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Yin Z, Huang W, Li K, Fernie AR, Yan S. Advances in mass spectrometry imaging for plant metabolomics-Expanding the analytical toolbox. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2168-2180. [PMID: 38990529 DOI: 10.1111/tpj.16924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024]
Abstract
Mass spectrometry imaging (MSI) has become increasingly popular in plant science due to its ability to characterize complex chemical, spatial, and temporal aspects of plant metabolism. Over the past decade, as the emerging and unique features of various MSI techniques have continued to support new discoveries in studies of plant metabolism closely associated with various aspects of plant function and physiology, spatial metabolomics based on MSI techniques has positioned it at the forefront of plant metabolic studies, providing the opportunity for far higher resolution than was previously available. Despite these efforts, profound challenges at the levels of spatial resolution, sensitivity, quantitative ability, chemical confidence, isomer discrimination, and spatial multi-omics integration, undoubtedly remain. In this Perspective, we provide a contemporary overview of the emergent MSI techniques widely used in the plant sciences, with particular emphasis on recent advances in methodological breakthroughs. Having established the detailed context of MSI, we outline both the golden opportunities and key challenges currently facing plant metabolomics, presenting our vision as to how the enormous potential of MSI technologies will contribute to progress in plant science in the coming years.
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Affiliation(s)
- Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Institute of Advanced Science Facilities, Shenzhen, 518107, Guangdong, China
| | - Wenjie Huang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Kun Li
- Guangdong Key Laboratory of Crop Genetic Improvement, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
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2
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Chen J, Larsson L, Swarbrick A, Lundeberg J. Spatial landscapes of cancers: insights and opportunities. Nat Rev Clin Oncol 2024; 21:660-674. [PMID: 39043872 DOI: 10.1038/s41571-024-00926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2024] [Indexed: 07/25/2024]
Abstract
Solid tumours comprise many different cell types organized in spatially structured arrangements, with substantial intratumour and intertumour heterogeneity. Advances in spatial profiling technologies over the past decade hold promise to capture the complexity of these cellular architectures to build a holistic view of the intricate molecular mechanisms that shape the tumour ecosystem. Some of these mechanisms act at the cellular scale and are controlled by cell-autonomous programmes or communication between nearby cells, whereas other mechanisms result from coordinated efforts between large networks of cells and extracellular molecules organized into tissues and organs. In this Review we provide insights into the application of single-cell and spatial profiling tools, with a focus on spatially resolved transcriptomic tools developed to understand the cellular architecture of the tumour microenvironment and identify opportunities to use them to improve clinical management of cancers.
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Affiliation(s)
- Julia Chen
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Department of Medical Oncology, St George Hospital, Sydney, New South Wales, Australia
| | - Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
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3
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Leontyev D, Olivos H, Shrestha B, Datta Roy PM, LaPlaca MC, Fernández FM. Desorption Electrospray Ionization Cyclic Ion Mobility-Mass Spectrometry Imaging for Traumatic Brain Injury Spatial Metabolomics. Anal Chem 2024; 96:13598-13606. [PMID: 39106040 PMCID: PMC11339727 DOI: 10.1021/acs.analchem.4c02394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/20/2024] [Accepted: 07/25/2024] [Indexed: 08/07/2024]
Abstract
Lipidomics focuses on investigating alterations in a wide variety of lipids that harness important information on metabolic processes and disease pathology. However, the vast structural diversity of lipids and the presence of isobaric and isomeric species creates serious challenges in feature identification, particularly in mass spectrometry imaging experiments that lack front-end separations. Ion mobility has emerged as a potential solution to address some of these challenges and is increasingly being utilized as part of mass spectrometry imaging platforms. Here, we present the results of a pilot mass spectrometry imaging study on rat brains subjected to traumatic brain injury (TBI) to evaluate the depth and quality of the information yielded by desorption electrospray ionization cyclic ion mobility mass spectrometry (DESI cIM MSI). Imaging data were collected with one and six passes through the cIM cell. Increasing the number of passes increased the ion mobility resolving power and the resolution of isobaric lipids, enabling the creation of more specific maps. Interestingly, drift time data enabled the recognition of multiply charged phosphoinositide species in the complex data set generated. These species have not been previously reported in TBI MSI studies and were found to decrease in the hippocampus region following injury. These changes were attributed to increased enzymatic activity after TBI, releasing arachidonic acid that is converted to eicosanoids to control inflammation. A substantial reduction in NAD and alterations in other adenine metabolites were also observed, supporting the hypothesis that energy metabolism in the brain is severely disrupted in TBI.
