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Metabolites
Special Issues
Mass Spectrometry Imaging and Spatial Metabolomics
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Mass Spectrometry Imaging and Spatial Metabolomics

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Metabolomic Profiling Technology".

Deadline for manuscript submissions: 30 October 2025 | Viewed by 4547

Special Issue Editors

Dr. Zhonghua Wang

E-Mail Website
Guest Editor
Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, Beijing, China
Interests: mass spectrometry imaging and metabolomics
Special Issues, Collections and Topics in MDPI journals
Dr. Chenglong Sun

E-Mail Website
Guest Editor
Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
Interests: spatially resolved metabolomics

Special Issue Information

Dear Colleagues, 

Mass spectrometry imaging (MSI) combined with spatial metabolomics has emerged as a powerful tool for understanding the spatial distribution of metabolites in various biological contexts. This Special Issue aims to showcase cutting-edge research and advancements in MSI and spatial metabolomics, highlighting their applications in disease diagnostics, drug development, and biomarker discovery. We invite contributions that explore novel methodologies, technical improvements, and interdisciplinary approaches that push the boundaries of these technologies.

Dr. Zhonghua Wang
Dr. Chenglong Sun
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • mass spectrometry imaging (MSI)
  • spatial metabolomics
  • biomarker discovery
  • disease diagnostics
  • drug development
  • technical advancements
  • interdisciplinary approaches
  • imaging techniques

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Published Papers (4 papers)

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Research

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11 pages, 3387 KB  
Article
Imprint Desorption Electrospray Ionization Mass Spectrometry Imaging (IDESI-MSI) Reveals Absorption of Triclopyr-Based Herbicide in Plants and Mouse Organs
by Hanzhi Liu, Yunshuo Tian, Ruolun Wei, Yifan Meng and Richard N. Zare
Metabolites 2025, 15(7), 437; https://doi.org/10.3390/metabo15070437 - 30 Jun 2025
Viewed by 422
Abstract
Background: Understanding the absorption and distribution of herbicides in plants and animal tissues is essential for assessing their potential risks to human health. Method: In this study, we employed imprint desorption electrospray ionization mass spectrometry imaging (IDESI-MSI) to visualize in both vegetable and [...] Read more.
Background: Understanding the absorption and distribution of herbicides in plants and animal tissues is essential for assessing their potential risks to human health. Method: In this study, we employed imprint desorption electrospray ionization mass spectrometry imaging (IDESI-MSI) to visualize in both vegetable and animal tissues the absorption of Roundup which is a widely used herbicide. Results: Using IDESI-MSI with a pixel size of 150 µm, we detected the herbicide alongside several endogenous metabolites on oil-absorbing films applied to carrot sections. Time-course experiments revealed progressive herbicide penetration into carrot tissue, with penetration depth increasing linearly over time at a rate of approximately 0.25 mm/h. In contrast, green pepper samples showed minimal herbicide infiltration, likely owing to their hydrophobic cuticle barrier. Additionally, mice fed with herbicide-treated carrots exhibited detectable levels of herbicide in liver and kidney tissues. Conclusions: These findings highlight the utility of IDESI-MSI as a powerful analytical platform for the rapid evaluation of chemical migration and absorption in food and biological systems, with important implications for food safety and toxicological research. Full article
(This article belongs to the Special Issue Mass Spectrometry Imaging and Spatial Metabolomics)
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12 pages, 8273 KB  
Article
Spatial Metabolomics Profiling Reveals Curcumin Induces Metabolic Reprogramming in Three-Dimensional Tumor Spheroids
by Zihan Zhu, Yaqi Zhang, Lei Wang, Haoyuan Geng, Min Li, Shiping Chen, Xiao Wang, Panpan Chen, Chenglong Sun and Chao Zhang
Metabolites 2024, 14(9), 482; https://doi.org/10.3390/metabo14090482 - 2 Sep 2024
Cited by 3 | Viewed by 2113
Abstract
Curcumin is widely recognized for its diverse antitumor properties, ranging from breast cancer to many other types of cancers. However, its role in the tumor microenvironment remains to be elucidated. In this study, we established a 3D tumor spheroids model that can simulate [...] Read more.
Curcumin is widely recognized for its diverse antitumor properties, ranging from breast cancer to many other types of cancers. However, its role in the tumor microenvironment remains to be elucidated. In this study, we established a 3D tumor spheroids model that can simulate the growth environment of tumor cells and visualized the antitumor metabolic alteration caused by curcumin using mass spectrometry imaging technology. Our results showed that curcumin not only exerts a profound impact on the growth and proliferation of breast cancer cells but in situ multivariate statistical analysis also reveals the significant effect on the overall metabolic profile of tumor spheroids. Meanwhile, our visualization map characterized curcumin metabolic processes of reduction and glucuronidation in tumor spheroids. More importantly, abnormal metabolic pathways related to lipid metabolism and polyamine metabolism were also remodeled at the metabolite and gene levels after curcumin intervention. These insights deepen our comprehension of the regulatory mechanism of curcumin on the tumor metabolic network, furnishing powerful references for antitumor treatment. Full article
(This article belongs to the Special Issue Mass Spectrometry Imaging and Spatial Metabolomics)
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Review

