A liquid chromatography-mass spectrometry-based metabolome database for tomato
A liquid chromatography-mass spectrometry-based metabolome database for tomato
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DOI：
10.1104/pp.106.078428
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发表时间：
2006-08-01
期刊：
影响因子：
7.4
通讯作者：
de Vos, C. H. Ric
中科院分区：
文献类型：
--
作者：
Moco, Sofia;Bino, Raoul J.;de Vos, C. H. Ric
对于描述生物体的代谢组来说，共同代谢物数据库的开发是至关重要的。在这里，我们介绍了代谢番茄数据库(Moto DB)，一个致力于基于液-质联用(LC-MS)的番茄果实代谢组学的代谢物数据库(MOTO DB)。建立了一种反相高效液相色谱与四极杆飞行时间质谱仪联用和光电二极管阵列检测(PDA)相结合的分析方法，用于大规模检测和鉴定植物中的主要半极性代谢物，并将番茄果实代谢物数据纳入MOTO DB。使用软件工具处理色谱图，以提取和比对质量信号，并根据强度进行准确的质量计算。通过将其准确的质量信号与文献报道的番茄化合物进行匹配来指定所检测的质量，并通过PDA和MS/MS信息以及使用参考化合物来尽可能地补充所检测的质量。用这种方法鉴定了几种以前没有报道过的番茄果实的新化合物，并将其添加到数据库中。MOTO DB可在http://appliedbioinformatics.wur.nl上获得，其中包含到目前为止使用LC-PDA-四极飞行时间MS平台收集的所有信息，包括保留时间、计算的准确质量、PDA光谱、MS/MS碎片和文献参考。对番茄果皮和果肉组织的无偏代谢谱分析和比较验证了MOTO DB的适用性，结果表明，所有的类黄酮和α-西红柿碱都专门存在于番茄果皮中，而其他几种生物碱和一些特殊的苯丙烷类化合物主要存在于果肉组织中。
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, PDAspectra, 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.