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Updated: Nov 4, 2025
Sample Preparation for Single Cell Mass Spectrometry Metabolomics Studies: Combined Cell Washing, Quenching, Drying, and Storage
Published on: September 16, 2025
Mass spectrometry-based strategies for single-cell metabolomics
Rui Hu1,2, Ying Li1,2, Yunhuang Yang1,2
1Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China.
Single-cell metabolomics (SCM) analyzes cellular heterogeneity, offering new biomarker discovery. Despite challenges like metabolite instability, mass spectrometry-based SCM advances offer powerful insights.
Area of Science:
- Biochemistry
- Cell Biology
- Analytical Chemistry
Background:
- Single-cell analysis reveals cellular heterogeneity, crucial for tissue classification and biomarker discovery.
- Multi-omics at the single-cell level (genomics, transcriptomics, metabolomics, proteomics) are increasingly feasible.
- Single-cell metabolomics (SCM) is challenging due to metabolite instability and concentration ranges, unlike other omics.
Purpose of the Study:
- To review recent advancements in mass spectrometry-based single-cell metabolomics (SCM).
- To discuss progress in SCM platforms, sample preparation, and applications across diverse cell types.
- To highlight current limitations and future research avenues in SCM.
Main Methods:
- Review of mass spectrometry (MS) platforms for SCM.
- Analysis of sample preparation techniques for SCM.
- Summary of SCM applications in plant, cancer, neuron, embryo, and yeast cells.
Main Results:
- Significant progress in MS-based SCM technologies and biochemical applications over the last decade.
- Development of various MS platforms and sample preparation methods tailored for SCM.
- Demonstrated SCM applicability across a wide range of cell types.
Conclusions:
- SCM is a rapidly advancing field with growing potential for biological research.
- Overcoming challenges in metabolite handling is key to unlocking SCM's full capabilities.
- Future research should focus on refining SCM techniques and expanding its applications.