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Affiliation(s)
- Dmitry Leontyev
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United State
| | - Hernando Olivos
- Waters
Corporation, Milford, Massachusetts 01757, United State
| | | | - Pooja M. Datta Roy
- Coulter
Department of Biomedical Engineering, Georgia
Institute of Technology/Emory University, Atlanta, Georgia 30332, United State
| | - Michelle C. LaPlaca
- Coulter
Department of Biomedical Engineering, Georgia
Institute of Technology/Emory University, Atlanta, Georgia 30332, United State
- Parker
H. Petit Institute for Bioengineering and Bioscience, Atlanta, Georgia 30332, United
States
| | - Facundo M. Fernández
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United State
- Parker
H. Petit Institute for Bioengineering and Bioscience, Atlanta, Georgia 30332, United
States
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4
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de Almeida CM, Dos Santos NA, Lacerda V, Ma X, Fernández FM, Romão W. Applications of MALDI mass spectrometry in forensic science. Anal Bioanal Chem 2024:10.1007/s00216-024-05470-y. [PMID: 39160439 DOI: 10.1007/s00216-024-05470-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 08/21/2024]
Abstract
Forensic chemistry literature has grown exponentially, with many analytical techniques being used to provide valuable information to help solve criminal cases. Among them, matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), particularly MALDI MS imaging (MALDI MSI), has shown much potential in forensic applications. Due to its high specificity, MALDI MSI can analyze a wide variety of compounds in complex samples without extensive sample preparation, providing chemical profiles and spatial distributions of given analyte(s). This review introduces MALDI MS(I) to forensic scientists with a focus on its basic principles and the applications of MALDI MS(I) to the analysis of fingerprints, drugs of abuse, and their metabolites in hair, medicine samples, animal tissues, and inks in documents.
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Affiliation(s)
- Camila M de Almeida
- Laboratory of Petroleomics and Forensics, Universidade Federal Do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Goiabeiras, Vitória, Espírito Santo, 29075-910, Brazil
| | - Nayara A Dos Santos
- Laboratory of Petroleomics and Forensics, Universidade Federal Do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Goiabeiras, Vitória, Espírito Santo, 29075-910, Brazil
- Instituto Nacional de Ciência E Tecnologia Forense (INCT Forense), Vila Velha, Brazil
| | - Valdemar Lacerda
- Laboratory of Petroleomics and Forensics, Universidade Federal Do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Goiabeiras, Vitória, Espírito Santo, 29075-910, Brazil
| | - Xin Ma
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wanderson Romão
- Laboratory of Petroleomics and Forensics, Universidade Federal Do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Goiabeiras, Vitória, Espírito Santo, 29075-910, Brazil.
- Instituto Nacional de Ciência E Tecnologia Forense (INCT Forense), Vila Velha, Brazil.
- Instituto Federal Do Espírito Santo (IFES), Av. Ministro Salgado Filho, Soteco, Vila Velha, Espírito Santo, 29106-010, Brazil.
