Dereplication of natural products using GC-TOF mass spectrometry

Improved metabolite identification by spectral deconvolution ratio analysis

Fausto Carnevale Neto, Alan C. Pilon, Denise M. Selegato, Rafael T. Freire, Haiwei Gu, Daniel Raftery, Norberto P. Lopes, Ian Castro-Gamboa

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number59
JournalFrontiers in Molecular Biosciences
Volume3
Issue numberSEP
DOIs
StatePublished - Sep 30 2016
Externally publishedYes

Fingerprint

Deconvolution
Metabolites
Biological Products
Mass spectrometry
Mass Spectrometry
Software
Identification (control systems)
Chrysobalanaceae
Euphorbiaceae
Solanaceae
Aptitude
Metabolomics
Plant Extracts
Ions
Design of experiments
Recovery

Keywords

  • Compound identification
  • GC-MS
  • Peak deconvolution
  • Plant metabolomics
  • Ratio analysis

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

Cite this

Dereplication of natural products using GC-TOF mass spectrometry : Improved metabolite identification by spectral deconvolution ratio analysis. / Neto, Fausto Carnevale; Pilon, Alan C.; Selegato, Denise M.; Freire, Rafael T.; Gu, Haiwei; Raftery, Daniel; Lopes, Norberto P.; Castro-Gamboa, Ian.

In: Frontiers in Molecular Biosciences, Vol. 3, No. SEP, 59, 30.09.2016.

Research output: Contribution to journalArticle

Neto, Fausto Carnevale ; Pilon, Alan C. ; Selegato, Denise M. ; Freire, Rafael T. ; Gu, Haiwei ; Raftery, Daniel ; Lopes, Norberto P. ; Castro-Gamboa, Ian. / Dereplication of natural products using GC-TOF mass spectrometry : Improved metabolite identification by spectral deconvolution ratio analysis. In: Frontiers in Molecular Biosciences. 2016 ; Vol. 3, No. SEP.
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