Dereplication of natural products using GC-TOF mass spectrometry: Improved metabolite identification by spectral deconvolution ratio analysis
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3389/fmolb.2016.00059 http://hdl.handle.net/11449/174487 |
Resumo: | Dereplication based on hyphenated techniques has been extensively applied in plant metabolomics, thereby avoiding re-isolation of known natural products. However, due to the complex nature of biological samples and their large concentration range, dereplication requires the use of chemometric tools to comprehensively extract information from the acquired data. In this work we developed a reliable GC-MS-based method for the identification of non-targeted plant metabolites by combining the Ratio Analysis of Mass Spectrometry deconvolution tool (RAMSY) with Automated Mass Spectral Deconvolution and Identification System software (AMDIS). Plants species from Solanaceae, Chrysobalanaceae and Euphorbiaceae were selected as model systems due to their molecular diversity, ethnopharmacological potential, and economical value. The samples were analyzed by GC-MS after methoximation and silylation reactions. Dereplication was initiated with the use of a factorial design of experiments to determine the best AMDIS configuration for each sample, considering linear retention indices and mass spectral data. A heuristic factor (CDF, compound detection factor) was developed and applied to the AMDIS results in order to decrease the false-positive rates. Despite the enhancement in deconvolution and peak identification, the empirical AMDIS method was not able to fully deconvolute all GC-peaks, leading to low MF values and/or missing metabolites. RAMSY was applied as a complementary deconvolution method to AMDIS to peaks exhibiting substantial overlap, resulting in recovery of low-intensity co-eluted ions. The results from this combination of optimized AMDIS with RAMSY attested to the ability of this approach as an improved dereplication method for complex biological samples such as plant extracts. |
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Dereplication of natural products using GC-TOF mass spectrometry: Improved metabolite identification by spectral deconvolution ratio analysisCompound identificationGC-MSPeak deconvolutionPlant metabolomicsRatio analysisDereplication based on hyphenated techniques has been extensively applied in plant metabolomics, thereby avoiding re-isolation of known natural products. However, due to the complex nature of biological samples and their large concentration range, dereplication requires the use of chemometric tools to comprehensively extract information from the acquired data. In this work we developed a reliable GC-MS-based method for the identification of non-targeted plant metabolites by combining the Ratio Analysis of Mass Spectrometry deconvolution tool (RAMSY) with Automated Mass Spectral Deconvolution and Identification System software (AMDIS). Plants species from Solanaceae, Chrysobalanaceae and Euphorbiaceae were selected as model systems due to their molecular diversity, ethnopharmacological potential, and economical value. The samples were analyzed by GC-MS after methoximation and silylation reactions. Dereplication was initiated with the use of a factorial design of experiments to determine the best AMDIS configuration for each sample, considering linear retention indices and mass spectral data. A heuristic factor (CDF, compound detection factor) was developed and applied to the AMDIS results in order to decrease the false-positive rates. Despite the enhancement in deconvolution and peak identification, the empirical AMDIS method was not able to fully deconvolute all GC-peaks, leading to low MF values and/or missing metabolites. RAMSY was applied as a complementary deconvolution method to AMDIS to peaks exhibiting substantial overlap, resulting in recovery of low-intensity co-eluted ions. The results from this combination of optimized AMDIS with RAMSY attested to the ability of this approach as an improved dereplication method for complex biological samples such as plant extracts.National Natural Science Foundation of ChinaNúcleo de Pesquisas em Produtos Naturais e Sintéticos Departamento de Física e Química Universidade de São Paulo Faculdade de Ciências Farmacêuticas de Ribeirão PretoNúcleo de Bioensaios Biossíntese e Ecofisiologia de Produtos Naturais Departamento de Química Orgânica Instituto de Química Universidade Estadual Paulista UNESPCentro de Imagens e Espectroscopia in vivo por Ressonância Magnética Instituto de Física de São Carlos Universidade de São PauloDepartment of Anesthesiology and Pain Medicine Northwest Metabolomics Research Center University of WashingtonJiangxi Key Laboratory for Mass Spectrometry and Instrumentation East China Institute of TechnologyPublic Health Sciences Division Fred Hutchinson Cancer Research CenterNúcleo de Bioensaios Biossíntese e Ecofisiologia de Produtos Naturais Departamento de Química Orgânica Instituto de Química Universidade Estadual Paulista UNESPNational Natural Science Foundation of China: 21365001Universidade de São Paulo (USP)Universidade Estadual Paulista (Unesp)University of WashingtonEast China Institute of TechnologyFred Hutchinson Cancer Research CenterNeto, Fausto Carnevale [UNESP]Pilon, Alan C. [UNESP]Selegato, Denise M. [UNESP]Freire, Rafael T. [UNESP]Gu, HaiweiRaftery, DanielLopes, Norberto P.Castro-Gamboa, Ian [UNESP]2018-12-11T17:11:23Z2018-12-11T17:11:23Z2016-09-30info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://dx.doi.org/10.3389/fmolb.2016.00059Frontiers in Molecular Biosciences, v. 3, n. SEP, 2016.2296-889Xhttp://hdl.handle.net/11449/17448710.3389/fmolb.2016.000592-s2.0-850182000342-s2.0-85018200034.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers in Molecular Biosciencesinfo:eu-repo/semantics/openAccess2023-10-06T06:02:08Zoai:repositorio.unesp.br:11449/174487Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-10-06T06:02:08Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Dereplication of natural products using GC-TOF mass spectrometry: Improved metabolite identification by spectral deconvolution ratio analysis |
