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ICBM-OCEAN: Processing Ultrahigh-Resolution Mass Spectrometry Data of Complex Molecular Mixtures

  • Julian Merder*
    Julian Merder
    Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
    *Email: [email protected] (J.M.).
  • Jan A. Freund
    Jan A. Freund
    Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
  • Ulrike Feudel
    Ulrike Feudel
    Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
  • Christian T. Hansen
    Christian T. Hansen
    Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
  • Jeffrey A. Hawkes
    Jeffrey A. Hawkes
    Department of Chemistry−BMC, Uppsala University, Husargatan 3 (D5), 752 37 Uppsala, Sweden
  • Benjamin Jacob
    Benjamin Jacob
    Helmholtz-Centre Geesthacht, Centre for Materials and Coastal Research, Max-Planck-Straße 1, 21502 Geesthacht, Germany
  • Katrin Klaproth
    Katrin Klaproth
    Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
  • Jutta Niggemann
    Jutta Niggemann
    Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
  • Beatriz E. Noriega-Ortega
    Beatriz E. Noriega-Ortega
    Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
  • Helena Osterholz
    Helena Osterholz
    Leibniz Institute for Baltic Sea Research Warnemuende, Seestraße 15, 18119 Rostock, Germany
  • Pamela E. Rossel
    Pamela E. Rossel
    Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
  • Michael Seidel
    Michael Seidel
    Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
  • Gabriel Singer
    Gabriel Singer
    Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
    Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
  • Aron Stubbins
    Aron Stubbins
    Departments of Marine and Environmental Science, Chemistry and Chemical Biology, and Civil and Environmental Engineering, Northeastern University, 102 HT, Boston, Massachusetts 02115, United States
  • Hannelore Waska
    Hannelore Waska
    Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
  • , and 
  • Thorsten Dittmar*
    Thorsten Dittmar
    Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
    *Email: [email protected] (T.D.).
Cite this: Anal. Chem. 2020, 92, 10, 6832–6838
Publication Date (Web):April 16, 2020
https://doi.org/10.1021/acs.analchem.9b05659
Copyright © 2020 American Chemical Society

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    Supporting Info (1)»

    Abstract

    Abstract Image

    Untargeted molecular analyses of complex mixtures are relevant for many fields of research, including geochemistry, pharmacology, and medicine. Ultrahigh-resolution mass spectrometry is one of the most powerful tools in this context. The availability of open scripts and online tools for specific data processing steps such as noise removal or molecular formula assignment is growing, but an integrative tool where all crucial steps are reproducibly evaluated and documented is lacking. We developed a novel, server-based tool (ICBM-OCEAN, Institute for Chemistry and Biology of the Marine Environment, Oldenburg–complex molecular mixtures, evaluation & analysis) that integrates published and novel approaches for standardized processing of ultrahigh-resolution mass spectrometry data of complex molecular mixtures. Different from published approaches, we offer diagnostic and validation tools for all relevant steps. Among other features, we included objective and reproducible reduction of noise and systematic errors, spectra recalibration and alignment, and identification of likeliest molecular formulas. With 15 chemical elements, the tool offers high flexibility in formula attribution. Alignment of mass spectra among different samples prior to molecular formula assignment improves mass error and facilitates molecular formula confirmation with the help of isotopologues. The online tool and the detailed instruction manual are freely accessible at www.icbm.de/icbm-ocean.

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.analchem.9b05659.

    • Major features of ICBM-OCEAN; common chemical parameters in DOM geochemistry and parameters used in ICBM-OCEAN (PDF)