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27 pages, 1703 KB  
Review
Spatially Resolved Plant Metabolomics
by Ronald J. Myers, Jr., Zachary M. Tretter, Abigail G. Daffron, Eric X. Fritschi, William Thives Santos, Maiya L. Foster, Matthew Klotz, Kristin M. Stafford, Christina Kasch, Thomas J. Taylor, Lillian C. Tellefson, Tyler Hartman, Dru Hackler, Preston Stephen and Lloyd W. Sumner
Metabolites 2025, 15(8), 539; https://doi.org/10.3390/metabo15080539 - 8 Aug 2025
Viewed by 580
Abstract
Research and innovation in metabolomics tools to measure metabolite accumulation within plants have led to important discoveries with respect to the improvement of plant stress tolerance, development, and crop yield. Traditional metabolomics analyses have commonly utilized gas chromatography–mass spectrometry and liquid chromatography–mass spectrometry, [...] Read more.
Research and innovation in metabolomics tools to measure metabolite accumulation within plants have led to important discoveries with respect to the improvement of plant stress tolerance, development, and crop yield. Traditional metabolomics analyses have commonly utilized gas chromatography–mass spectrometry and liquid chromatography–mass spectrometry, but these methods are often performed without regard for the spatial locations of metabolites within tissues. Methods for mass spectral imaging (MSI) have recently been developed to detect and spatially resolve metabolite accumulation and are rapidly being adopted on a wider scale. Since 2010, the number of publications incorporating mass spectral imaging has grown from approximately 80 articles to over 378 on a yearly basis, constituting an increase of at least 350% during this time frame. Spatially resolved metabolite accumulation data provides unique insights into the function and regulation of plant biochemical pathways. Mass spectral imaging is commonly paired with desorption ionization technologies, including matrix-assisted laser desorption ionization (MALDI) and desorption electrospray ionization (DESI), to generate accurate, spatially resolved metabolomics data from prepared tissue segments. Here, we describe the most recent advancements in sample preparation methods, mass spectral imaging technologies, and data processing tools that have been developed to address the limits of MSI technology. Additionally, we summarize recent applications of MSI technologies in plant metabolomics and discuss potential avenues for future research advancements within the plant biology community through the use of these technologies. Full article
(This article belongs to the Special Issue Mass Spectrometry Imaging and Spatial Metabolomics)
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Other

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10 pages, 1562 KB  
Technical Note
SMQVP: A Web Application for Spatial Metabolomics Quality Visualization and Processing
by Zhanlong Mei, Wan Sun, Yun Zhao, Haoke Deng, Xiaolian Ning, Chunlu Feng and Jin Zi
Metabolites 2025, 15(6), 354; https://doi.org/10.3390/metabo15060354 - 27 May 2025
Viewed by 653
Abstract
Background: Spatial metabolomics is a powerful technique that enables spatially resolved mapping of metabolite distributions at the tissue and cellular levels, providing valuable insights into biological processes. However, challenges in data quality control and preprocessing remain significant bottlenecks, critically impacting the reliability of [...] Read more.
Background: Spatial metabolomics is a powerful technique that enables spatially resolved mapping of metabolite distributions at the tissue and cellular levels, providing valuable insights into biological processes. However, challenges in data quality control and preprocessing remain significant bottlenecks, critically impacting the reliability of downstream analyses and the robustness of findings. Methods: To address these limitations, we present Spatial Metabolomics data Quality Visualization and Processing (SMQVP v1.0), a novel software with a user-friendly graphical interface designed for the systematic quality assessment and preprocessing of spatial metabolomics data. SMQVP incorporates eight comprehensive quality visualization and evaluation modules, including background consistency assessments, noise ion filtering, intensity distribution analyses, and the identification of isotopic and adduct ions. Results: We demonstrated SMQVP’s effectiveness using AFADESI-based mouse brain data, showing that the tool successfully identified and removed noise signals. This rigorous preprocessing resulted in improved clustering outcomes that more accurately reflected the underlying tissue morphology compared with analyses performed on unprocessed data. Conclusions: SMQVP is the first systematic approach focused on quality visualization, specifically for spatial metabolomics. It offers researchers an accessible and comprehensive solution for enhancing data integrity and mitigating the impact of technical noise, thereby improving the reliability and robustness of their spatial metabolomics findings. Full article
(This article belongs to the Special Issue Mass Spectrometry Imaging and Spatial Metabolomics)
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