Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data

Abstract

Time of flight secondary ion mass spectrometry (ToF SIMS) is one of the most powerful characterization tools allowing imaging of the chemical properties of various systems and materials. It allows precise studies of the chemical composition with sub-100-nm lateral and nanometer depth spatial resolution. However, comprehensive interpretation of ToF SIMS results is challengeable, because of the data volume and its multidimensionality. Furthermore, investigation of the samples with pronounced topographical features are complicated by the spectral shift. In this work we developed approach for the comprehensive ToF SIMS data interpretation based on the data analytics and automated extraction of the sample topography based on time of flight shift. We further applied this approach to investigate correlation between biological function and chemical composition in Arabidopsis roots.

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1];  [2]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
+ Show Author Affiliations
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1412060
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Ievlev, Anton V., Belianinov, Alexei, Jesse, Stephen, Allison, David P., Doktycz, Mitchel John, Retterer, Scott T., Kalinin, Sergei V., and Ovchinnikova, Olga S. Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data. United States: N. p., 2017. Web. doi:10.1038/s41598-017-17049-y.
Copy to clipboard
Ievlev, Anton V., Belianinov, Alexei, Jesse, Stephen, Allison, David P., Doktycz, Mitchel John, Retterer, Scott T., Kalinin, Sergei V., & Ovchinnikova, Olga S. Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data. United States. https://doi.org/10.1038/s41598-017-17049-y
Copy to clipboard
Ievlev, Anton V., Belianinov, Alexei, Jesse, Stephen, Allison, David P., Doktycz, Mitchel John, Retterer, Scott T., Kalinin, Sergei V., and Ovchinnikova, Olga S. Wed . "Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data". United States. https://doi.org/10.1038/s41598-017-17049-y. https://www.osti.gov/servlets/purl/1412060.
Copy to clipboard
@article{osti_1412060,
title = {Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data},
author = {Ievlev, Anton V. and Belianinov, Alexei and Jesse, Stephen and Allison, David P. and Doktycz, Mitchel John and Retterer, Scott T. and Kalinin, Sergei V. and Ovchinnikova, Olga S.},
abstractNote = {Time of flight secondary ion mass spectrometry (ToF SIMS) is one of the most powerful characterization tools allowing imaging of the chemical properties of various systems and materials. It allows precise studies of the chemical composition with sub-100-nm lateral and nanometer depth spatial resolution. However, comprehensive interpretation of ToF SIMS results is challengeable, because of the data volume and its multidimensionality. Furthermore, investigation of the samples with pronounced topographical features are complicated by the spectral shift. In this work we developed approach for the comprehensive ToF SIMS data interpretation based on the data analytics and automated extraction of the sample topography based on time of flight shift. We further applied this approach to investigate correlation between biological function and chemical composition in Arabidopsis roots.},
doi = {10.1038/s41598-017-17049-y},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {Wed Dec 06 00:00:00 EST 2017},
month = {Wed Dec 06 00:00:00 EST 2017}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1038/s41598-017-17049-y
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 15 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Quantitative Analysis of the Local Phase Transitions Induced by Laser Heating
journal, October 2015

  • Ievlev, Anton V.; Susner, Michael A.; McGuire, Michael A.
  • ACS Nano, Vol. 9, Issue 12
  • DOI: 10.1021/acsnano.5b05818

Time-of-flight secondary ion mass spectrometry: techniques and applications for the characterization of biomaterial surfaces
journal, September 2003

Cluster secondary ion mass spectrometry: an insight into “super-efficient” collision cascades
journal, June 2004

  • Rickman, Richard D.; Verkhoturov, Stanislav V.; Schweikert, Emile A.
  • Applied Surface Science, Vol. 231-232
  • DOI: 10.1016/j.apsusc.2004.03.026

Principal Component Analysis of TOF-SIMS Images of Organic Monolayers
journal, November 2002

  • Biesinger, Mark C.; Paepegaey, Pierre-Yves; McIntyre, N. Stewart
  • Analytical Chemistry, Vol. 74, Issue 22
  • DOI: 10.1021/ac020311n

Principal component and spatial correlation analysis of spectroscopic-imaging data in scanning probe microscopy
journal, February 2009

