MS/MS, GC-MS and FTIR. SEM-EDS analysis showed that they were formed by polycrystalline structures mainly composed by Cu (46.5% m/m) and positioned concentrically. MALDI-TOF-MS/MS and GCMS showed that peptide bonds of CuLp were broken, producing lipid chains and amino acids free. The FTIR of BS showed three nitro groups: CN, NN and NO, which were not found in the control. These data suggest that the CuLp amino acid produced a CN group linked to copper, as CuCN blocks, that auto-assembled in supramolecular structures. This phenomenon could be explored as a method to recover copper and to obtain supramolecular CuCN structures, which in turn may be used as template for superconductor or computing devices.
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Affiliation(s)
- Enrique E Rozas
- Dempster-Poli-USP, Chemical Engineering Department, University of São Paulo (USP), Av. Prof. Lineu Prestes 580, block 21, CEP: 05508-910, São Paulo, Brazil.
| | - Maria Anita Mendes
- Dempster-Poli-USP, Chemical Engineering Department, University of São Paulo (USP), Av. Prof. Lineu Prestes 580, block 21, CEP: 05508-910, São Paulo, Brazil
| | - Marcio Reis Custódio
- Department of General Physiology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, 101, CEP: 05508-090, Brazil
| | - Denise C R Espinosa
- LAREX, Chemical Engineering Department, University of São Paulo, Av. Prof. Lineu Prestes 580, block 21, CEP: 05508-910, São Paulo (USP), Brazil
| | - Claudio A O do Nascimento
- Dempster-Poli-USP, Chemical Engineering Department, University of São Paulo (USP), Av. Prof. Lineu Prestes 580, block 21, CEP: 05508-910, São Paulo, Brazil
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5
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Abstract
Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, the authors provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analyses, and current outlooks. Specifically, the authors offer an overview of SIMS and development of the NanoSIMS. The authors describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includes an in-depth discussion of appropriate colormaps. Additionally, the authors provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Finally, the authors present a perspective on the future of this technology and where they think it will have the greatest impact in near future.
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6
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Moss FR, Boxer SG. Atomic Recombination in Dynamic Secondary Ion Mass Spectrometry Probes Distance in Lipid Assemblies: A Nanometer Chemical Ruler. J Am Chem Soc 2016; 138:16737-16744. [PMID: 27977192 DOI: 10.1021/jacs.6b10655] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The lateral organization of biological membranes is thought to take place on the nanometer length scale. However, this length scale and the dynamic nature of small lipid and protein domains have made characterization of such organization in biological membranes and model systems difficult. Here we introduce a new method for measuring the colocalization of lipids in monolayers and bilayers using stable isotope labeling. We take advantage of a process that occurs in dynamic SIMS called atomic recombination, in which atoms on different molecules combine to form diatomic ions that are detected with a NanoSIMS instrument. This process is highly sensitive to the distance between molecules. By measuring the efficiency of the formation of 13C15N- ions from 13C and 15N atoms on different lipid molecules, we measure variations in the lateral organization of bilayers even though these heterogeneities occur on a length scale of only a few nm, well below the diameter of the primary ion beam of the NanoSIMS instrument or even the best super-resolution fluorescence methods. Using this technique, we provide direct evidence for nanoscale phase separation in a model membrane, which may provide a better model for the organization of biological membranes than lipid mixtures with microscale phase separation. We expect this technique to be broadly applicable to any assembly where very short scale proximity is of interest or unknown, both in chemical and biological systems.
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Affiliation(s)
- Frank R Moss
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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7
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Kabatas S, Vreja IC, Saka SK, Höschen C, Kröhnert K, Opazo F, Rizzoli SO, Diederichsen U. A contamination-insensitive probe for imaging specific biomolecules by secondary ion mass spectrometry. Chem Commun (Camb) 2016. [PMID: 26195041 DOI: 10.1039/c5cc03895b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Imaging techniques should differentiate between specific signals, from the biomolecules of interest, and non-specific signals, from the background. We present a probe containing (15)N and (14)N isotopes in approximately equal proportion, for secondary ion mass spectrometry imaging. This probe designed for a precise biomolecule analysis is insensitive to background signals.
