Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2006 Aug;141(4):1205-18.
doi: 10.1104/pp.106.078428.

A Liquid Chromatography-Mass Spectrometry-Based Metabolome Database for Tomato

Affiliations
Free PMC article
Comparative Study

A Liquid Chromatography-Mass Spectrometry-Based Metabolome Database for Tomato

Sofia Moco et al. Plant Physiol. .
Free PMC article

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 alpha-tomatine were specifically present in the peel, while several other alkaloids and some particular phenylpropanoids were mainly present in the flesh tissue.

Figures

Figure 1.
Figure 1.
Typical chromatograms obtained from reversed-phase LC-PDA-ESI-QTOF-MS analysis of tomato peel extract. A, Total ion signal (QTOF MS). B, Absorbance signal (PDA). Retention times (in minutes) are indicated for the most intense peaks (difference between the two detectors is 0.15 min). Inserts in A show accurate mass (I) and MS/MS spectrum (II), and in B absorbance spectrum (III) obtained for the compound rutin eluting at 23.3 min.
Figure 2.
Figure 2.
Peak intensity ratios, in logarithmic scale, of mass signals (peak height) obtained in positive and negative ionization modes for some metabolites found in tomato peel extracts.
Figure 3.
Figure 3.
Difference between observed and theoretical monoisotopic masses, calculated as Δppm (y axis), as a function of the parent ion signal intensity, expressed as ion counts/scan at center of peak (x axis, log10-transformed data) for some identified compounds in tomato peel extracts. Threshold levels for mass accuracies between +5 and −5 ppm, and for analyte mass signal intensities between 0.25 and 2.0 times the lock mass signal intensity are indicated with dotted lines.
Figure 4.
Figure 4.
A, Strategy applied for data analysis and identification of metabolites in tomato fruit, using LC-PDA-QTOF MS. Key entry into the database is the (intensity-corrected) accurate mass. B, Screenshot from the MoTo database query frame. Detected masses can be filled in (in this example m/z 609 in negative-ionization mode) and searched against the database at user-defined mass accuracy (first frame). If at least one mass hit is found in the database, the elemental compositions, deviations from accurate masses, and IUPAC names of the corresponding metabolites are indicated, as well as links to PubChem, if applicable, and our own experimental data (second frame). The last frame shows the experimental and literature information available for the selected compound.
Figure 5.
Figure 5.
Unbiased LC-QTOF MS-based comparative profiling of aqueous-methanol extracts from peel and flesh tissues from ripe tomato fruit (var. Moneymaker). Mass chromatograms (m/z 100–1,500) were acquired in ESI-negative mode. Retention times (in minutes) and nominal masses of the most intense signals are indicated in the chromatograms (plotted as base peak intensities [BPI], from 4–50 min). A, Representative original chromatogram of peel tissue. B, Representative original chromatogram of flesh tissue. C, Differential chromatogram for metabolites that are significantly (P < 0.05; n = 8 extracts) at least 1.5-fold higher in extracts from peel compared to flesh tissue (peaks pointing upwards) or higher in extracts from flesh compared to peel tissue (peaks pointing downwards). a, Coumaric acid-hexose II; b, quercetin-hexose-deoxyhexose-pentose; c, rutin; d, kaempferol-hexose-deoxyhexose-pentose or quercetin-dideoxyhexose-pentose; e, α-tomatine; f, naringenin; g, naringenin chalcone; h, caffeic acid-hexose II; i, 3-caffeoylquinic acid; j, spirosolanol-trihexose; and k, hydroxyfurastanol tetrahexoside.

Similar articles

See all similar articles

Cited by 96 articles

See all "Cited by" articles

Publication types

LinkOut - more resources

Feedback