Analysis of the failure mechanism for a stable organic photovoltaic during 10 000 h of testing
journal, January 2007

  • Krebs, Frederik C.; Norrman, Kion
  • Progress in Photovoltaics: Research and Applications, Vol. 15, Issue 8
  • DOI: 10.1002/pip.794

Postacquisition Mass Resolution Improvement in Time-of-Flight Secondary Ion Mass Spectrometry
journal, January 2012

  • Pachuta, Steven J.; Vlasak, Paul R.
  • Analytical Chemistry, Vol. 84, Issue 3
  • DOI: 10.1021/ac203229m

Graphene engineering by neon ion beams
journal, February 2016

Atomic and Molecular Imaging at the Single-Cell Level with TOF-SIMS
journal, July 1997

  • Colliver, Thomas L.; Brummel, Christopher L.; Pacholski, Michaeleen L.
  • Analytical Chemistry, Vol. 69, Issue 13
  • DOI: 10.1021/ac9701748

Organic ion imaging of biological tissue with secondary ion mass spectrometry and matrix-assisted laser desorption/ionization
journal, January 2001

  • Todd, Peter J.; Schaaff, T. Gregory; Chaurand, Pierre
  • Journal of Mass Spectrometry, Vol. 36, Issue 4
  • DOI: 10.1002/jms.153

Transport of 13C-oleate in adipocytes measured using multi imaging mass spectrometry
journal, November 2004

  • Kleinfeld, Alan M.; Kampf, J. Patrick; Lechene, Claude
  • Journal of the American Society for Mass Spectrometry, Vol. 15, Issue 11, p. 1572-1580
  • DOI: 10.1016/j.jasms.2004.07.010

Imaging with Mass Spectrometry
journal, October 1999

  • Pacholski, M. L.; Winograd, N.
  • Chemical Reviews, Vol. 99, Issue 10
  • DOI: 10.1021/cr980137w

Using Matrix Peaks To Map Topography:  Increased Mass Resolution and Enhanced Sensitivity in Chemical Imaging
journal, September 2003

  • McDonnell, Liam A.; Mize, Todd H.; Luxembourg, Stefan L.
  • Analytical Chemistry, Vol. 75, Issue 17
  • DOI: 10.1021/ac034401j

Imaging mass spectrometry
journal, January 2007

  • McDonnell, Liam A.; Heeren, Ron M. A.
  • Mass Spectrometry Reviews, Vol. 26, Issue 4
  • DOI: 10.1002/mas.20124

Multivariate Statistical Analysis of Three-Spatial-Dimension TOF-SIMS Raw Data Sets
journal, October 2007

  • Smentkowski, V. S.; Ostrowski, S. G.; Braunstein, E.
  • Analytical Chemistry, Vol. 79, Issue 20
  • DOI: 10.1021/ac071019o

Mapping chemical and bonding information using multivariate analysis of electron energy-loss spectrum images
journal, October 2006

Mass Spectrometric Imaging of Lipids in Brain Tissue
journal, August 2004

  • Sjövall, Peter; Lausmaa, Jukka; Johansson, Björn
  • Analytical Chemistry, Vol. 76, Issue 15
  • DOI: 10.1021/ac049389p

Correction of topographic artefacts of ToF-SIMS element distributions: Correction of topographic artefacts of ToF-SIMS element distributions
journal, July 2012

  • Ziegler, Georg; Hutter, Herbert
  • Surface and Interface Analysis, Vol. 45, Issue 1
  • DOI: 10.1002/sia.5127

Full information acquisition in piezoresponse force microscopy
journal, December 2015

  • Somnath, Suhas; Belianinov, Alexei; Kalinin, Sergei V.
  • Applied Physics Letters, Vol. 107, Issue 26
  • DOI: 10.1063/1.4938482

Multivariate analysis of ToF-SIMS data for biological applications
journal, August 2009

  • Park, Ji-Won; Min, Hyegeun; Kim, Young-Pil
  • Surface and Interface Analysis, Vol. 41, Issue 8
  • DOI: 10.1002/sia.3049