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Affiliation(s)
- Selda Kabatas
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, D-37077 Göttingen, Germany.
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8
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Kruse J, Abraham M, Amelung W, Baum C, Bol R, Kühn O, Lewandowski H, Niederberger J, Oelmann Y, Rüger C, Santner J, Siebers M, Siebers N, Spohn M, Vestergren J, Vogts A, Leinweber P. Innovative methods in soil phosphorus research: A review. JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE = ZEITSCHRIFT FUR PFLANZENERNAHRUNG UND BODENKUNDE 2015; 178:43-88. [PMID: 26167132 PMCID: PMC4497464 DOI: 10.1002/jpln.201400327] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/16/2014] [Indexed: 05/18/2023]
Abstract
Phosphorus (P) is an indispensable element for all life on Earth and, during the past decade, concerns about the future of its global supply have stimulated much research on soil P and method development. This review provides an overview of advanced state-of-the-art methods currently used in soil P research. These involve bulk and spatially resolved spectroscopic and spectrometric P speciation methods (1 and 2D NMR, IR, Raman, Q-TOF MS/MS, high resolution-MS, NanoSIMS, XRF, XPS, (µ)XAS) as well as methods for assessing soil P reactions (sorption isotherms, quantum-chemical modeling, microbial biomass P, enzymes activity, DGT, 33P isotopic exchange, 18O isotope ratios). Required experimental set-ups and the potentials and limitations of individual methods present a guide for the selection of most suitable methods or combinations.
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Affiliation(s)
- Jens Kruse
- Soil Science, Faculty for Agricultural and Environmental Sciences, University of RostockJustus-von-Liebig Weg 6, 18051 Rostock, Germany
- Institute of Crop Science and Resource Conservation, Soil Science and Soil Ecology, University of BonnNussallee 13, 53115 Bonn, Germany
| | - Marion Abraham
- Leibniz Institute for Baltic Sea ResearchSeestraße 15, 18119 Rostock, Germany
| | - Wulf Amelung
- Institute of Crop Science and Resource Conservation, Soil Science and Soil Ecology, University of BonnNussallee 13, 53115 Bonn, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and GeosciencesIBG-3: Agrosphere, 52425 Jülich, Germany
| | - Christel Baum
- Soil Science, Faculty for Agricultural and Environmental Sciences, University of RostockJustus-von-Liebig Weg 6, 18051 Rostock, Germany
| | - Roland Bol
- Forschungszentrum Jülich GmbH, Institute of Bio- and GeosciencesIBG-3: Agrosphere, 52425 Jülich, Germany
| | - Oliver Kühn
- Institute of Physics, Faculty of Mathematics and Natural Sciences, University of RostockWismarsche Straße 43–45,18057 Rostock, Germany
| | - Hans Lewandowski
- Forschungszentrum Jülich GmbH, Institute of Bio- and GeosciencesIBG-3: Agrosphere, 52425 Jülich, Germany
| | - Jörg Niederberger
- Chair of Silviculture, Albert Ludwig University FreiburgTennenbacherstraße 4, 79085 Freiburg im Breisgau, Germany
| | - Yvonne Oelmann
- Geoecology, Geosciences, University of TübingenRümelinstraße 19–23.72070 Tübingen, Germany
| | - Christopher Rüger
- Analytical Chemistry, Faculty of Mathematics and Natural Sciences, University of RostockDr.-Lorenzweg 1, 18059 Rostock, Germany
| | - Jakob Santner
- Institute of Soil Research, University of Natural Resources and Life Sciences ViennaKonrad Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Meike Siebers
- Institute of Molecular Physiology and Biotechnology of Plants, University of BonnKarlrobert-Kreiten-Str. 13, 53115 Bonn, Germany
| | - Nina Siebers
- Forschungszentrum Jülich GmbH, Institute of Bio- and GeosciencesIBG-3: Agrosphere, 52425 Jülich, Germany
| | - Marie Spohn
- Department of Soil Ecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University BayreuthDr.-Hans-Frisch-Str. 1–3, 95448 Bayreuth, Germany
| | - Johan Vestergren
- Chemistry, Umeå University, Kemi A, plan 4, Linnaeus väg10 Umeå, Sweden
| | - Angela Vogts
- Leibniz Institute for Baltic Sea ResearchSeestraße 15, 18119 Rostock, Germany
| | - Peter Leinweber
- Soil Science, Faculty for Agricultural and Environmental Sciences, University of RostockJustus-von-Liebig Weg 6, 18051 Rostock, Germany
- *
Soil Science, Faculty for Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig Weg 6, 18051 Rostock, Germany e-mail:
