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Nakatani Kohta Last modified date:2023.09.29

Graduate School

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The overall profile of metabolites present in living organisms, represented by amino acids that make up proteins and nucleotides such as ATP that make up DNA, is referred to as the metabolome. Within the metabolome, various metabolites closely related to diseases have been discovered. I am currently working on the development of analytical methods that can simultaneously measure these thousands of metabolites. .
Academic Degree
ph.D. in Engineering
Country of degree conferring institution (Overseas)
Field of Specialization
Analytical Science in Metabolomics
ORCID(Open Researcher and Contributor ID)
Total Priod of education and research career in the foreign country
Outline Activities
In my research activities, I am involved in the development of measurement techniques for metabolome analysis. The metabolome refers to the overall profile of metabolites present in living organisms, represented by amino acids that make up proteins and nucleotides such as ATP that make up DNA. Within the metabolome, numerous substances closely related to various diseases have been discovered, and there is a pressing need for the development of analytical methods that can simultaneously measure these thousands of metabolites.

To develop an analytical method that captures the complete picture of the metabolome, which can range from thousands to tens of thousands of metabolites, it requires continuous work such as developing essential techniques, optimizing analysis conditions using those techniques, extracting individual metabolites from the metabolome for evaluation of the analysis system, and iterative improvement of the techniques based on feedback. I strategically conduct the development of analytical methods by grouping the metabolome.

In terms of educational activities, I teach separation chemistry and analytical chemistry, which are fundamental knowledge necessary for the measurement science of metabolomics. I also cover biochemistry to understand life phenomena related to metabolism.

As for my contributions to society, I engage in activities to strengthen the research network within Japan and establish cooperative relationships with international networks. I believe that scientific and technological advancements are essential for the transformation of human welfare, and tackling these challenges requires a united global effort. Therefore, I aspire to contribute to the promotion of scientific and technological advancements through the establishment of a sound international network. Specifically, I organize and manage young researcher associations within various domestic academic societies to build cooperative networks with young communities abroad.
Research Interests

