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Dereplication of microbial metabolites through database search of mass spectra

Author

Listed:
  • Hosein Mohimani

    (Carnegie Mellon University
    University of California, San Diego)

  • Alexey Gurevich

    (St. Petersburg State University)

  • Alexander Shlemov

    (St. Petersburg State University)

  • Alla Mikheenko

    (St. Petersburg State University)

  • Anton Korobeynikov

    (St. Petersburg State University
    St. Petersburg State University)

  • Liu Cao

    (Carnegie Mellon University)

  • Egor Shcherbin

    (National Research University Higher School of Economics)

  • Louis-Felix Nothias

    (University of California, San Diego)

  • Pieter C. Dorrestein

    (University of California, San Diego
    University of California, San Diego)

  • Pavel A. Pevzner

    (University of California, San Diego
    St. Petersburg State University)

Abstract

Natural products have traditionally been rich sources for drug discovery. In order to clear the road toward the discovery of unknown natural products, biologists need dereplication strategies that identify known ones. Here we report DEREPLICATOR+, an algorithm that improves on the previous approaches for identifying peptidic natural products, and extends them for identification of polyketides, terpenes, benzenoids, alkaloids, flavonoids, and other classes of natural products. We show that DEREPLICATOR+ can search all spectra in the recently launched Global Natural Products Social molecular network and identify an order of magnitude more natural products than previous dereplication efforts. We further demonstrate that DEREPLICATOR+ enables cross-validation of genome-mining and peptidogenomics/glycogenomics results.

Suggested Citation

  • Hosein Mohimani & Alexey Gurevich & Alexander Shlemov & Alla Mikheenko & Anton Korobeynikov & Liu Cao & Egor Shcherbin & Louis-Felix Nothias & Pieter C. Dorrestein & Pavel A. Pevzner, 2018. "Dereplication of microbial metabolites through database search of mass spectra," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06082-8
    DOI: 10.1038/s41467-018-06082-8
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    Cited by:

    1. Nicholas J. Morehouse & Trevor N. Clark & Emily J. McMann & Jeffrey A. Santen & F. P. Jake Haeckl & Christopher A. Gray & Roger G. Linington, 2023. "Annotation of natural product compound families using molecular networking topology and structural similarity fingerprinting," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    2. Yi-Yuan Lee & Mustafa Guler & Desnor N. Chigumba & Shen Wang & Neel Mittal & Cameron Miller & Benjamin Krummenacher & Haodong Liu & Liu Cao & Aditya Kannan & Keshav Narayan & Samuel T. Slocum & Bryan , 2023. "HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search," Nature Communications, Nature, vol. 14(1), pages 1-17, December.

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