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9
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Jiang H, Favaro E, Goulbourne CN, Rakowska PD, Hughes GM, Ryadnov MG, Fong LG, Young SG, Ferguson DJP, Harris AL, Grovenor CRM. Stable isotope imaging of biological samples with high resolution secondary ion mass spectrometry and complementary techniques. Methods 2014; 68:317-24. [PMID: 24556558 PMCID: PMC4222523 DOI: 10.1016/j.ymeth.2014.02.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 01/07/2014] [Accepted: 02/06/2014] [Indexed: 02/07/2023] Open
Abstract
Stable isotopes are ideal labels for studying biological processes because they have little or no effect on the biochemical properties of target molecules. The NanoSIMS is a tool that can image the distribution of stable isotope labels with up to 50 nm spatial resolution and with good quantitation. This combination of features has enabled several groups to undertake significant experiments on biological problems in the last decade. Combining the NanoSIMS with other imaging techniques also enables us to obtain not only chemical information but also the structural information needed to understand biological processes. This article describes the methodologies that we have developed to correlate atomic force microscopy and backscattered electron imaging with NanoSIMS experiments to illustrate the imaging of stable isotopes at molecular, cellular, and tissue scales. Our studies make it possible to address 3 biological problems: (1) the interaction of antimicrobial peptides with membranes; (2) glutamine metabolism in cancer cells; and (3) lipoprotein interactions in different tissues.
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Affiliation(s)
- H Jiang
- Materials Department, Oxford University, Oxford, UK.
| | - E Favaro
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - C N Goulbourne
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - P D Rakowska
- National Physical Laboratory, Teddington, UK; Department of Chemistry, University College London, London, UK
| | - G M Hughes
- Materials Department, Oxford University, Oxford, UK
| | - M G Ryadnov
- National Physical Laboratory, Teddington, UK; School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - L G Fong
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - S G Young
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA; Department of Human Genetics, University of California Los Angeles, Los Angeles, USA
| | - D J P Ferguson
- Nuffield Department of Clinical Laboratory Science, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - A L Harris
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
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10
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Baboo S, Bhushan B, Jiang H, Grovenor CRM, Pierre P, Davis BG, Cook PR. Most human proteins made in both nucleus and cytoplasm turn over within minutes. PLoS One 2014; 9:e99346. [PMID: 24911415 PMCID: PMC4050049 DOI: 10.1371/journal.pone.0099346] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 05/13/2014] [Indexed: 12/25/2022] Open
Abstract
In bacteria, protein synthesis can be coupled to transcription, but in eukaryotes it is believed to occur solely in the cytoplasm. Using pulses as short as 5 s, we find that three analogues – L-azidohomoalanine, puromycin (detected after attaching fluors using ‘click’ chemistry or immuno-labeling), and amino acids tagged with ‘heavy’ 15N and 13C (detected using secondary ion mass spectrometry) – are incorporated into the nucleus and cytoplasm in a process sensitive to translational inhibitors. The nuclear incorporation represents a significant fraction of the total, and labels in both compartments have half-lives of less than a minute; results are consistent with most newly-made peptides being destroyed soon after they are made. As nascent RNA bearing a premature termination codon (detected by fluorescence in situ hybridization) is also eliminated by a mechanism sensitive to a translational inhibitor, the nuclear turnover of peptides is probably a by-product of proof-reading the RNA for stop codons (a process known as nonsense-mediated decay). We speculate that the apparently-wasteful turnover of this previously-hidden (‘dark-matter’) world of peptide is involved in regulating protein production.