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5
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Liu T, Wang P, Chen Y, Sun B, Li Q, Wan H, Yang W, Ma P, Zhang D, Dong G, Chen S, Chen Q, Ma W, Sun W. LC-MS and MALDI-MSI-based metabolomic approaches provide insights into the spatial-temporal metabolite profiles of Tartary buckwheat achene development. Food Chem 2024; 449:139183. [PMID: 38604028 DOI: 10.1016/j.foodchem.2024.139183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/03/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Tartary buckwheat, celebrated as the "king of grains" for its flavonoid and phenolic acid richness, has health-promoting properties. Despite significant morphological and metabolic variations in mature achenes, research on their developmental process is limited. Utilizing Liquid chromatography-mass spectrometry and atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry imaging, we conducted spatial-temporal metabolomics on two cultivars during achene development. Metabolic profiles including 17 phenolic acids and 83 flavonoids are influenced by both varietal distinctions and developmental intricacies. Notably, flavonols, as major flavonoids, accumulated with achene ripening and showed a tissue-specific distribution. Specifically, flavonol glycosides and aglycones concentrated in the embryo, while methylated flavonols and procyanidins in the hull. Black achenes at the green achene stage have higher bioactive compounds and enhanced antioxidant capacity. These findings provide insights into spatial and temporal characteristics of metabolites in Tartary buckwheat achenes and serve as a theoretical guide for selecting optimal resources for food production.
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Affiliation(s)
- Tingxia Liu
- College of Pharmaceutical Sciences, Heilongjiang University of Chinese Medicine, Harbin 150040, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Peng Wang
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Yiling Chen
- Amway (China) Botanical R&D Centre, Wuxi 214115, China
| | - Boshi Sun
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Qing Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Huihua Wan
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wei Yang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Pengda Ma
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Dong Zhang
- College of Agriculture, South China Agricultural University, Guangzhou Laboratory for Lingnan Modern Agriculture Science and Technology, Guangzhou 510642, China
| | | | - Shilin Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qingfu Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Baoshan Beilu15 116, Guiyang 550001, China
| | - Wei Ma
- College of Pharmaceutical Sciences, Heilongjiang University of Chinese Medicine, Harbin 150040, China.
| | - Wei Sun
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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6
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Ruman T, Krupa Z, Nizioł J. Direct Three-Dimensional Mass Spectrometry Imaging with Laser Ablation Remote Atmospheric Pressure Photoionization/Chemical Ionization. Anal Chem 2024; 96:13326-13334. [PMID: 39077860 PMCID: PMC11325297 DOI: 10.1021/acs.analchem.4c03402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The laser ablation remote atmospheric pressure photoionization/chemical ionization (LARAPPI/CI) platform coupled to an ultrahigh resolution quadrupole-time-of-flight (QToF) mass spectrometer was developed and employed for the first direct three-dimensional (3D) mass spectrometry imaging (MSI) of metabolites in human and plant tissues. Our solution for 3D MSI does not require sample modification or cutting into thin slices. Ablation characteristics of an optical system based on a diffraction optical element are studied and used for voxel stacking to directly remove layers of tissues. Agar gel, red radish, kiwi, human kidney cancer, and normal tissue samples were used for the tests of this new system. The 2D and 3D ion images vividly illustrate differences in the abundances of selected metabolites between cancerous and noncancerous regions of the kidney tissue and also between different parts of plant tissues. The LARAPPI/CI MSI setup is also the first example of the successful use of combined dopant-assisted atmospheric pressure photoionization (DA-APPI) and atmospheric pressure chemical ionization (APCI) ion source for mass spectrometry imaging.
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Affiliation(s)
- Tomasz Ruman
- Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, Rzeszów University of Technology, 6 Powstan ́ców Warszawy Ave., Rzeszów 35-959. Poland
| | - Zuzanna Krupa
- Doctoral School of Engineering and Technical Sciences at the Rzeszów University of Technology, 8 Powstan ́ców Warszawy Ave., Rzeszów 35-959, Poland
| | - Joanna Nizioł
- Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, Rzeszów University of Technology, 6 Powstan ́ców Warszawy Ave., Rzeszów 35-959. Poland
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7
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Shen X, Guan Z, Zhang C, Yan Z, Sun C. The multicellular compartmentation of plant specialized metabolism. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102616. [PMID: 39142253 DOI: 10.1016/j.pbi.2024.102616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/16/2024]
Abstract
The phenomenon of multicellular compartmentation in biosynthetic pathways has been documented for only a limited subset of specialized metabolites, despite its hypothesized significance in facilitating plant survival and adaptation to environmental stress. Transporters that shuttle metabolic intermediates between cells are hypothesized to be integral components enabling compartmentalized biosynthesis. Nevertheless, our understanding of the multicellular compartmentation of plant specialized metabolism and the associated intermediate transporters remains incomplete. The emergence of single-cell and spatial multiomics techniques holds promise for shedding light on unresolved questions in this field, such as the prevalence of multicellular compartmentation across the plant kingdom and the specific types of specialized metabolites whose biosynthetic pathways are prone to compartmentation. Advancing our understanding of the mechanisms underlying multicellular compartmentation will contribute to improving the production of specialized target metabolites through metabolic engineering or synthetic biology.
