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LipidCreator workbench to probe the lipidomic landscape

Author

Listed:
  • Bing Peng

    (Leibniz-Institut für Analytische Wissenschaften – ISAS - e.V.
    Karolinska Institutet, Karolinska University Hospital)

  • Dominik Kopczynski

    (Leibniz-Institut für Analytische Wissenschaften – ISAS - e.V.)

  • Brian S. Pratt

    (University of Washington, Department of Genome Sciences)

  • Christer S. Ejsing

    (University of Southern Denmark, DK-
    European Molecular Biology Laboratory)

  • Bo Burla

    (Life Sciences Institute, National University of Singapore)

  • Martin Hermansson

    (University of Southern Denmark, DK-
    Wihuri Research Institute)

  • Peter Imre Benke

    (Yong Loo Lin School of Medicine, National University of Singapore)

  • Sock Hwee Tan

    (National University Hospital
    National University of Singapore)

  • Mark Y. Chan

    (National University Hospital
    National University of Singapore
    National University Health System)

  • Federico Torta

    (Yong Loo Lin School of Medicine, National University of Singapore)

  • Dominik Schwudke

    (Research Center Borstel, Leibniz Lung Center
    German Center for Infection Research (DZIF)
    Airway Research Center North Member of the German Center for Lung Research (DZL))

  • Sven W. Meckelmann

    (University of Duisburg-Essen)

  • Cristina Coman

    (Leibniz-Institut für Analytische Wissenschaften – ISAS - e.V.
    University of Vienna)

  • Oliver J. Schmitz

    (University of Duisburg-Essen)

  • Brendan MacLean

    (University of Washington, Department of Genome Sciences)

  • Mailin-Christin Manke

    (University of Tübingen)

  • Oliver Borst

    (University of Tübingen)

  • Markus R. Wenk

    (Life Sciences Institute, National University of Singapore
    Yong Loo Lin School of Medicine, National University of Singapore)

  • Nils Hoffmann

    (Leibniz-Institut für Analytische Wissenschaften – ISAS - e.V.)

  • Robert Ahrends

    (Leibniz-Institut für Analytische Wissenschaften – ISAS - e.V.
    University of Vienna)

Abstract

Mass spectrometry (MS)-based targeted lipidomics enables the robust quantification of selected lipids under various biological conditions but comprehensive software tools to support such analyses are lacking. Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.

Suggested Citation

  • Bing Peng & Dominik Kopczynski & Brian S. Pratt & Christer S. Ejsing & Bo Burla & Martin Hermansson & Peter Imre Benke & Sock Hwee Tan & Mark Y. Chan & Federico Torta & Dominik Schwudke & Sven W. Meck, 2020. "LipidCreator workbench to probe the lipidomic landscape," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15960-z
    DOI: 10.1038/s41467-020-15960-z
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