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Affiliation(s)
- Sabyasachi Baboo
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Bhaskar Bhushan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Haibo Jiang
- Department of Materials, University of Oxford, Oxford, United Kingdom
| | | | - Philippe Pierre
- Centre d′Immunologie de Marseille-Luminy, Aix-Marseille Université, Marseille, France
- Institut National de la Santé et de la Recherche Médicale, U1104, Marseille, France
- Centre National de la Recherche Scientifique, Unités Mixtes de Recherche 7280, Marseille, France
| | - Benjamin G. Davis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Peter R. Cook
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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11
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Steinhauser ML, Lechene CP. Quantitative imaging of subcellular metabolism with stable isotopes and multi-isotope imaging mass spectrometry. Semin Cell Dev Biol 2013; 24:661-7. [PMID: 23660233 DOI: 10.1016/j.semcdb.2013.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multi-isotope imaging mass spectrometry (MIMS) is the quantitative imaging of stable isotope labels in cells with a new type of secondary ion mass spectrometer (NanoSIMS). The power of the methodology is attributable to (i) the immense advantage of using non-toxic stable isotope labels, (ii) high resolution imaging that approaches the resolution of usual transmission electron microscopy and (iii) the precise quantification of label down to 1 part-per-million and spanning several orders of magnitude. Here we review the basic elements of MIMS and describe new applications of MIMS to the quantitative study of metabolic processes including protein and nucleic acid synthesis in model organisms ranging from microbes to humans.
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Affiliation(s)
- Matthew L Steinhauser
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, United States; Division of Genetics, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, United States; Division of Cardiovascular Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, United States
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12
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Delaune A, Cabin-Flaman A, Legent G, Gibouin D, Smet-Nocca C, Lefebvre F, Benecke A, Vasse M, Ripoll C. 50nm-scale localization of single unmodified, isotopically enriched, proteins in cells. PLoS One 2013; 8:e56559. [PMID: 23431383 PMCID: PMC3576336 DOI: 10.1371/journal.pone.0056559] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 01/02/2013] [Indexed: 02/01/2023] Open
Abstract
Imaging single proteins within cells is challenging if the possibility of artefacts due to tagging or to recognition by antibodies is to be avoided. It is generally believed that the biological properties of proteins remain unaltered when 14N isotopes are replaced with 15N. 15N-enriched proteins can be localised by dynamic Secondary Ion Mass Spectrometry (D-SIMS). We describe here a novel imaging analysis algorithm to detect a few 15N-enriched proteins - and even a single protein - within a cell using D-SIMS. The algorithm distinguishes statistically between a low local increase in 15N isotopic fraction due to an enriched protein and a stochastic increase due to the background. To determine the number of enriched proteins responsible for the increase in the isotopic fraction, we use sequential D-SIMS images in which we compare the measured isotopic fractions to those expected if 1, 2 or more enriched proteins are present. The number of enriched proteins is the one that gives the best fit between the measured and the expected values. We used our method to localise 15N-enriched thymine DNA glycosylase (TDG) and retinoid X receptor α (RXRα) proteins delivered to COS-7 cells. We show that both a single TDG and a single RXRα can be detected. After 4 h incubation, both proteins were found mainly in the nucleus; RXRα as a monomer or dimer and TDG only as a monomer. After 7 h, RXRα was found in the nucleus as a monomer, dimer or tetramer, whilst TDG was no longer in the nucleus and instead formed clusters in the cytoplasm. After 24 h, RXRα formed clusters in the cytoplasm, and TDG was no longer detectable. In conclusion, single unmodified proteins in cells can be counted and localised with 50 nm resolution by combining D-SIMS with our method of analysis.
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Affiliation(s)
- Anthony Delaune
- Laboratoire MERCI EA3829, équipe AMMIS, Faculté des Sciences de l'Université de Rouen, Mont Saint Aignan, France.
