IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v9y2018i1d10.1038_s41467-018-06082-8.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-018-06082-8
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-018-06082-8?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    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.
    3. Donghui Yan & Muqing Zhou & Abhinav Adduri & Yihao Zhuang & Mustafa Guler & Sitong Liu & Hyonyoung Shin & Torin Kovach & Gloria Oh & Xiao Liu & Yuting Deng & Xiaofeng Wang & Liu Cao & David H. Sherman, 2024. "Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06082-8. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.