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Sample Set Information

Title Integrated LC-MS/MS system for plant metabolomics
Description Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is highly sensitive, selective, and enables extensive detection of metabolites within a sample. The result allows us to characterize comprehensive metabolite accumulation patterns without dependence on authentic standard compounds and isolation of the individual metabolites. A reference database search is essential for the structural assignment process of un-targeted MS and MS/MS data. Moreover, the characterization of unknown metabolites is challenging, since these cannot be assigned a candidate structure by using a reference database. In this case study, integrated LC-MS/MS based plant metabolomics allows us to detect several hundred metabolites in a sample; and integrated omics analyses, e.g., large-scale reverse genetics, linkage mapping, and association mapping, provides a powerful tool for candidate structure selection or rejection. We also examine emerging technology and applications for LC-MS/MS-based un-targeted plant metabolomics. These activities promote the characterization of massive extended detectable metabolites.
Authors Yuji Sawada, Masami Yokota Hirai
Reference Sawada and Hirai (2013) Computational and Structural Biotechnology Journal 23;4:e201301011. doi: 10.5936/csbj.201301011. eCollection 2013

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The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

Analytical Method Details Information

Instrument HPLC: Waters Acquity UPLC system; MS: Waters Q-TOF Premier
Instrument Type UPLC-QTOF-MS
Ionization ESI
Ion Mode Positive and Negative
Description The UPLC (Waters) conditions were manually optimized based on the separation patterns of 12 methionine-derived glucosinolates and were as follows: fl ow rate 0.24 ml min –1 ; solvents A, 0.1% formic acid in water and B, 0.1% formic acid in acetonitrile; gradient program of B (0 min, 0%; 0.25 min, 0%; 0.4 min, 9%; 0.8 min, 17%; 1.9 min, 100%; 2.1 min, 100%; 2.11 min, 0%); 3 min cycles with a temperature of 38°C.The TQMS detection conditions were the same as those for FIA-TQMS, except that the source temperature was 130°C.
Comment_of_details Sawada et al. Plant Cell Physiol. 2009 Jan;50(1):37-47

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