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13
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Piani L, Remusat L, Robert F. Determination of the H isotopic composition of individual components in fine-scale mixtures of organic matter and phyllosilicates with the nanoscale secondary ion mass spectrometry. Anal Chem 2012; 84:10199-206. [PMID: 23121456 DOI: 10.1021/ac301099u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
When organic matter is mixed on a nanometer scale with clay minerals, the individual D/H ratios of the two H-bearing phases cannot be directly measured even with the nominal spatial resolution of nanoscale secondary ion mass spectrometry (NanoSIMS, 50-100 nm). To overcome this limitation, a new analytical protocol is proposed based on the deconvolution of the D(-)/H(-) and (16)OD(-)/(16)OH(-) ionic ratios measured by NanoSIMS. Indeed, since the yields of H(-) and (16)OH(-) are different for organics and clays, it should be theoretically possible to determine the mixing ratio of these two components in the area analyzed by the ion probe. Using organics with different D/H ratios, the interdependence of the D(-)/H(-) and (16)OD(-)/(16)OH(-) ionic ratios was determined in pure samples. Then using the H(-) and (16)OH(-) yields and the isotopic ratios measured on pure organic matter and clays, the expected D(-)/H(-) and (16)OD(-)/(16)OH(-) variations as a function of the mixing proportions were determined. These numerical predictions are consistent with measurements on laboratory prepared mixtures of D-rich organic matter and D-poor phyllosilicates, validating both the proposed experimental protocol and its use for meteorites. With an improvement of the precision of the ionic ratios by a factor of 10, it should possible to expend this protocol to samples having natural terrestrial D/H variations. Such an improvement could be attainable with the development of synthetic deuterated reference samples.
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Affiliation(s)
- Laurette Piani
- Laboratoire de Minéralogie et Cosmochimie du Muséum, Muséum National d'Histoire Naturelle, Paris, France.
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14
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Hatton PJ, Remusat L, Zeller B, Derrien D. A multi-scale approach to determine accurate elemental and isotopic ratios by nano-scale secondary ion mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1363-1371. [PMID: 22555930 DOI: 10.1002/rcm.6228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE Nano-scale secondary ion mass spectrometry (NanoSIMS) is still hampered by a lack of appropriate calibration method for the quantification of elemental and isotopic ratios in heterogeneous materials such as soil samples. The potential of (13)C-(15)N-labeled density fractions of soil to calibrate the C/N, (13)C/(12)C and (15)N/(14)N ratios provided by NanoSIMS was evaluated. METHODS The spatial organization of soil particles found at the macro- and micro-scales were compared. The C/N, (13)C/(12)C and (15)N/(14)N ratios measured at the macroscopic scale from different density fractions using an elemental analyzer coupled to an isotope ratio mass spectrometer (EA/IRMS) were compared with the corresponding micro-scale NanoSIMS measurements. When the macro- and micro-scales patterns were similar, macroscopic scale measurements obtained by EA/IRMS and the corresponding NanoSIMS C/N and (15)N/(14)N ratios averaged per fraction were used to obtain correction equations. The correction method using the internal calibration procedure was compared with the traditional one using a single organic standard. RESULTS It was demonstrated that the correction method using an internal calibration procedure was applicable for NanoSIMS images acquired on more than 500 µm(2) per fraction and provided more accurate C/N and (15)N/(14)N ratios than the traditional correction method. CONCLUSIONS As long as the NanoSIMS sampling was representative of the macroscopic properties, the correction method using an internal calibration procedure allowed better quantification of the isotope tracers and characterization of the C/N ratios. This method not only produced qualitative images, but also accurate quantitative parameters from which ecological interpretations can be derived.
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Affiliation(s)
- Pierre-Joseph Hatton
- INRA, Laboratoire de Biogéochimie des Ecosystèmes Forestiers, UR 1138, INRA Nancy, 54280 Champenoux, France.
