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Spatial Molecular Imaging of the Glycome Using Mass Spectrometry
Published on: November 28, 2025
Authentic Spatial Metabolomics by Avoiding Hidden Pitfalls in MSI Workflows
Jinyu Zhou1,2, Shengxi Li1,2, Yinghao Cao1,3
1State Key Laboratory of Common Mechanism Research for Major Disease, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing100730, China.
Analytical Chemistry
|July 16, 2026
Summary
This study identifies four overlooked pitfalls in mass spectrometry imaging (MSI) workflows, including metabolic quenching and matrix effects. Actionable strategies are provided for more reliable spatial metabolomics in research.
Area of Science:
- Analytical Chemistry
- Biochemistry
- Molecular Imaging
Background:
- Mass spectrometry imaging (MSI) enables visualization of molecular distribution in tissues.
- Challenges in MSI include sample preparation and instrumental limitations, hindering reproducible metabolic maps.
Purpose of the Study:
- To identify and address critical, overlooked pitfalls in mass spectrometry imaging (MSI) workflows.
- To provide practical strategies for enhancing the reliability of spatial metabolomics.
Main Methods:
- Evaluation of four key pitfalls: metabolic quenching, matrix effects, mass resolving power, and quadrupole isolation width.
- Implementation of heat stabilization, isotope-labeled internal standards, ultrahigh resolution, and spatial correlation analysis.
Main Results:
- Thaw-mounting reactivates enzymes; heat stabilization mitigates this.
- Matrix effects can be corrected using isotope-labeled internal standards.
- Ultrahigh resolution is crucial for distinguishing isobaric species; spatial correlation analysis deconvolutes MS/MS spectra.
Conclusions:
- Overcoming identified pitfalls is essential for authentic and reproducible metabolic maps.
- The study offers a practical framework for improving spatial metabolomics in preclinical and clinical research.