Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 93

MS2T/PRIMe
The MS/MS spectral tag (MS2T) libraries at the Riken Metabolomics (PRIMe)
website provides access to libraries of phytochemical LC-MS2 spectra obtained
from various plant species.
LC-ESI-Q TOF/MS
By using the automatic MS2 retreval function of LC-ESI-QTOF/MS (Matsuda et al.
2009 ), MS2T/PRIMe and LC-ESI-Q TOF/MS databases can play crucial roles as
information resources and repositories of large amount of new data. They also serve
as tools for further integration of metabolic profiles containing comprehensive data
acquired from other 'omics' research (Akiyama et al. 2008 ).
CombinedApproachesinMetabolomics
Metabolome research can help in the understanding of metabolic activity at the
cell, tissue and organ levels, and achieving profiles complementary to other 'omics'
research; which can aid genetic variation studies. At present these combination of
methods have been demonstrated mostly in the model plant Arabidopsis by utilising
the many other 'omics' web sites and resources that currently exist for this model
plant; including whole-genome sequencing, large-scale transcriptome data and re-
lated expression data, bioresources from mutants, and full-length cDNA clones.
The experimental scheme for systematic information retrieval of gene-to-metab-
olite data through a combination of transcriptome and metabolome resources has
been demonstrated by Saito's group at the RIKEN Plant Science Centre (Saito et al.
2008 ). The URL list and resources below are also listed in Table 2.10 .
map (BL-SOM)
Data containing transcriptome and metabolome changes in Arabidopsis under stress
conditions induced by deficiency of sulfur and nitrogen were analysed using batch-
learning, self-organizing map (BL-SOM) analysis, which enabled the identification
of genes involved in glucosinolate biosynthesis (Hirai et al. 2004 ). An integrated
approach with an activation-tagged mutant line with overexpressed genes wasd
used to identify genes involved in anthocyanin biosynthesis (Tohge et al. 2005 ).