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Affiliation(s)
- Xiaofeng Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing, 100700, China
| | - Zhijing Guan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Chuyi Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Zhaojiu Yan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Chao Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing, 100700, China.
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8
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McKinnon JC, Balez R, Young RSE, Brown ML, Lum JS, Robinson L, Belov ME, Ooi L, Tortorella S, Mitchell TW, Ellis SR. MALDI-2-Enabled Oversampling for the Mass Spectrometry Imaging of Metabolites at Single-Cell Resolution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39137242 DOI: 10.1021/jasms.4c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can provide valuable insights into the metabolome of complex biological systems such as organ tissues and cells. However, obtaining metabolite data at single-cell spatial resolutions presents a few technological challenges. Generally, spatial resolution is defined by the increment the sample stage moves between laser ablation spots. Stage movements less than the diameter of the focused laser beam (i.e., oversampling) can improve spatial resolution; however, such oversampling conditions result in a reduction in sensitivity. To overcome this, we combine an oversampling approach with laser postionization (MALDI-2), which allows for both higher spatial resolution and improved analyte ionization efficiencies. This approach provides significant enhancements to sensitivity for various metabolite classes (e.g., amino acids, purines, carbohydrates etc.), with mass spectral intensities from 6 to 8 μm pixel sizes (from a laser spot size of ∼13 μm) being commensurate with or higher than those obtained by conventional MALDI at 20 μm pixel sizes for many different metabolites. This technique has been used to map the distribution of metabolites throughout mouse spinal cord tissue to observe how metabolite localizations change throughout specific anatomical regions, such as those distributed to the somatosensory area of the dorsal horn, white matter, gray matter, and ventral horn. Furthermore, this method is utilized for single-cell metabolomics of human iPSC-derived astrocytes at 10 μm pixel sizes whereby many different metabolites, including nucleotides, were detected from individual cells while providing insight into cellular localizations.
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Affiliation(s)
- Jayden C McKinnon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia
| | - Rachelle Balez
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia
| | - Reuben S E Young
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia
| | - Mikayla L Brown
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia
| | - Jeremy S Lum
- Molecular Horizons, School of Medical, Indigenous and Health Science, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia
| | - Liam Robinson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia
| | - Mikhail E Belov
- Spectroglyph LLC, Kennewick, Washington 99338, United States
| | - Lezanne Ooi
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia
| | - Sara Tortorella
- Molecular Horizon srl, Via Montelino 30, Bettona, PG 06084, Italy
| | - Todd W Mitchell
- Molecular Horizons, School of Medical, Indigenous and Health Science, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia
| | - Shane R Ellis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia
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9
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Djambazova K, Gibson-Corley KN, Freiberg JA, Caprioli RM, Skaar EP, Spraggins JM. MALDI TIMS IMS Reveals Ganglioside Molecular Diversity within Murine S. aureus Kidney Tissue Abscesses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1692-1701. [PMID: 39052897 PMCID: PMC11311236 DOI: 10.1021/jasms.4c00089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/11/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
Gangliosides play important roles in innate and adaptive immunity. The high degree of structural heterogeneity results in significant variability in ganglioside expression patterns and greatly complicates linking structure and function. Structural characterization at the site of infection is essential in elucidating host ganglioside function in response to invading pathogens, such as Staphylococcus aureus (S. aureus). Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) enables high-specificity spatial investigation of intact gangliosides. Here, ganglioside structural and spatial heterogeneity within an S. aureus-infected mouse kidney abscess was characterized. Differences in spatial distributions were observed for gangliosides of different classes and those that differ in ceramide chain composition and oligosaccharide-bound sialic acid. Furthermore, integrating trapped ion mobility spectrometry (TIMS) allowed for the gas-phase separation and visualization of monosialylated ganglioside isomers that differ in sialic acid type and position. The isomers differ in spatial distributions within the host-pathogen interface, where molecular patterns revealed new molecular zones in the abscess previously unidentified by traditional histology.
