Open Access

Nature Communications, volume 9, issue 1, publication number 4035

Dereplication of microbial metabolites through database search of mass spectra

Mohimani Hosein ^{1, 2}

Gurevich Alexey ³

Shlemov Alex ³

Mikheenko Alla ³

Korobeynikov Anton ^{3, 4}

Cao Liu ¹

Shcherbin Egor ⁵

Nothias Louis-Felix ⁶

Dorrestein Pieter C. ^{6, 7}

Pevzner Pavel A. ^{2, 3}

Hide authors affiliations Show authors affiliations: 7 affiliations

Computational Biology Department, School of Computer Sciences, Carnegie Mellon University, Pittsburgh, USA |

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA |

Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia |

⁴

Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia |

⁵

National Research University Higher School of Economics, St. Petersburg, Russia |

⁶

Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA |

⁷

Department of Pharmacology and Pediatrics, University of California, San Diego, La Jolla, USA |

Publication type: Journal Article

Publication date: 2018-10-02

Springer Nature

Journal: Nature Communications

Quartile SCImago

Quartile WOS

Impact factor: 16.6

ISSN: 20411723

DOI: 10.1038/s41467-018-06082-8

Copy DOI

PubMed ID: 30279420

General Chemistry

General Biochemistry, Genetics and Molecular Biology

General Physics and Astronomy

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.New natural products can be identified via mass spectrometry by excluding all known ones from the analysis, a process called dereplication. Here, the authors extend a previously published dereplication algorithm to different classes of secondary metabolites.

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Citations by journals

	2 4 6 8 10 12
Marine Drugs	Marine Drugs, 12, 5.88% Marine Drugs 12 publications, 5.88%
Analytical Chemistry	Analytical Chemistry, 8, 3.92% Analytical Chemistry 8 publications, 3.92%
Journal of Natural Products	Journal of Natural Products, 8, 3.92% Journal of Natural Products 8 publications, 3.92%
Natural Product Reports	Natural Product Reports, 8, 3.92% Natural Product Reports 8 publications, 3.92%
Molecules	Molecules, 7, 3.43% Molecules 7 publications, 3.43%
Frontiers in Microbiology	Frontiers in Microbiology, 6, 2.94% Frontiers in Microbiology 6 publications, 2.94%
Metabolites	Metabolites, 5, 2.45% Metabolites 5 publications, 2.45%
Nature Communications	Nature Communications, 5, 2.45% Nature Communications 5 publications, 2.45%
Scientific Reports	Scientific Reports, 3, 1.47% Scientific Reports 3 publications, 1.47%
Nature Reviews Microbiology	Nature Reviews Microbiology, 3, 1.47% Nature Reviews Microbiology 3 publications, 1.47%
Food Chemistry	Food Chemistry, 3, 1.47% Food Chemistry 3 publications, 1.47%
Chemistry and Biodiversity	Chemistry and Biodiversity, 3, 1.47% Chemistry and Biodiversity 3 publications, 1.47%
RSC Advances	RSC Advances, 3, 1.47% RSC Advances 3 publications, 1.47%
Advances in Experimental Medicine and Biology	Advances in Experimental Medicine and Biology, 3, 1.47% Advances in Experimental Medicine and Biology 3 publications, 1.47%
Antibiotics	Antibiotics, 2, 0.98% Antibiotics 2 publications, 0.98%
Journal of Cheminformatics	Journal of Cheminformatics, 2, 0.98% Journal of Cheminformatics 2 publications, 0.98%
Toxins	Toxins, 2, 0.98% Toxins 2 publications, 0.98%
Frontiers in Plant Science	Frontiers in Plant Science, 2, 0.98% Frontiers in Plant Science 2 publications, 0.98%
Nature Protocols	Nature Protocols, 2, 0.98% Nature Protocols 2 publications, 0.98%
Nature Microbiology	Nature Microbiology, 2, 0.98% Nature Microbiology 2 publications, 0.98%
Synthetic and Systems Biotechnology	Synthetic and Systems Biotechnology, 2, 0.98% Synthetic and Systems Biotechnology 2 publications, 0.98%
ChemBioChem	ChemBioChem, 2, 0.98% ChemBioChem 2 publications, 0.98%
FEMS Microbiology Letters	FEMS Microbiology Letters, 2, 0.98% FEMS Microbiology Letters 2 publications, 0.98%
Journal of Agricultural and Food Chemistry	Journal of Agricultural and Food Chemistry, 2, 0.98% Journal of Agricultural and Food Chemistry 2 publications, 0.98%
mBio	mBio, 2, 0.98% mBio 2 publications, 0.98%
mSystems	mSystems, 2, 0.98% mSystems 2 publications, 0.98%
Applied and Environmental Microbiology	Applied and Environmental Microbiology, 2, 0.98% Applied and Environmental Microbiology 2 publications, 0.98%
PNAS Nexus	PNAS Nexus, 2, 0.98% PNAS Nexus 2 publications, 0.98%
Current Topics in Medicinal Chemistry	Current Topics in Medicinal Chemistry, 1, 0.49% Current Topics in Medicinal Chemistry 1 publication, 0.49%
	2 4 6 8 10 12