In pursuit of resolution in time-of-flight mass spectrometry: A historical perspective: IN PURSUIT OF RESOLUTION IN TOF MASS SPECTROMETRY
journal, May 2015

  • Radionova, Anna; Filippov, Igor; Derrick, Peter J.
  • Mass Spectrometry Reviews, Vol. 35, Issue 6
  • DOI: 10.1002/mas.21470

Multivariate analysis of extremely large ToFSIMS imaging datasets by a rapid PCA method: Extremely large ToFSIMS imaging by rapid PCA
journal, August 2015

  • Cumpson, Peter J.; Sano, Naoko; Fletcher, Ian W.
  • Surface and Interface Analysis, Vol. 47, Issue 10
  • DOI: 10.1002/sia.5800

Multi-component analysis: blind extraction of pure components mass spectra using sparse component analysis
journal, September 2009

  • Kopriva, Ivica; Jerić, Ivanka
  • Journal of Mass Spectrometry, Vol. 44, Issue 9
  • DOI: 10.1002/jms.1627

BEAM: A Computational Workflow System for Managing and Modeling Material Characterization Data in HPC Environments
journal, January 2016

Multivariate Analysis of ToF-SIMS Data from Multicomponent Systems: The Why, When, and How
journal, December 2012

Organosulfate Formation in Biogenic Secondary Organic Aerosol
journal, September 2008

  • Surratt, Jason D.; Gómez-González, Yadian; Chan, Arthur W. H.
  • The Journal of Physical Chemistry A, Vol. 112, Issue 36
  • DOI: 10.1021/jp802310p

Local coexistence of VO2 phases revealed by deep data analysis
journal, July 2016

  • Strelcov, Evgheni; Ievlev, Anton; Belianinov, Alex
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep29216

Organic ion imaging of biological tissue with secondary ion mass spectrometry and matrix-assisted laser desorption/ionization
journal, January 2001

  • Todd, Peter J.; Schaaff, T. Gregory; Chaurand, Pierre
  • Journal of Mass Spectrometry, Vol. 36, Issue 4
  • DOI: 10.1002/jms.153

Multi-component analysis: blind extraction of pure components mass spectra using sparse component analysis
journal, September 2009

  • Kopriva, Ivica; Jerić, Ivanka
  • Journal of Mass Spectrometry, Vol. 44, Issue 9
  • DOI: 10.1002/jms.1627

In pursuit of resolution in time-of-flight mass spectrometry: A historical perspective: IN PURSUIT OF RESOLUTION IN TOF MASS SPECTROMETRY
journal, May 2015

  • Radionova, Anna; Filippov, Igor; Derrick, Peter J.
  • Mass Spectrometry Reviews, Vol. 35, Issue 6
  • DOI: 10.1002/mas.21470

Analysis of the failure mechanism for a stable organic photovoltaic during 10 000 h of testing
journal, January 2007

  • Krebs, Frederik C.; Norrman, Kion
  • Progress in Photovoltaics: Research and Applications, Vol. 15, Issue 8
  • DOI: 10.1002/pip.794

Multivariate analysis of ToF-SIMS data for biological applications
journal, August 2009

  • Park, Ji-Won; Min, Hyegeun; Kim, Young-Pil
  • Surface and Interface Analysis, Vol. 41, Issue 8
  • DOI: 10.1002/sia.3049

Multivariate analysis of extremely large ToFSIMS imaging datasets by a rapid PCA method: Extremely large ToFSIMS imaging by rapid PCA
journal, August 2015

  • Cumpson, Peter J.; Sano, Naoko; Fletcher, Ian W.
  • Surface and Interface Analysis, Vol. 47, Issue 10
  • DOI: 10.1002/sia.5800

High-resolution chemical imaging with scanning ion probe SIMS
journal, May 1995

  • Chabala, J. M.; Soni, K. K.; Li, J.
  • International Journal of Mass Spectrometry and Ion Processes, Vol. 143
  • DOI: 10.1016/0168-1176(94)04119-r

Scanning secondary ion analytical microscopy with parallel detection
journal, January 1992

Cluster secondary ion mass spectrometry: an insight into “super-efficient” collision cascades
journal, June 2004

