A liquid chromatography-mass spectrometry-based metabolome database for tomato

S.I.A. Moco, R.J. Bino, O.F.J. Vorst, H.A. Verhoeven, J.C.W. de Groot, T.A. van Beek, J.J.M. Vervoort, C.H. de Vos

Research output: Contribution to journalArticleAcademicpeer-review

364 Citations (Scopus)

Abstract

For the description of the metabolome of an organism, the development of common metabolite databases is of utmost importance. Here we present the Metabolome Tomato Database (MoTo DB), a metabolite database dedicated to liquid chromatography-mass spectrometry (LC-MS)- based metabolomics of tomato fruit (Solanum lycopersicum). A reproducible analytical approach consisting of reversed-phase LC coupled to quadrupole time-of-flight MS and photodiode array detection (PDA) was developed for large-scale detection and identification of mainly semipolar metabolites in plants and for the incorporation of the tomato fruit metabolite data into the MoTo DB. Chromatograms were processed using software tools for mass signal extraction and alignment, and intensity-dependent accurate mass calculation. The detected masses were assigned by matching their accurate mass signals with tomato compounds reported in literature and complemented, as much as possible, by PDA and MS/MS information, as well as by using reference compounds. Several novel compounds not previously reported for tomato fruit were identified in this manner and added to the database. The MoTo DB is available at http://appliedbioinformatics.wur.nl and contains all information so far assembled using this LC-PDA-quadrupole time-of-flight MS platform, including retention times, calculated accurate masses, PDA spectra, MS/MS fragments, and literature references. Unbiased metabolic profiling and comparison of peel and flesh tissues from tomato fruits validated the applicability of the MoTo DB, revealing that all flavonoids and -tomatine were specifically present in the peel, while several other alkaloids and some particular phenylpropanoids were mainly present in the flesh tissue
Original languageEnglish
Pages (from-to)1205-1218
JournalPlant Physiology
Volume141
Issue number4
DOIs
Publication statusPublished - 2006

Fingerprint

metabolome
Metabolome
Lycopersicon esculentum
Liquid Chromatography
liquid chromatography
Mass Spectrometry
tomatoes
mass spectrometry
Databases
Fruit
metabolites
fruits
metabolomics
Tomatine
Solanum lycopersicum
phenylpropanoids
Metabolomics
Alkaloids
Flavonoids
alkaloids

Keywords

  • steroidal alkaloid glycosides
  • solid-phase extraction
  • lycopersicon-esculentum
  • hydroxycinnamic acids
  • alpha-tomatine
  • quantitative-analysis
  • antioxidant activity
  • phenolic-compounds
  • fruit
  • vegetables

Cite this

@article{72772e95acbf411292d80f7c3d0d8125,
title = "A liquid chromatography-mass spectrometry-based metabolome database for tomato",
abstract = "For the description of the metabolome of an organism, the development of common metabolite databases is of utmost importance. Here we present the Metabolome Tomato Database (MoTo DB), a metabolite database dedicated to liquid chromatography-mass spectrometry (LC-MS)- based metabolomics of tomato fruit (Solanum lycopersicum). A reproducible analytical approach consisting of reversed-phase LC coupled to quadrupole time-of-flight MS and photodiode array detection (PDA) was developed for large-scale detection and identification of mainly semipolar metabolites in plants and for the incorporation of the tomato fruit metabolite data into the MoTo DB. Chromatograms were processed using software tools for mass signal extraction and alignment, and intensity-dependent accurate mass calculation. The detected masses were assigned by matching their accurate mass signals with tomato compounds reported in literature and complemented, as much as possible, by PDA and MS/MS information, as well as by using reference compounds. Several novel compounds not previously reported for tomato fruit were identified in this manner and added to the database. The MoTo DB is available at http://appliedbioinformatics.wur.nl and contains all information so far assembled using this LC-PDA-quadrupole time-of-flight MS platform, including retention times, calculated accurate masses, PDA spectra, MS/MS fragments, and literature references. Unbiased metabolic profiling and comparison of peel and flesh tissues from tomato fruits validated the applicability of the MoTo DB, revealing that all flavonoids and -tomatine were specifically present in the peel, while several other alkaloids and some particular phenylpropanoids were mainly present in the flesh tissue",
keywords = "steroidal alkaloid glycosides, solid-phase extraction, lycopersicon-esculentum, hydroxycinnamic acids, alpha-tomatine, quantitative-analysis, antioxidant activity, phenolic-compounds, fruit, vegetables",
author = "S.I.A. Moco and R.J. Bino and O.F.J. Vorst and H.A. Verhoeven and {de Groot}, J.C.W. and {van Beek}, T.A. and J.J.M. Vervoort and {de Vos}, C.H.",
year = "2006",
doi = "10.1104/pp.106.078428",
language = "English",
volume = "141",
pages = "1205--1218",
journal = "Plant Physiology",
issn = "0032-0889",
publisher = "American Society of Plant Biologists",
number = "4",

}

A liquid chromatography-mass spectrometry-based metabolome database for tomato. / Moco, S.I.A.; Bino, R.J.; Vorst, O.F.J.; Verhoeven, H.A.; de Groot, J.C.W.; van Beek, T.A.; Vervoort, J.J.M.; de Vos, C.H.