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Affiliation(s)
- Katerina
V. Djambazova
- Department
of Cell and Developmental Biology, Vanderbilt
University, Nashville, Tennessee 37232, United States
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37232, United States
| | - Katherine N. Gibson-Corley
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Jeffrey A. Freiberg
- Vanderbilt
Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Division
of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Richard M. Caprioli
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37232, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Eric P. Skaar
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Institute for Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37232, United States
| | - Jeffrey M. Spraggins
- Department
of Cell and Developmental Biology, Vanderbilt
University, Nashville, Tennessee 37232, United States
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37232, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
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10
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Vallianatou T, Angerer TB, Kaya I, Nilsson A, Shariatgorji R, Svenningsson P, Andrén PE. Applying Spatial Metabolomics To Investigate Age- and Drug-Induced Neurochemical Changes. ACS Chem Neurosci 2024; 15:2822-2829. [PMID: 39072364 PMCID: PMC11311129 DOI: 10.1021/acschemneuro.4c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/14/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024] Open
Abstract
In an era when population aging is increasing the burden of neurodegenerative conditions, deciphering the mechanisms underlying brain senescence is more important than ever. Here, we present a spatial metabolomics analysis of age-induced neurochemical alterations in the mouse brain using negative ionization mode mass spectrometry imaging. The age-dependent effects of the acetylcholinesterase inhibitor tacrine were simultaneously examined. For ultrahigh mass resolution analysis, we utilized a Fourier-transform ion cyclotron resonance spectrometer. To complement this, a trapped ion mobility spectrometry time-of-flight analyzer provided high speed and lateral resolution. The chosen approach facilitated the detection and identification of a wide range of metabolites, from amino acids to sphingolipids. We reported significant, age-dependent alterations in brain lipids which were most evident for sulfatides and lysophosphatidic acids. Sulfatide species, which are mainly localized to white matter, either increased or decreased with age, depending on the carbon chain length and hydroxylation stage. Lysophosphatidic acids were found to decrease with age in the detailed cortical and hippocampal subregions. An age-dependent increase in the glutamine/glutamate ratio, an indicator of glia-neuron interconnection and neurotoxicity, was detected after tacrine administration. The presented metabolic mapping approach was able to provide visualizations of the lipid signaling and neurotransmission alterations induced by early aging and can thus be beneficial to further elucidating age-related neurochemical pathways.
