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RIKEN Center for Biosystems Dynamics Research Laboratory for Single Cell Mass Spectrometry

Team Leader: Eisuke Nishida (Ph.D.)

Research Summary

Eisuke Nishida (Ph.D.)

Cells, the building blocks of life, show various responses to stimuli. Clarification of these cellular dynamics by comprehensive and quantitative evaluation of the changes over time can help us to understand various aspects of life, such as cellular responses to environmental changes, molecular mechanisms of development, and mechanisms of carcinogenesis of cells etc. The Laboratory for Single Cell Mass Spectrometry aims to develop technologies to comprehensively reveal intracellular metabolites and proteins at a single cell level by using a single cell mass spectrometry technique with a nanospray chip and a capillary electrophoresis mass spectrometry technique. We also aim to further develop the established technologies for single cell drug discovery and novel diagnostic techniques.

Main Research Fields

  • Chemistry

Related Research Fields

  • Engineering
  • Biological Sciences
  • Biology
  • Medicine, Dentistry & Pharmacy
  • Analytical chemistry


  • Mass spectrometry
  • Single cell analysis
  • Metabolomics
  • Proteome
  • Capillary electrophoresis

Research Subjects

  • Development of Live Single Cell Mass Spectrometry (Live MS)
  • Application of Live MS to Cell Molecular Dynamism
  • Application of Live MS to Developmental Biology
  • Pico-Medicine and Pico-Diagnosis
  • Probe-imaging Single Cell Mass Spectrometry

Selected Publications

  • 1. Kawai T, Ota N, Okada K, et al.:
    "Ultrasensitive single cell metabolomics by capillary electrophoresis-mass spectrometry with a thin-walled tapered emitter and large-volume dual sample preconcentration"
    Analytical Chemistry 91, 10564-10572 (2019) doi: 10.1021/acs.analchem.9b01578
  • 2. Ali A, Abouleila Y, Shimizu Y, et al.:
    "Single-cell screening of tamoxifen abundance and effect using mass spectrometry and Raman-spectroscopy"
    Analytical Chemistry 91(4). 2710-2718 (2019) doi: 10.1021/acs.analchem.8b04393
  • 3. Kawai T, Ota N, Imasato A, et al.:
    "Profiling of N-linked glycans from 100 cells by capillary electrophoresis with large-volume dual preconcentration by isotachophoresis and stacking"
    Journal of Chromatography A 1563. 138-144 (2018) doi: 10.1016/j.chroma.2018.06.034
  • 4. Narumi R, Masuda K, Tomonaga T, et al.:
    "Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics"
    Synthetic and Systems Biotechnology 3. 97-104 doi:10.1016/j.synbio.2018.02.004
  • 5. Masuda K, Abouleila Y, Ali A, et al.:
    "Live Single-Cell Mass Spectrometry for Plant Metabolomics"
    Methods in Molecular Biology 1778. 269-282 (2018) doi:10.1007/978-1-4939-7819-9_19
  • 6. Emara S, Amer S, Ali A, et al.:
    "Single-Cell Metabolomics"
    Advances in Experimental Medicine and Biology 965. 323-343 (2017) doi:10.1007/978-3-319-47656-8_13
  • 7. Ali A, Abouleila Y, Amer S, et al.:
    "Quantitative Live Single-cell Mass Spectrometry with Spatial Evaluation by Three-Dimensional Holographic and Tomographic Laser Microscopy"
    Analytical Sciences 32(2). 125-127 (2016) doi:10.2116/analsci.32.125
  • 8. Yamamoto K, Takahashi K, Mizuno H, et al.:
    "Cell-specific localization of alkaloids in Catharanthus roseus stem tissue measured with Imaging MS and Single-cell MS"
    Proceedings of the National Academy of Sciences of the United States of America 113(14). 3891-3896 (2016) doi:10.1073/pnas.1521959113
  • 9. Hiyama E, Ali A, Amer S, et al.:
    "Direct Lipido-Metabolomics of Single Floating Cells for Analysis of Circulating Tumor Cells by Live Single-cell Mass Spectrometry"
    Analytical Sciences 31(12). 1215-1217 (2015) doi:10.2116/analsci.31.1215
  • 10. Esaki T, Masujima T.:
    "Fluorescence Probing Live Single-cell Mass Spectrometry for Direct Analysis of Organelle Metabolism"
    Analytical Sciences 31(12). 1211-1213. (2015) doi:10.2116/analsci.31.1211

Related Links

Lab Members

Principal investigator

Eisuke Nishida
Team Leader

Core members

Yoshihiro Shimizu
Senior Scientist
Keiko Masuda
Postdoctoral Researcher
Ahmed Ali
Research Associate
Yasmine Abouleila
Research Associate
Takayuki Kawai
Special Postdoctoral Researcher

Contact Information

Quantitative Biology Building B
6-2-4, Furuedai, Suita, Osaka
Tel: +81-(0)6-6155-0448
Fax: +81-(0)6-6872-4853
Email: yshimizu [at] riken.jp