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15
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Goto K, Waki M, Takahashi T, Kadowaki M, Setou M. High-Resolution Multi-isotope Imaging Mass Spectrometry Enables Visualisation of Stem Cell Division and Metabolism. Chembiochem 2012; 13:1103-6. [DOI: 10.1002/cbic.201200146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Indexed: 11/11/2022]
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16
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Remusat L, Hatton PJ, Nico PS, Zeller B, Kleber M, Derrien D. NanoSIMS study of organic matter associated with soil aggregates: advantages, limitations, and combination with STXM. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:3943-3949. [PMID: 22360342 DOI: 10.1021/es203745k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Direct observations of processes occurring at the mineral-organic interface are increasingly seen as relevant for the cycling of both natural soil organic matter and organic contaminants in soils and sediments. Advanced analytical tools with the capability to visualize and characterize organic matter at the submicrometer scale, such as Nano Secondary Ion Mass Spectrometry (NanoSIMS) and Scanning Transmission X-ray Microscopy (STXM) coupled to Near Edge X-ray Absorption Fine Structure Spectroscopy (NEXAFS), may be combined to locate and characterize mineral-associated organic matter. Taking advantage of samples collected from a decadal (15)N litter labeling experiment in a temperate forest, we demonstrate the potential of NanoSIMS to image intact soil particles and to detect spots of isotopic enrichment even at low levels of (15)N application. We show how microsites of isotopic enrichment detected by NanoSIMS can be speciated by STXM-NEXAFS performed on the same particle. Finally, by showing how (15)N enrichment at one microsite could be linked to the presence of microbial metabolites, we emphasize the potential of this combined imaging and spectroscopic approach to link microenvironment with geochemical process and/or location with ecological function.
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Affiliation(s)
- Laurent Remusat
- Laboratoire de Minéralogie et Cosmochimie du Muséum, UMR 7202 CNRS/MNHN, Muséum National d'Histoire Naturelle, Paris, France
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17
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Lanni EJ, Rubakhin SS, Sweedler JV. Mass spectrometry imaging and profiling of single cells. J Proteomics 2012; 75:5036-5051. [PMID: 22498881 DOI: 10.1016/j.jprot.2012.03.017] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/08/2012] [Accepted: 03/13/2012] [Indexed: 11/25/2022]
Abstract
Mass spectrometry imaging and profiling of individual cells and subcellular structures provide unique analytical capabilities for biological and biomedical research, including determination of the biochemical heterogeneity of cellular populations and intracellular localization of pharmaceuticals. Two mass spectrometry technologies-secondary ion mass spectrometry (SIMS) and matrix assisted laser desorption/ionization mass spectrometry (MALDI MS)-are most often used in micro-bioanalytical investigations. Recent advances in ion probe technologies have increased the dynamic range and sensitivity of analyte detection by SIMS, allowing two- and three-dimensional localization of analytes in a variety of cells. SIMS operating in the mass spectrometry imaging (MSI) mode can routinely reach spatial resolutions at the submicron level; therefore, it is frequently used in studies of the chemical composition of subcellular structures. MALDI MS offers a large mass range and high sensitivity of analyte detection. It has been successfully applied in a variety of single-cell and organelle profiling studies. Innovative instrumentation such as scanning microprobe MALDI and mass microscope spectrometers enables new subcellular MSI measurements. Other approaches for MS-based chemical imaging and profiling include those based on near-field laser ablation and inductively-coupled plasma MS analysis, which offer complementary capabilities for subcellular chemical imaging and profiling.
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Affiliation(s)
- Eric J Lanni
- Department of Chemistry and the Beckman Institute of Science and Technology, University of Illinois, Urbana IL 61801, USA
| | - Stanislav S Rubakhin
- Department of Chemistry and the Beckman Institute of Science and Technology, University of Illinois, Urbana IL 61801, USA
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute of Science and Technology, University of Illinois, Urbana IL 61801, USA.