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    62. Alexandra L. Klodt, Marley Adamek, Monica Dibley, Sergey A. Nizkorodov, Rachel E. O'Brien. Effects of the sample matrix on the photobleaching and photodegradation of toluene-derived secondary organic aerosol compounds. Atmospheric Chemistry and Physics 2022, 22 (15) , 10155-10171. https://doi.org/10.5194/acp-22-10155-2022
    63. Julian Merder, Heidelinde Röder, Thorsten Dittmar, Ulrike Feudel, Jan A. Freund, Gunnar Gerdts, Alexandra Kraberg, Jutta Niggemann. Dissolved organic compounds with synchronous dynamics share chemical properties and origin. Limnology and Oceanography 2021, 66 (11) , 4001-4016. https://doi.org/10.1002/lno.11938
    64. Teresa S. Catalá, Spencer Shorte, Thorsten Dittmar. Marine dissolved organic matter: a vast and unexplored molecular space. Applied Microbiology and Biotechnology 2021, 105 (19) , 7225-7239. https://doi.org/10.1007/s00253-021-11489-3
    65. Thorsten Dittmar, Sinikka T. Lennartz, Hagen Buck-Wiese, Dennis A. Hansell, Chiara Santinelli, Chiara Vanni, Bernd Blasius, Jan-Hendrik Hehemann. Enigmatic persistence of dissolved organic matter in the ocean. Nature Reviews Earth & Environment 2021, 2 (8) , 570-583. https://doi.org/10.1038/s43017-021-00183-7
    66. Julius Degenhardt, Julian Merder, Benedikt Heyerhoff, Heike Simon, Bert Engelen, Hannelore Waska. Cross-Shore and Depth Zonations in Bacterial Diversity Are Linked to Age and Source of Dissolved Organic Matter across the Intertidal Area of a Sandy Beach. Microorganisms 2021, 9 (8) , 1720. https://doi.org/10.3390/microorganisms9081720
    67. Gonzalo V. Gomez-Saez, Thorsten Dittmar, Moritz Holtappels, Anika M. Pohlabeln, Anna Lichtschlag, Bernhard Schnetger, Antje Boetius, Jutta Niggemann. Sulfurization of dissolved organic matter in the anoxic water column of the Black Sea. Science Advances 2021, 7 (25) https://doi.org/10.1126/sciadv.abf6199
    68. Stephan L. Seibert, Michael E. Böttcher, Hannelore Waska, Tobias Holt, Thomas Pollmann, Janek Greskowiak, Gudrun Massmann. Hydrogeochemistry of near-surface groundwater on a developing barrier island (Spiekeroog, Germany): The role of inundation, season and vegetation. Journal of Hydrology 2021, 597 , 126139. https://doi.org/10.1016/j.jhydrol.2021.126139
    69. Helena Osterholz, David P.A. Kilgour, Dominik Sebastian Storey, Gaute Lavik, Timothy G. Ferdelman, Jutta Niggemann, Thorsten Dittmar. Accumulation of DOC in the South Pacific Subtropical Gyre from a molecular perspective. Marine Chemistry 2021, 231 , 103955. https://doi.org/10.1016/j.marchem.2021.103955
    70. Hannelore Waska, Heike Simon, Soeren Ahmerkamp, Janek Greskowiak, Janis Ahrens, Stephan L. Seibert, Kai Schwalfenberg, Oliver Zielinski, Thorsten Dittmar. Molecular Traits of Dissolved Organic Matter in the Subterranean Estuary of a High-Energy Beach: Indications of Sources and Sinks. Frontiers in Marine Science 2021, 8 https://doi.org/10.3389/fmars.2021.607083
    71. Erin N MacDonald, Suzanne E Tank, Steven V Kokelj, Duane G Froese, Ryan H S Hutchins. Permafrost-derived dissolved organic matter composition varies across permafrost end-members in the western Canadian Arctic. Environmental Research Letters 2021, 16 (2) , 024036. https://doi.org/10.1088/1748-9326/abd971
    72. Brandon M. Stephens, Keri Opalk, Daniel Petras, Shuting Liu, Jacqueline Comstock, Lihini I. Aluwihare, Dennis A. Hansell, Craig A. Carlson. Organic Matter Composition at Ocean Station Papa Affects Its Bioavailability, Bacterioplankton Growth Efficiency and the Responding Taxa. Frontiers in Marine Science 2020, 7 https://doi.org/10.3389/fmars.2020.590273
    73. Teresa S. Catalá, Pamela E. Rossel, Félix Álvarez-Gómez, Jan Tebben, Félix L. Figueroa, Thorsten Dittmar. Antioxidant Activity and Phenolic Content of Marine Dissolved Organic Matter and Their Relation to Molecular Composition. Frontiers in Marine Science 2020, 7 https://doi.org/10.3389/fmars.2020.603447