In: Plant Physiology, Vol. 141, No. 4, 2006, p. 1205-1218.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - A liquid chromatography-mass spectrometry-based metabolome database for tomato

AU - Moco, S.I.A.

AU - Bino, R.J.

AU - Vorst, O.F.J.

AU - Verhoeven, H.A.

AU - de Groot, J.C.W.

AU - van Beek, T.A.

AU - Vervoort, J.J.M.

AU - de Vos, C.H.

PY - 2006

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N2 - For the description of the metabolome of an organism, the development of common metabolite databases is of utmost importance. Here we present the Metabolome Tomato Database (MoTo DB), a metabolite database dedicated to liquid chromatography-mass spectrometry (LC-MS)- based metabolomics of tomato fruit (Solanum lycopersicum). A reproducible analytical approach consisting of reversed-phase LC coupled to quadrupole time-of-flight MS and photodiode array detection (PDA) was developed for large-scale detection and identification of mainly semipolar metabolites in plants and for the incorporation of the tomato fruit metabolite data into the MoTo DB. Chromatograms were processed using software tools for mass signal extraction and alignment, and intensity-dependent accurate mass calculation. The detected masses were assigned by matching their accurate mass signals with tomato compounds reported in literature and complemented, as much as possible, by PDA and MS/MS information, as well as by using reference compounds. Several novel compounds not previously reported for tomato fruit were identified in this manner and added to the database. The MoTo DB is available at http://appliedbioinformatics.wur.nl and contains all information so far assembled using this LC-PDA-quadrupole time-of-flight MS platform, including retention times, calculated accurate masses, PDA spectra, MS/MS fragments, and literature references. Unbiased metabolic profiling and comparison of peel and flesh tissues from tomato fruits validated the applicability of the MoTo DB, revealing that all flavonoids and -tomatine were specifically present in the peel, while several other alkaloids and some particular phenylpropanoids were mainly present in the flesh tissue

AB - For the description of the metabolome of an organism, the development of common metabolite databases is of utmost importance. Here we present the Metabolome Tomato Database (MoTo DB), a metabolite database dedicated to liquid chromatography-mass spectrometry (LC-MS)- based metabolomics of tomato fruit (Solanum lycopersicum). A reproducible analytical approach consisting of reversed-phase LC coupled to quadrupole time-of-flight MS and photodiode array detection (PDA) was developed for large-scale detection and identification of mainly semipolar metabolites in plants and for the incorporation of the tomato fruit metabolite data into the MoTo DB. Chromatograms were processed using software tools for mass signal extraction and alignment, and intensity-dependent accurate mass calculation. The detected masses were assigned by matching their accurate mass signals with tomato compounds reported in literature and complemented, as much as possible, by PDA and MS/MS information, as well as by using reference compounds. Several novel compounds not previously reported for tomato fruit were identified in this manner and added to the database. The MoTo DB is available at http://appliedbioinformatics.wur.nl and contains all information so far assembled using this LC-PDA-quadrupole time-of-flight MS platform, including retention times, calculated accurate masses, PDA spectra, MS/MS fragments, and literature references. Unbiased metabolic profiling and comparison of peel and flesh tissues from tomato fruits validated the applicability of the MoTo DB, revealing that all flavonoids and -tomatine were specifically present in the peel, while several other alkaloids and some particular phenylpropanoids were mainly present in the flesh tissue

KW - steroidal alkaloid glycosides

KW - solid-phase extraction

KW - lycopersicon-esculentum

KW - hydroxycinnamic acids

KW - alpha-tomatine

KW - quantitative-analysis

KW - antioxidant activity

KW - phenolic-compounds

KW - fruit

KW - vegetables

U2 - 10.1104/pp.106.078428

DO - 10.1104/pp.106.078428

M3 - Article

VL - 141

SP - 1205

EP - 1218

JO - Plant Physiology

JF - Plant Physiology

SN - 0032-0889

IS - 4

ER -