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18
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Gormanns P, Reckow S, Poczatek JC, Turck CW, Lechene C. Segmentation of multi-isotope imaging mass spectrometry data for semi-automatic detection of regions of interest. PLoS One 2012; 7:e30576. [PMID: 22347386 PMCID: PMC3276494 DOI: 10.1371/journal.pone.0030576] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 12/21/2011] [Indexed: 11/18/2022] Open
Abstract
Multi-isotope imaging mass spectrometry (MIMS) associates secondary ion mass spectrometry (SIMS) with detection of several atomic masses, the use of stable isotopes as labels, and affiliated quantitative image-analysis software. By associating image and measure, MIMS allows one to obtain quantitative information about biological processes in sub-cellular domains. MIMS can be applied to a wide range of biomedical problems, in particular metabolism and cell fate [1], [2], [3]. In order to obtain morphologically pertinent data from MIMS images, we have to define regions of interest (ROIs). ROIs are drawn by hand, a tedious and time-consuming process. We have developed and successfully applied a support vector machine (SVM) for segmentation of MIMS images that allows fast, semi-automatic boundary detection of regions of interests. Using the SVM, high-quality ROIs (as compared to an expert's manual delineation) were obtained for 2 types of images derived from unrelated data sets. This automation simplifies, accelerates and improves the post-processing analysis of MIMS images. This approach has been integrated into "Open MIMS," an ImageJ-plugin for comprehensive analysis of MIMS images that is available online at http://www.nrims.hms.harvard.edu/NRIMS_ImageJ.php.
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Affiliation(s)
- Philipp Gormanns
- Max Planck Institute of Psychiatry, Proteomics and Biomarkers, Munich, Germany
| | - Stefan Reckow
- Max Planck Institute of Psychiatry, Proteomics and Biomarkers, Munich, Germany
| | - J. Collin Poczatek
- National Resource for Imaging Mass Spectrometry, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, Massachusetts, United States of America
| | - Christoph W. Turck
- Max Planck Institute of Psychiatry, Proteomics and Biomarkers, Munich, Germany
| | - Claude Lechene
- National Resource for Imaging Mass Spectrometry, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, Massachusetts, United States of America
- * E-mail:
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19
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Abstract
Recent advances in high-resolution imaging secondary ion mass spectrometry (SIMS) (J Biol 5: 20, 2006) have made isotopic tracing at the single-cell level a standard technique for microbial ecology and systems biology; elemental and metal cofactor analyses are also showing significant promise. For example, with the NanoSIMS, metabolic activities of single microbial cells can be tracked by imaging natural isotopic/elemental composition or isotope distribution after stable isotope probing. When linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. We broadly call this combination of methods nanoSIP, for nanometer-scale stable isotope probing. Here we present the primary materials and methods used for nanoSIP, with an emphasis on key steps and potential pitfalls. Applications to pure cultures, cocultures, and complex communities are discussed.
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Affiliation(s)
- Jennifer Pett-Ridge
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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20
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Dekas AE, Orphan VJ. Identification of diazotrophic microorganisms in marine sediment via fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Methods Enzymol 2011; 486:281-305. [PMID: 21185440 DOI: 10.1016/b978-0-12-381294-0.00012-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Growing appreciation for the biogeochemical significance of uncultured microorganisms is changing the focus of environmental microbiology. Techniques designed to investigate microbial metabolism in situ are increasingly popular, from mRNA-targeted fluorescence in situ hybridization (FISH) to the "-omics" revolution, including metagenomics, transcriptomics, and proteomics. Recently, the coupling of FISH with nanometer-scale secondary ion mass spectrometry (NanoSIMS) has taken this movement in a new direction, allowing single-cell metabolic analysis of uncultured microbial phylogenic groups. The main advantage of FISH-NanoSIMS over previous noncultivation-based techniques to probe metabolism is its ability to directly link 16S rRNA phylogenetic identity to metabolic function. In the following chapter, we describe the procedures necessary to identify nitrogen-fixing microbes within marine sediment via FISH-NanoSIMS, using our work on nitrogen fixation by uncultured deep-sea methane-consuming archaea as a case study.