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Affiliation(s)
- Theodosia Vallianatou
- Department
of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science
for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Tina B. Angerer
- Department
of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science
for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Ibrahim Kaya
- Department
of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science
for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Anna Nilsson
- Department
of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science
for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Reza Shariatgorji
- Department
of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science
for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Per Svenningsson
- Department
of Clinical Neuroscience, Karolinska Institute, Stockholm SE-17177, Sweden
| | - Per E. Andrén
- Department
of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science
for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
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11
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Sohn AL, Bowman AP, Barnes MM, Kullman SW, Muddiman DC. Oversampling for Enhanced Spatial Resolution of Zebrafish by Top-Hat IR-MALDESI-MSI. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1959-1968. [PMID: 38985437 DOI: 10.1021/jasms.4c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Mass spectrometry imaging (MSI) has become a significant tool for measuring chemical species in biological tissues, where much of the impact of these platforms lies in their capability to report the spatial distribution of analytes for correlation to sample morphology. As a result, enhancement of spatial resolution has become a frontier of innovation in the field, and necessary developments are dependent on the ionization source. More particularly, laser-based imaging sources may require modifications to the optical train or alternative sampling techniques. These challenges are heightened for systems with infrared (IR) lasers, as their operating wavelength generates spot sizes that are inherently larger than their ultraviolet counterparts. Recently, the infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) source has shown the utility of a diffractive optical element (DOE) to produce square ablation patterns, termed top-hat IR-MALDESI. If the DOE optic is combined with oversampling methods, smaller ablation volumes can be sampled to render higher spatial resolution imaging experiments. Further, this approach enables reproducible spot sizes and ablation volumes for better comparison between scans. Herein, we investigate the utility of oversampling with top-hat IR-MALDESI to enhance the spatial resolution of measured lipids localized within the head of sectioned zebrafish tissue. Four different spatial resolutions were evaluated for data quality (e.g., mass measurement accuracy, spectral accuracy) and quantity of annotations. Other experimental parameters to consider for high spatial resolution imaging are also discussed. Ultimately, 20 μm spatial resolution was achieved in this work and supports feasibility for use in future IR-MALDESI studies.
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Affiliation(s)
- Alexandria L Sohn
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | | | - Morgan M Barnes
- Toxicology Program, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Seth W Kullman
- Toxicology Program, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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12
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Bhushan V, Nita-Lazar A. Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology. J Proteome Res 2024; 23:2700-2722. [PMID: 38451675 PMCID: PMC11296931 DOI: 10.1021/acs.jproteome.3c00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell equilibrium. Cellular processes such as signaling, growth, proliferation, motility, and programmed cell death require dynamic protein movements between cell compartments. Aberrant protein localization is associated with a wide range of diseases. Therefore, analyzing the subcellular proteome of the cell can provide a comprehensive overview of cellular biology. With recent advancements in mass spectrometry, imaging technology, computational tools, and deep machine learning algorithms, studies pertaining to subcellular protein localization and their dynamic distributions are gaining momentum. These studies reveal changing interaction networks because of "moonlighting proteins" and serve as a discovery tool for disease network mechanisms. Consequently, this review aims to provide a comprehensive repository for recent advancements in subcellular proteomics subcontexting methods, challenges, and future perspectives for method developers. In summary, subcellular proteomics is crucial to the understanding of the fundamental cellular mechanisms and the associated diseases.
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Affiliation(s)
- Vanya Bhushan
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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13
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Geng Z, Jin Q, Liu L, Huang Y, Zhou X, Zhang X, Sun W. Enhanced MALDI-2 Sensitivity with Reflecting Post-Ionization Laser for High-Resolution MS Imaging Combined with Real-Time Microscope Imaging. Anal Chem 2024. [PMID: 39093983 DOI: 10.1021/acs.analchem.4c00576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Laser-induced matrix-assisted laser desorption/ionization post-ionization (MALDI-2) could improve the MALDI sensitivity of biological metabolites by over 1 order of magnitude. Herein, we demonstrate that MALDI-2 sensitivity can be further enhanced with reflecting post-ionization laser that multiplies the intersection times between laser and MALDI plume. This method, which we named MALDI-2+, typically brought over 2 times sensitivity improvement from conventional MALDI-2. Advancing in sensitivity thereby prompted us to pursue higher mass spectrometry imaging (MSI) spatial resolution. A dedicated T-shaped ion guide was designed to allow perpendicular incidence of ablation laser in reflection geometry MALDI. Although 8-10 μm pixel was used in MALDI imaging due to the limited precision of the motorized stage, the laser spot diameter could be down to 2.5 μm for potentially higher spatial resolution. In addition, this ion source enabled real-time and high-quality microscope imaging from backward of the sample plate. Beneficially, we were able to monitor the actual laser spot condition in real time as well as obtain high-resolution microscopic sample images that inherently register with MSI images. All of these benefits have been demonstrated by analyzing standard samples and imaging of cells. We believe that the enhancement in sensitivity, spatial resolution, and microscope capacity of our design could facilitate spatial omics studies.