  • Rickman, Richard D.; Verkhoturov, Stanislav V.; Schweikert, Emile A.
  • Applied Surface Science, Vol. 231-232
  • DOI: 10.1016/j.apsusc.2004.03.026

BEAM: A Computational Workflow System for Managing and Modeling Material Characterization Data in HPC Environments
journal, January 2016

Mapping chemical and bonding information using multivariate analysis of electron energy-loss spectrum images
journal, October 2006

Inferring ejection distances and a surface energy profile in keV particle bombardment experiments
journal, November 2000

  • Delcorte, A.; Segda, B. G.; Garrison, B. J.
  • Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Vol. 171, Issue 3
  • DOI: 10.1016/s0168-583x(00)00263-9

Using Matrix Peaks To Map Topography:  Increased Mass Resolution and Enhanced Sensitivity in Chemical Imaging
journal, September 2003

  • McDonnell, Liam A.; Mize, Todd H.; Luxembourg, Stefan L.
  • Analytical Chemistry, Vol. 75, Issue 17
  • DOI: 10.1021/ac034401j

Quantitative Analysis of the Local Phase Transitions Induced by Laser Heating
journal, October 2015

  • Ievlev, Anton V.; Susner, Michael A.; McGuire, Michael A.
  • ACS Nano, Vol. 9, Issue 12
  • DOI: 10.1021/acsnano.5b05818

Imaging with Mass Spectrometry
journal, October 1999

  • Pacholski, M. L.; Winograd, N.
  • Chemical Reviews, Vol. 99, Issue 10
  • DOI: 10.1021/cr980137w

Organosulfate Formation in Biogenic Secondary Organic Aerosol
journal, September 2008

  • Surratt, Jason D.; Gómez-González, Yadian; Chan, Arthur W. H.
  • The Journal of Physical Chemistry A, Vol. 112, Issue 36
  • DOI: 10.1021/jp802310p

Data encoding based on the shape of the ferroelectric domains produced by using a scanning probe microscope tip
journal, January 2015

  • Ievlev, Anton V.; Kalinin, Sergei V.
  • Nanoscale, Vol. 7, Issue 25
  • DOI: 10.1039/c5nr02443a

Full information acquisition in piezoresponse force microscopy
journal, December 2015

  • Somnath, Suhas; Belianinov, Alexei; Kalinin, Sergei V.
  • Applied Physics Letters, Vol. 107, Issue 26
  • DOI: 10.1063/1.4938482

Principal component and spatial correlation analysis of spectroscopic-imaging data in scanning probe microscopy
journal, February 2009

    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Self‐Assembled Room Temperature Multiferroic BiFeO 3 ‐LiFe 5 O 8 Nanocomposites
    journal, October 2019

    • Sharma, Yogesh; Agarwal, Radhe; Collins, Liam
    • Advanced Functional Materials, Vol. 30, Issue 3
    • DOI: 10.1002/adfm.201906849

    Application of pan-sharpening algorithm for correlative multimodal imaging using AFM-IR
    journal, April 2019

    • Borodinov, Nikolay; Bilkey, Natasha; Foston, Marcus
    • npj Computational Materials, Vol. 5, Issue 1
    • DOI: 10.1038/s41524-019-0186-z

    An artificial intelligence atomic force microscope enabled by machine learning
    journal, January 2018

    • Huang, Boyuan; Li, Zhenghao; Li, Jiangyu
    • Nanoscale, Vol. 10, Issue 45
    • DOI: 10.1039/c8nr06734a

    Rapid evaluation of immobilized immunoglobulins using automated mass-segmented ToF-SIMS
    journal, November 2019

    • Madiona, Robert M. T.; Welch, Nicholas G.; Muir, Benjamin W.
    • Biointerphases, Vol. 14, Issue 6
    • DOI: 10.1063/1.5121450

    Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform
    journal, April 2018

    • Kannan, R.; Ievlev, A. V.; Laanait, N.
    • Advanced Structural and Chemical Imaging, Vol. 4, Issue 1
    • DOI: 10.1186/s40679-018-0055-8

    Artificial Intelligent Atomic Force Microscope Enabled by Machine Learning
    text, January 2018

      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: