Standard Spectrum Search

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About Standard Spectrum Search

Standard spectrum search is one of the major services offered by the PRIMe project. Although comparison of standard compounds with measured metabolite mixture data is a key step in metabolome analysis, the quantity of standardized experimental spectral data around the world is insufficient to identify all measurable metabolites. Therefore, we engaged in a collaborative project to measure or collect standard spectral data in order to make these resources available to researchers.

Chemical complexity, metabolic heterogeneity, dynamic range, and the ease of extraction remain the main challenges in developing an effective metabolomics platform. Our PRIMe project performs standard measurements of metabolites by means of multidimensional Nuclear Magnetic Resonance (NMR) spectroscopy, Gas Chromatography-Mass Spectrometry (GC/MS), Liquid Chromatography-MS (LC/MS), and Capillary Electrophoresis-MS (CE/MS). Since these instruments measure different metabolites using differ solvent systems, it should therefore be possible to obtain data for a wide range of natural metabolites. By talking advantage of this range of technologies to obtain standardized metabolite measurements, this database will become a general-purpose Web service for facilitating metabolome analysis.


A schematic illustration of the standard metabolites that have already been measured and accumulated in the Standard Spectrum Search database: The standard metabolites are shown for mass spectrometry (282 compounds, labeled in red) and NMR (80 compounds, labeled in blue) in a map that contains the 134 KEGG External Link reference pathways, which correspond to 3230 metabolites (gray rectangles) and 4744 reactions (gray lines). The colored rectangles are redundant because different metabolic pathways can contain the same metabolite.

Measurement technologies

Nuclear Magnetic Resonance (NMR)

The NMR technique, which is based on the observation and characterization of the magnetizations of nuclear spins in different chemical environments, plays an important role in investigating the physiology and metabolism of living systems. NMR spectrometry has also been used for metabolic screening approaches that reveal the metabolic phenotype of many species.

Although one-dimensional(1D)-1H NMR spectral analysis has provided fast, inexpensive data to support the metabolic fingerprinting of samples, it has limitations: most of the chemical compounds represented in the chemical shift are largely unknown, and many of them have overlapping 1D spectra and are thus difficult to assign. An attractive alternative wolud be to introduce 13C chemical shifts as a second dimension. The low signal strength of 13C chemical shifts that results from the low natural abundance of 13C can be overcome by labeling materials with the stable 13C isotope. Plants can be easily labeled by feeding seedlings with 13C labeled sugars or 13CO2 (Kikuchi et al. 2004; Kikuchi & Hirayama 2007a,b). Simultaneously, this technique provides an excellent method for tracing carbon movements among metabolites, providing additional data for understanding metabolic flows at the atomic level, although this approach would require more detailed analysis.

  • Tian C, Chikayama E, Tsuboi Y, Kuromori T, Shinozaki K, Kikuchi J, Hirayama T. (2007) Top-down phenomics of Arabidopsis thaliana: metabolic profiling by one- and two-dimensional nuclear magnetic resonance spectroscopy and transcriptome analysis of albino mutants. J Biol Chem. 2007 Jun 22;282(25):18532–41. [PubMed] External Link
  • Kikuchi J, Hirayama T. (2007) Practical aspects of uniform stable isotope labeling of higher plants for heteronuclear NMR-based metabolomics. Methods Mol Biol. 2007;358:273–86. [PubMed] External Link
  • Kikuchi J, Shinozaki K, Hirayama T. (2004) Stable Isotope Labeling of Arabidopsis thaliana for an NMR-Based Metabolomics Approach. Plant Cell Physiol. 2004 Aug;45(8):1099–104. [PubMed] External Link

Gas Chromatography-Mass Spectrometry (GC/MS)

GC/MS is currently proving to be the most popular method for metabolome analysis due to the robustness of both the separation and the electron-impact spectrometry techniques. Furthermore, the availability of some excellent deconvolution and metabolic identification software is also contributing to the spread of this technology among metabolome researchers. The capillary columns used in GC enable the separation of more than 100 compounds in a single analysis. The use of GC/MS in metabolome analysis can be divided into two parts: (1) naturally occurring volatile metabolites and (2) non-volatile, polar metabolites that can be synthesized by means of chemical derivatization.

Liquid Chromatography-MS (LC/MS)

LC/MS provides molecular identification and the quantification of polar and neutral metabolites, even when they are present in a mixture. Advances in chromatographic technologies, such as the ultra-performance liquid chromatography (UPLC) system from Waters Corporation External Link, combined with advances in column chemistry, such as hydrophilic interaction chromatography (HILIC) and the use of long monolithic columns, are yielding significantly improved resolution. However, several difficulties remain to be solved, such as the incompatibility caused by the liquid flow rate into the high vacuum of the mass spectrometer and the ionization of non-volatile and thermally labile compounds during LC/MS analyses. The introduction of powerful soft-ionization techniques, such as thermospraying, atmospheric-pressure chemical ionization (APCI), photo-ionization (PI), and electrospraying can overcome these problems.

Capillary Electrophoresis-MS (CE/MS)

Compared to the LC/MS technique, one major drawback of CE/MS is the high limit of detection (i.e., the low sensitivity of the technique) as a result of the low injection volume used in CE. High-resolution separation capability and sensitive detection of water soluble extracts will provide a strong combination suitable for the analysis of a diverse range of primary and secondary metabolites.

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