De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments

Bahar Behsaz, Hosein Mohimani, Alexey Gurevich, Andrey Prjibelski, Mark F. Fisher, Fernando Vargas, Larry Smarr, Pieter C. Dorrestein, Joshua S Mylne, Pavel A. Pevzner

Результат исследований: Научные публикации в периодических изданияхстатья

Выдержка

Cyclic and branch cyclic peptides (cyclopeptides) represent a class of bioactive natural products that include many antibiotics and anti-tumor compounds. Despite the recent advances in metabolomics analysis, still little is known about the cyclopeptides in the human gut and their possible interactions due to a lack of computational analysis pipelines that are applicable to such compounds. Here, we introduce CycloNovo, an algorithm for automated de novo cyclopeptide analysis and sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms, to identify cyclopeptides in spectral datasets. CycloNovo reconstructed 32 previously unreported cyclopeptides (to the best of our knowledge) in the human gut and reported over a hundred cyclopeptides in other environments represented by various spectra on Global Natural Products Social Molecular Network (GNPS).
Язык оригиналаанглийский
ЖурналCell Systems
DOI
СостояниеЭлектронная публикация перед печатью - 18 дек 2019

Отпечаток

Cyclic Peptides
Peptides
Biological Products
Metabolomics
DNA Sequence Analysis
Social Support
Anti-Bacterial Agents

Цитировать

Behsaz, B., Mohimani, H., Gurevich, A., Prjibelski, A., Fisher, M. F., Vargas, F., ... Pevzner, P. A. (2019). De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Cell Systems. https://doi.org/10.1016/j.cels.2019.11.007
Behsaz, Bahar ; Mohimani, Hosein ; Gurevich, Alexey ; Prjibelski, Andrey ; Fisher, Mark F. ; Vargas, Fernando ; Smarr, Larry ; Dorrestein, Pieter C. ; Mylne, Joshua S ; Pevzner, Pavel A. . / De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. В: Cell Systems. 2019.
@article{744a02521c8743adae128d7a16b42d94,
title = "De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments",
abstract = "Cyclic and branch cyclic peptides (cyclopeptides) represent a class of bioactive natural products that include many antibiotics and anti-tumor compounds. Despite the recent advances in metabolomics analysis, still little is known about the cyclopeptides in the human gut and their possible interactions due to a lack of computational analysis pipelines that are applicable to such compounds. Here, we introduce CycloNovo, an algorithm for automated de novo cyclopeptide analysis and sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms, to identify cyclopeptides in spectral datasets. CycloNovo reconstructed 32 previously unreported cyclopeptides (to the best of our knowledge) in the human gut and reported over a hundred cyclopeptides in other environments represented by various spectra on Global Natural Products Social Molecular Network (GNPS).",
keywords = "Natural products, peptide sequencing, Mass Spectrometry, Metabolomics, Microbiome, antimicrobial peptides",
author = "Bahar Behsaz and Hosein Mohimani and Alexey Gurevich and Andrey Prjibelski and Fisher, {Mark F.} and Fernando Vargas and Larry Smarr and Dorrestein, {Pieter C.} and Mylne, {Joshua S} and Pevzner, {Pavel A.}",
year = "2019",
month = "12",
day = "18",
doi = "10.1016/j.cels.2019.11.007",
language = "English",
journal = "Cell Systems",
issn = "2405-4712",
publisher = "Cell Press",

}

Behsaz, B, Mohimani, H, Gurevich, A, Prjibelski, A, Fisher, MF, Vargas, F, Smarr, L, Dorrestein, PC, Mylne, JS & Pevzner, PA 2019, 'De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments', Cell Systems. https://doi.org/10.1016/j.cels.2019.11.007

De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. / Behsaz, Bahar; Mohimani, Hosein; Gurevich, Alexey ; Prjibelski, Andrey ; Fisher, Mark F.; Vargas, Fernando ; Smarr, Larry; Dorrestein, Pieter C.; Mylne, Joshua S; Pevzner, Pavel A. .

В: Cell Systems, 18.12.2019.

Результат исследований: Научные публикации в периодических изданияхстатья

TY - JOUR

T1 - De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments

AU - Behsaz, Bahar

AU - Mohimani, Hosein

AU - Gurevich, Alexey

AU - Prjibelski, Andrey

AU - Fisher, Mark F.

AU - Vargas, Fernando

AU - Smarr, Larry

AU - Dorrestein, Pieter C.

AU - Mylne, Joshua S

AU - Pevzner, Pavel A.

PY - 2019/12/18

Y1 - 2019/12/18

N2 - Cyclic and branch cyclic peptides (cyclopeptides) represent a class of bioactive natural products that include many antibiotics and anti-tumor compounds. Despite the recent advances in metabolomics analysis, still little is known about the cyclopeptides in the human gut and their possible interactions due to a lack of computational analysis pipelines that are applicable to such compounds. Here, we introduce CycloNovo, an algorithm for automated de novo cyclopeptide analysis and sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms, to identify cyclopeptides in spectral datasets. CycloNovo reconstructed 32 previously unreported cyclopeptides (to the best of our knowledge) in the human gut and reported over a hundred cyclopeptides in other environments represented by various spectra on Global Natural Products Social Molecular Network (GNPS).

AB - Cyclic and branch cyclic peptides (cyclopeptides) represent a class of bioactive natural products that include many antibiotics and anti-tumor compounds. Despite the recent advances in metabolomics analysis, still little is known about the cyclopeptides in the human gut and their possible interactions due to a lack of computational analysis pipelines that are applicable to such compounds. Here, we introduce CycloNovo, an algorithm for automated de novo cyclopeptide analysis and sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms, to identify cyclopeptides in spectral datasets. CycloNovo reconstructed 32 previously unreported cyclopeptides (to the best of our knowledge) in the human gut and reported over a hundred cyclopeptides in other environments represented by various spectra on Global Natural Products Social Molecular Network (GNPS).

KW - Natural products

KW - peptide sequencing

KW - Mass Spectrometry

KW - Metabolomics

KW - Microbiome

KW - antimicrobial peptides

U2 - 10.1016/j.cels.2019.11.007

DO - 10.1016/j.cels.2019.11.007

M3 - Article

JO - Cell Systems

JF - Cell Systems

SN - 2405-4712

ER -

Behsaz B, Mohimani H, Gurevich A, Prjibelski A, Fisher MF, Vargas F и соавт. De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Cell Systems. 2019 Дек. 18. https://doi.org/10.1016/j.cels.2019.11.007