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Affiliation(s)
- Anne E Dekas
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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21
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Boxer SG, Kraft ML, Weber PK. Advances in imaging secondary ion mass spectrometry for biological samples. Annu Rev Biophys 2009; 38:53-74. [PMID: 19086820 DOI: 10.1146/annurev.biophys.050708.133634] [Citation(s) in RCA: 206] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Imaging mass spectrometry combines the power of mass spectrometry to identify complex molecules based on mass with sample imaging. Recent advances in secondary ion mass spectrometry have improved sensitivity and spatial resolution, so that these methods have the potential to bridge between high-resolution structures obtained by X-ray crystallography and cyro-electron microscopy and ultrastructure visualized by conventional light microscopy. Following background information on the method and instrumentation, we address the key issue of sample preparation. Because mass spectrometry is performed in high vacuum, it is essential to preserve the lateral organization of the sample while removing bulk water, and this has been a major barrier for applications to biological systems. Recent applications of imaging mass spectrometry to cell biology, microbial communities, and biosynthetic pathways are summarized briefly, and studies of biological membrane organization are described in greater depth.
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Affiliation(s)
- Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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22
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Legent G, Delaune A, Norris V, Delcorte A, Gibouin D, Lefebvre F, Misevic G, Thellier M, Ripoll C. Method for macromolecular colocalization using atomic recombination in dynamic SIMS. J Phys Chem B 2008; 112:5534-46. [PMID: 18399679 DOI: 10.1021/jp7100489] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Localizing two or more components of assemblies in biological systems requires both continued development of fluorescence techniques and invention of entirely new techniques. Candidates for the latter include dynamic secondary ion mass spectrometry (D-SIMS). The latest generation of D-SIMS, the Cameca NanoSIMS 50, permits the localization of specific, isotopically labeled molecules and macromolecules in sections of biological material with a resolution in the tens of nanometers and with a sensitivity approaching in principle that of a single protein. Here we use two different systems, crystals of glycine and mixtures of proteins, to show that the formation of recombinant CN secondary ions under Cs bombardment can be exploited to create a new colocalization technique. We show experimentally that the formation of the recombinant (13)C(15)N secondary ion between (13)C- and (15)N-labeled macromolecules is indeed an indicator of the distance between the interacting macromolecules and on their shape. We build up a convolution model of the mixing-recombination process in D-SIMS that allows quantitative interpretations of the distance-dependent formation of the recombinant CN. Our results show that macromolecules can be colocalized if they are within 2 nm of one another. We discuss the potential advantages of this new technique for biological applications.
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Affiliation(s)
- G Legent
- Laboratoire Assemblages moléculaires: modélisation, et imagerie SIMS, Faculté des Sciences de l'Université de Rouen, 76821 Mont Saint Aignan Cedex, France
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23
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Harton SE, Zhu Z, Stevie FA, Aoyama Y, Ade H. Carbon-13 Labeling for Quantitative Analysis of Molecular Movement in Heterogeneous Organic Materials Using Secondary Ion Mass Spectrometry. Anal Chem 2007; 79:5358-63. [PMID: 17555299 DOI: 10.1021/ac070437q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Secondary ion mass spectrometry (SIMS) is used to probe the movement of macromolecules in heterogeneous organic systems. Using 13C tracer labeling and two model systems, polystyrene/poly(2-vinylpyridine) (PS/P2VP) and polystyrene/poly(4-bromostyrene) (PS/P4BrS), the diffusion of 13C-labeled PS has been investigated near the respective heterogeneous interfaces using a CAMECA-IMS-6F magnetic sector mass spectrometer. 13C labeling has been shown to greatly minimize matrix effects (i.e., changes in secondary ion yields due to changing chemical environment) in heterogeneous systems. P2VP is a nitrogen-rich polymer (C7H7N monomer composition), making it an excellent model polymer for exploration of this technique for potential future use in biological applications, and probing the PS/P4BrS interface demonstrates the versatility of this technique for analysis of various heteroatom-containing materials. Results confirm that the 13C-labeling method does indeed allow for quantitative analysis of molecular movement in heterogeneous organic systems containing matrix-enhancing heteroatoms such as nitrogen. Therefore, extension of this method to more complicated biological systems involving multiple heteroatoms (oxygen, nitrogen, etc.), layers, and heterogeneous interfaces, as well as two- and three-dimensional profiling and imaging using SIMS, can be envisaged.
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Affiliation(s)
- Shane E Harton
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA.
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24
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:547-558. [PMID: 17385794 DOI: 10.1002/jms.1073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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