title |
Dereplication of natural products using GC-TOF mass spectrometry: Improved metabolite identification by spectral deconvolution ratio analysis |
spellingShingle |
Dereplication of natural products using GC-TOF mass spectrometry: Improved metabolite identification by spectral deconvolution ratio analysis Neto, Fausto Carnevale [UNESP] Compound identification GC-MS Peak deconvolution Plant metabolomics Ratio analysis |
title_short |
Dereplication of natural products using GC-TOF mass spectrometry: Improved metabolite identification by spectral deconvolution ratio analysis |
title_full |
Dereplication of natural products using GC-TOF mass spectrometry: Improved metabolite identification by spectral deconvolution ratio analysis |
title_fullStr |
Dereplication of natural products using GC-TOF mass spectrometry: Improved metabolite identification by spectral deconvolution ratio analysis |
title_full_unstemmed |
Dereplication of natural products using GC-TOF mass spectrometry: Improved metabolite identification by spectral deconvolution ratio analysis |
title_sort |
Dereplication of natural products using GC-TOF mass spectrometry: Improved metabolite identification by spectral deconvolution ratio analysis |
author |
Neto, Fausto Carnevale [UNESP] |
author_facet |
Neto, Fausto Carnevale [UNESP] Pilon, Alan C. [UNESP] Selegato, Denise M. [UNESP] Freire, Rafael T. [UNESP] Gu, Haiwei Raftery, Daniel Lopes, Norberto P. Castro-Gamboa, Ian [UNESP] |
author_role |
author |
author2 |
Pilon, Alan C. [UNESP] Selegato, Denise M. [UNESP] Freire, Rafael T. [UNESP] Gu, Haiwei Raftery, Daniel Lopes, Norberto P. Castro-Gamboa, Ian [UNESP] |
author2_role |
author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade de São Paulo (USP) Universidade Estadual Paulista (Unesp) University of Washington East China Institute of Technology Fred Hutchinson Cancer Research Center |
dc.contributor.author.fl_str_mv |
Neto, Fausto Carnevale [UNESP] Pilon, Alan C. [UNESP] Selegato, Denise M. [UNESP] Freire, Rafael T. [UNESP] Gu, Haiwei Raftery, Daniel Lopes, Norberto P. Castro-Gamboa, Ian [UNESP] |
dc.subject.por.fl_str_mv |
Compound identification GC-MS Peak deconvolution Plant metabolomics Ratio analysis |
topic |
Compound identification GC-MS Peak deconvolution Plant metabolomics Ratio analysis |
description |
Dereplication based on hyphenated techniques has been extensively applied in plant metabolomics, thereby avoiding re-isolation of known natural products. However, due to the complex nature of biological samples and their large concentration range, dereplication requires the use of chemometric tools to comprehensively extract information from the acquired data. In this work we developed a reliable GC-MS-based method for the identification of non-targeted plant metabolites by combining the Ratio Analysis of Mass Spectrometry deconvolution tool (RAMSY) with Automated Mass Spectral Deconvolution and Identification System software (AMDIS). Plants species from Solanaceae, Chrysobalanaceae and Euphorbiaceae were selected as model systems due to their molecular diversity, ethnopharmacological potential, and economical value. The samples were analyzed by GC-MS after methoximation and silylation reactions. Dereplication was initiated with the use of a factorial design of experiments to determine the best AMDIS configuration for each sample, considering linear retention indices and mass spectral data. A heuristic factor (CDF, compound detection factor) was developed and applied to the AMDIS results in order to decrease the false-positive rates. Despite the enhancement in deconvolution and peak identification, the empirical AMDIS method was not able to fully deconvolute all GC-peaks, leading to low MF values and/or missing metabolites. RAMSY was applied as a complementary deconvolution method to AMDIS to peaks exhibiting substantial overlap, resulting in recovery of low-intensity co-eluted ions. The results from this combination of optimized AMDIS with RAMSY attested to the ability of this approach as an improved dereplication method for complex biological samples such as plant extracts. |
publishDate |
2016 |
dc.date.none.fl_str_mv |
2016-09-30 2018-12-11T17:11:23Z 2018-12-11T17:11:23Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.3389/fmolb.2016.00059 Frontiers in Molecular Biosciences, v. 3, n. SEP, 2016. 2296-889X http://hdl.handle.net/11449/174487 10.3389/fmolb.2016.00059 2-s2.0-85018200034 2-s2.0-85018200034.pdf |
url |
http://dx.doi.org/10.3389/fmolb.2016.00059 http://hdl.handle.net/11449/174487 |
identifier_str_mv |
Frontiers in Molecular Biosciences, v. 3, n. SEP, 2016. 2296-889X 10.3389/fmolb.2016.00059 2-s2.0-85018200034 2-s2.0-85018200034.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers in Molecular Biosciences |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1799964450894118912 |