acids, carbohydrates and others. The central
dogma of biology states that genetic information
is transcribed into individual mRNA; each
mRNA contains the program for synthesis of a
particular protein. However, a large number of
proteins in fact serve as enzymes involved in
metabolic pathways whose metabolites largely
govern the phenotype. Gene perturbations lead to
changes in the transcript that result in changes in
the enzyme levels and in turn in the metabolic
profile. A comprehensive description of meta-
bolic behaviour is thus a critical piece of infor-
mation in biology.
Plant metabolomics is of particular interest
because plants are characterized by their diver-
sity of so-called secondary metabolites, also
referred to as natural products or phytochemicals.
To date, more than 100,000 metabolites have
been identified, and this number may well be less
than 10 % of the total (Wink 1988 ). The plant
metabolome—the complement of metabolites in
a plant species—represents enormous chemical
diversity owing to the complex set of metabolites
produced. Estimates of plant metabolomes vary
from 5,000 to 25,000; even in the absence of
definite data, the metabolomes of plants seem to
be larger than those of prokaryotes or animals.
Human beings use plants for their metabolites as
dyestuffs, resins, fibres, oils, fats, seasonings,
flavourings and pharmaceutical agents. It is well
accepted that phytochemicals play critical roles
in resistance against pathogens, herbivores and
other environmental stresses. Plant metabolomics
would provide fascinating data to researchers
working on plant metabolism. Plant metabolo-
mics not only contributes to functional genomics
and systems biology of plants but can also be
exploited in molecular breeding aimed at
improving productivity and functionality of
crops, incorporating stress tolerance, and pro-
ducing pharmaceutical materials, functional
foods, biomaterials and biofuels (Xu et al. 2013 ).
At present, there are large gaps in our
knowledge of genomics and metabolomics
because metabolites have more complex than the
elements of the classical central dogma. The
extreme complexity of metabolites, especially
plant metabolites, lies not only in their great
number but also in their chemical diversity.
High-throughput, high-sensitivity, high-selectiv-
ity and unbiased analytical methodologies that
permit better handling of phytochemicals have
been required ever since the beginning of plant
metabolomics. For instance, untargeted analyses
using MS-based technology have been developed
to provide the metabolic profiles of known and
unknown phytochemicals simultaneously (Sum-
ner et al. 2003 ; Weckwerth 2003 ; Schauer and
Fernie 2006 ; Guy et al. 2008 ; Hall et al. 2008 ;
Saito et al. 2008 ).
Reproducibility, another requirement of meta-
bolomics, would be ensured by unambiguous
identification of each metabolite measured, but in
general, it is not easy due to the vast diversity of
phytochemicals. MS provides two types of struc-
tural information: the molecular mass and the
fragment ion profile of the compound, i.e., its
mass spectrum. The reproducibility of fragmen-
tation depends on the ionization technique used.
Electron ionization (EI), the standard ionization
method in gas chromatography (GC)-MS, is
accompanied by the cleavage of the compounds,
generating a series of fragment ions according to
the ionization energy. The resultant MS spectrum
is highly reproducible, particularly when obtained
at 70 eV, and can be used for the identification of
the compound by searching a MS spectra library
containing more than 100,000 spectra. In contrast,
relatively soft ionization methods, such as elec-
trospray ionization (ESI) and atmospheric pres-
sure chemical ionization (APCI), which are
suitable for liquid chromatography (LC)-MS and
capillary electrophoresis (CE)-MS, generate only
a limited number of fragment ions. In the case of
LC- or CE-MS, tandem mass spectrometry (MS/
MS) is applied to obtain structural information on
the basis of the fragmentation pattern. LC(CE)-
ESI-MS and LC(CE)-APCI-MS are highly sen-
sitive techniques that provide information about
molecular mass. However, they are not useful for
the identification of compounds in a strict sense
because their ionization conditions are not stan-
dardized and only a few hundreds to thousands of
MS and MS/MS spectra obtained by ESI or APCI
are available in databases. Except in GC-EI-MS,
reproducibility of analysis may seem to be172 Y. Sawada and T. Aoki