  • Development of sample preparation and liquid chromatography mass spectrometry method for human blood steroid analysis
    keyword : steroidomics, reversed phase liquid chromatography, mass spectrometry
  • Development of sample preparation and analytical methods for lipidomics
    keyword : chromatography, mass spectrometry
  • Development of comprehensive metabolome analysis technology combining separation technology and mass spectrometry
    keyword : HILIC, AEX, Chromatography, Metabolomics, Lipidomics, Steroidomics
Academic Activities
1. Kohta Nakatani, Yoshihiro Izumi, Masatomo Takahashi, and Takeshi Bamba, Unified-Hydrophilic-Interaction/Anion-Exchange Liquid Chromatography Mass Spectrometry (Unified-HILIC/AEX/MS): A Single-Run Method for Comprehensive and Simultaneous Analysis of Polar Metabolome, 10.1021/acs.analchem.2c03986, 2022.11, One of the technical challenges in the field of metabolomics is the development of a single-run method to detect the full complement of polar metabolites in biological samples. However, an ideal method to meet this demand has not yet been developed. Herein, we proposed a simple methodology that enables the comprehensive and simultaneous analysis of polar metabolites using unified-hydrophilic-interaction/anion-exchange liquid chromatography mass spectrometry (unified-HILIC/AEX/MS) with a polymer-based mixed amines column composed of methacrylate-based polymer particles with primary, secondary, tertiary, and quaternary amines as functional groups. The optimized unified-HILIC/AEX/MS method is composed of two consecutive chromatographic separations, HILIC-dominant separation for cationic, uncharged, and zwitterionic polar metabolites [retention times (RTs) = 0–12.8 min] and AEX-dominant separation for polar anionic metabolites (RTs = 12.8–26.5 min), by varying the ratio of acetonitrile to 40 mM ammonium bicarbonate solution (pH 9.8). A total of 400 polar metabolites were analyzed simultaneously through a combination of highly efficient separation using unified-HILIC/AEX and remarkably sensitive detection using multiple reaction monitoring-based triple quadrupole mass spectrometry (unified-HILIC/AEX/MS/MS). A nontargeted metabolomic approach using unified-HILIC/AEX high-resolution mass spectrometry (unified-HILIC/AEX/HRMS) also provided more comprehensive information on polar metabolites (3242 metabolic features) in HeLa cell extracts than the conventional HILIC/HRMS method (2068 metabolic features). Our established unified-HILIC/AEX/MS/MS and unified-HILIC/AEX/HRMS methods have several advantages over conventional techniques, including polar metabolome coverage, throughput, and accurate quantitative performance, and represent potentially useful tools for in-depth studies on metabolism and biomarker discovery..
2. Kohta Nakatani, Yoshihiro Izumi, Kosuke Hata, Takeshi Bamba, An Analytical System for Single-Cell Metabolomics of Typical Mammalian Cells Based on Highly Sensitive Nano-Liquid Chromatography Tandem Mass Spectrometry,, 2020.01, The rapid development of next-generation sequencing techniques has enabled single-cell genomic and transcriptomic analyses, which have revealed the importance of heterogeneity in biological systems. However, analytical methods to accurately identify and quantify comprehensive metabolites from single mammalian cells with a typical diameter of 10–20 μm are still in the process of development. The aim of this study was to develop a single-cell metabolomic analytical system based on highly sensitive nano-liquid chromatography tandem mass spectrometry (nano-LC-MS/MS) with multiple reaction monitoring. A packed nano-LC column (3-μm particle-size pentafluorophenylpropyl Discovery HSF5 of dimensions 100 μm i.d.×180 mm) was prepared using a slurry technique. The optimized nano-LC-MS/MS method showed 3–132-fold (average value, 26-fold) greater sensitivity than semimicro-LC-MS/MS, and the detection limits for several hydrophilic metabolites, including amino acids and nucleic acid related metabolites were in the sub-fmol range. By combining live single-cell sampling and nano-LC-MS/MS, we successfully detected 18 relatively abundant hydrophilic metabolites (16 amino acids and 2 nucleic acid related metabolites) from single HeLa cells (n=22). Based on single-cell metabolic profiles, the 22 HeLa cells were classified into three distinct subclasses, suggesting differences in metabolic function in cultured HeLa cell populations. Our single-cell metabolomic analytical system represents a potentially useful tool for in-depth studies focused on cell metabolism and heterogeneity..
1. Kohta Nakatani, Yoshihiro Izumi, Kousuke Hata, Takeshi Hara, Takeshi Bamba, Development of an analytical system for single-cell metabolomics based on high-sensitive nano-LC/MS/MS, The 28th Hot Spring Harbor International Symposium 2018, 2018.10, A cell is the structural, functional, and biological minimum unit of all living organisms. Conventional metabolome analysis requires large amount of samples such as 10–15 mg of tissue or 105–106 cells due to the limitations on sensitivity of the analytical system and other techniques including cell sampling and sample pretreatment processes. However, it has been reported that minority cells occasionally have important functions. For example, cancer stem cells have tumorigenicity or chemotherapy resistance. Therefore, information garnered from the analysis of a specific tissue or a single-cell is expected to advance knowledge of the physiological heterogeneity. The aim of this study is to develop a single-cell metabolome analytical system by a combination of single-cell sample preparation technique and highly sensitive nano-liquid chromatography triple quadrupole mass spectrometry with multiple reaction monitoring (nano-LC/MS/MS). Since the LC/MS is a concentration-sensitive devise, the resultant signal mainly depends on the concentration of the analyte in the carrier flow. Theoretically, the sensitivity of LC/MS can be increased by lowering the flow rate obtained with narrow diameter LC column (i.e., nano-LC/MS). Prior to the development of the highly sensitive nano-LC/MS/MS method, we evaluated column packing materials with good retention and separation of hydrophilic metabolites. Among screened columns, LC with a silica-based pentafluorophenylpropyl column or a polymer-based amino column achieved good retention of hydrophilic metabolites, including amino acids, organic acids, nucleic acids, etc. We then fabricated nano-LC columns by packing the selected particles into 0.1 mm inner diameter (i.d.) fused silica capillary tubes. The sensitivity of our developed nano-LC/MS/MS system was about 100-fold higher than that of the conventional LC/MS/MS with 2.1 mm i.d. column, and the limits of detections of most hydrophilic metabolites were sub-fmol range. We also developed living single-cell sampling system consisting a fluorescence microscope, a micromanipulator, and a nano-syringe pump. By a combination of single-cell sampling, pretreatment techniques with reduced sample loss, and highly-sensitive nano-LC/MS/MS, we successfully detected relatively abundant hydrophilic metabolites from single HeLa cells. The developed analytical system is a new tool for single-cell metabolome analysis and thus will facilitate future research in tumor heterogeneity..
2. Kohta Nakatani, Yoshihiro Izumi, Masatomo Takahashi, Keita Sakurai, Michio Butsugan, Takeshi Bamba, Single-run comprehensive hydrophilic metabolome analysis by unified hydrophilic-interaction/anion-exchange liquid chromatography mass spectrometry, 8th ASIA-OCEANIA MASS SPECTROMETRY COMFERENCE 2020, 2020.01,  Introduction: 400 characters
Hydrophilic metabolome in biological samples is a complex mixture of metabolites with diverse chemical properties. At present, there is no analytical method that can analyze complex hydrophilic metabolome by a single-run analysis. Here, we report a "unified hydrophilic-interaction/anion-exchange liquid chromatography mass spectrometry" method for single-run hydrophilic metabolome analysis.
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 Method: 400 characters
An LC/MS system comprised of a Nexera X2 UHPLC system with wide pH tolerance coupled to an LCMS-8060 triple quadrupole mass spectrometer (TQMS) (Shimadzu Co., Ltd., Kyoto, Japan). GL-HilicAex column (Hitachi Chemical Techno Service Co., Ltd., Ibaraki, Japan) was used for LC separation. The optimal mobile phase was the gradient of acetonitrile (A) and 40 mM ammonium bicarbonate (pH 9.8).
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 Results: 900 characters
The unified hydrophilic-interaction/anion-exchange liquid chromatography tandem mass spectrometry (unified HILIC/AEX/MS/MS) method is composed of two separation phases: HILIC dominant phase (t = 0-12.8 min) and AEX dominant phase (t = 12.8-26.5 min). Cationic, uncharged, and zwitterionic metabolites are eluted under HILIC dominant phase, and then anionic metabolites are eluted under AEX dominant phase, which allows simultaneous analysis of hydrophilic metabolome by a single-run analysis. We comparatively evaluated the chromatographic performance of the unified HILIC/AEX method to those of conventional methods, which resulted in the demonstration of the best performance of the developed method. In addition, we applied the method to both targeted and non-targeted metabolomics of HeLa cells and the feasibility for metabolomics was demonstrated.
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 Novel Aspect: 150 characters
Unified HILIC and AEX chromatographic separation combined with MS improved coverage of metabolome analysis by single-run.
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Educational Activities
I provide the education necessary for metabolomics and its measurement science. Specifically, I develop human resources skilled in biochemistry, analytical chemistry, and separation chemistry.