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Enabling Live Single-Cell Metabolomics: Mass Spectrometry Technologies and Functional Applications

  • Simin Cheng 1,2,   
  • Danni Wu 2,   
  • Xiaoxiao Ma 2,*,   
  • Xiaoyun Gong 1,*

Received: 23 Jul 2025 | Revised: 06 Sep 2025 | Accepted: 18 Sep 2025 | Published: 12 Jan 2026

Abstract

As the fundamental unit of life, the metabolic state of an individual cell is regarded as a direct indicator of its physiological and pathological processes. Live single-cell mass spectrometry (Live-SCMS) has emerged as a key technique at the intersection of metabolomics and single-cell biology, with recent advancements in sampling strategies, signal detection, and biocompatibility. Conventional single-cell metabolite detection methods based on bulk-cell or fixed-cell analyses are often destructive and preclude further cellular analysis. In contrast, Live-SCMS enables in situ and dynamic profiling of cellular metabolism while preserving cellular integrity and viability. This review systematically outlines the core strategies of Live-SCMS, including minimally invasive sampling, low-perturbation workflows in buffered environments, biocompatible labeling, and isotope tracing. It emphasizes the unique advantages of the technique over traditional methods, such as higher sensitivity, improved spatial resolution, and real-time analysis capability, all achieved without compromising cell viability. Recent applications in cancer metabolism, drug response, immune cell functional profiling, and studies of plants, embryos, and microbial models are summarized. Future perspectives on technological advancement, broader biological applications, and clinical relevance are also provided

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DOI
10.53941/hm.2026.100004
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Volume 3, Issue 1
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Cheng, S.; Wu, D.; Ma, X.; Gong, X. Enabling Live Single-Cell Metabolomics: Mass Spectrometry Technologies and Functional Applications. Health and Metabolism 2026, 3 (1), 4. https://doi.org/10.53941/hm.2026.100004.
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