Citations by publishers

	5 10 15 20 25 30 35 40
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 36, 17.65% Multidisciplinary Digital Publishing Institute (MDPI) 36 publications, 17.65%
Springer Nature	Springer Nature, 32, 15.69% Springer Nature 32 publications, 15.69%
American Chemical Society (ACS)	American Chemical Society (ACS), 23, 11.27% American Chemical Society (ACS) 23 publications, 11.27%
Elsevier	Elsevier, 21, 10.29% Elsevier 21 publications, 10.29%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 13, 6.37% Royal Society of Chemistry (RSC) 13 publications, 6.37%
Frontiers Media S.A.	Frontiers Media S.A., 10, 4.9% Frontiers Media S.A. 10 publications, 4.9%
Wiley	Wiley, 8, 3.92% Wiley 8 publications, 3.92%
American Society for Microbiology	American Society for Microbiology, 7, 3.43% American Society for Microbiology 7 publications, 3.43%
Oxford University Press	Oxford University Press, 6, 2.94% Oxford University Press 6 publications, 2.94%
Portland Press	Portland Press, 2, 0.98% Portland Press 2 publications, 0.98%
KeAi Communications Co.	KeAi Communications Co., 2, 0.98% KeAi Communications Co. 2 publications, 0.98%
Taylor & Francis	Taylor & Francis, 2, 0.98% Taylor & Francis 2 publications, 0.98%
Bentham Science	Bentham Science, 1, 0.49% Bentham Science 1 publication, 0.49%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 1, 0.49% Public Library of Science (PLoS) 1 publication, 0.49%
Thieme	Thieme, 1, 0.49% Thieme 1 publication, 0.49%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 1, 0.49% American Association for the Advancement of Science (AAAS) 1 publication, 0.49%
	5 10 15 20 25 30 35 40

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Mohimani H. et al. Dereplication of microbial metabolites through database search of mass spectra // Nature Communications. 2018. Vol. 9. No. 1. 4035

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Mohimani H., Gurevich A., Shlemov A., Mikheenko A., Korobeynikov A., Cao L., Shcherbin E., Nothias L., Dorrestein P. C., Pevzner P. A. Dereplication of microbial metabolites through database search of mass spectra // Nature Communications. 2018. Vol. 9. No. 1. 4035

RIS |

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RIS Copy

TY - JOUR

DO - 10.1038/s41467-018-06082-8

UR - https://doi.org/10.1038%2Fs41467-018-06082-8

TI - Dereplication of microbial metabolites through database search of mass spectra

T2 - Nature Communications

AU - Mohimani, Hosein

AU - Gurevich, Alexey

AU - Shlemov, Alex

AU - Mikheenko, Alla

AU - Korobeynikov, Anton

AU - Cao, Liu

AU - Shcherbin, Egor

AU - Nothias, Louis-Felix

AU - Dorrestein, Pieter C.

AU - Pevzner, Pavel A.

PY - 2018

DA - 2018/10/02 00:00:00

PB - Springer Nature

IS - 1

VL - 9

PMID - 30279420

SN - 2041-1723

ER -

BibTex

Cite this

BibTex Copy

@article{2018_Mohimani,

author = {Hosein Mohimani and Alexey Gurevich and Alex Shlemov and Alla Mikheenko and Anton Korobeynikov and Liu Cao and Egor Shcherbin and Louis-Felix Nothias and Pieter C. Dorrestein and Pavel A. Pevzner},

title = {Dereplication of microbial metabolites through database search of mass spectra},

journal = {Nature Communications},

year = {2018},

volume = {9},

publisher = {Springer Nature},

month = {oct},

url = {https://doi.org/10.1038%2Fs41467-018-06082-8},

number = {1},

doi = {10.1038/s41467-018-06082-8}

}

Found error?

Publisher

Springer Nature

Journal

Nature Communications

Quartile SCImago

Quartile WOS

Impact factor

16.6

ISSN

20411723 (Print)