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Affiliation(s)
- Zhi Geng
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
| | - Qiao Jin
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
| | - Lin Liu
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
| | - Yuanyuan Huang
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
| | - Xinfeng Zhou
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
| | - Xiaoqiang Zhang
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
| | - Wenjian Sun
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
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14
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Zivko C, Hahm TH, Tressler C, Brown D, Glunde K, Mahairaki V. Mass Spectrometry Imaging of Organoids to Improve Preclinical Research. Adv Healthc Mater 2024; 13:e2302499. [PMID: 38247228 DOI: 10.1002/adhm.202302499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/18/2023] [Indexed: 01/23/2024]
Abstract
Preclinical models are essential research tools before novel therapeutic or diagnostic methods can be applied to humans. These range from in vitro cell monocultures to vastly more complex animal models, but clinical translation to humans often fails to deliver significant results. Three-dimensional (3D) organoid systems are being increasingly studied to establish physiologically relevant in vitro platforms in a trade-off between the complexity of the research question and the complexity of practical experimental setups. The sensitivity and precision of analytical tools are yet another limiting factors in what can be investigated, and mass spectrometry (MS) is one of the most powerful analytical techniques available to the scientific community. Its innovative use to spatially resolve biological samples has opened many research avenues in the field of MS imaging (MSI). Here, this work aims to explore the current scientific landscape in the application of MSI on organoids, with an emphasis on their combined potential to facilitate and improve preclinical studies.
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Affiliation(s)
- Cristina Zivko
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Tae-Hun Hahm
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Cay Tressler
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Dalton Brown
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Kristine Glunde
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Vasiliki Mahairaki
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
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15
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Veličković M, Wu R, Gao Y, Thairu MW, Veličković D, Munoz N, Clendinen CS, Bilbao A, Chu RK, Lalli PM, Zemaitis K, Nicora CD, Kyle JE, Orton D, Williams S, Zhu Y, Zhao R, Monroe ME, Moore RJ, Webb-Robertson BJM, Bramer LM, Currie CR, Piehowski PD, Burnum-Johnson KE. Mapping microhabitats of lignocellulose decomposition by a microbial consortium. Nat Chem Biol 2024; 20:1033-1043. [PMID: 38302607 PMCID: PMC11288888 DOI: 10.1038/s41589-023-01536-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
The leaf-cutter ant fungal garden ecosystem is a naturally evolved model system for efficient plant biomass degradation. Degradation processes mediated by the symbiotic fungus Leucoagaricus gongylophorus are difficult to characterize due to dynamic metabolisms and spatial complexity of the system. Herein, we performed microscale imaging across 12-µm-thick adjacent sections of Atta cephalotes fungal gardens and applied a metabolome-informed proteome imaging approach to map lignin degradation. This approach combines two spatial multiomics mass spectrometry modalities that enabled us to visualize colocalized metabolites and proteins across and through the fungal garden. Spatially profiled metabolites revealed an accumulation of lignin-related products, outlining morphologically unique lignin microhabitats. Metaproteomic analyses of these microhabitats revealed carbohydrate-degrading enzymes, indicating a prominent fungal role in lignocellulose decomposition. Integration of metabolome-informed proteome imaging data provides a comprehensive view of underlying biological pathways to inform our understanding of metabolic fungal pathways in plant matter degradation within the micrometer-scale environment.
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Affiliation(s)
- Marija Veličković
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Margaret W Thairu
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Dušan Veličković
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nathalie Munoz
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chaevien S Clendinen
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Aivett Bilbao
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rosalie K Chu
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Priscila M Lalli
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kevin Zemaitis
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarai Williams
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ying Zhu
- Department of Microchemistry, Proteomics, Lipidomics, and Next Generation Sequencing, Genentech, San Francisco, CA, USA
| | - Rui Zhao
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Paul D Piehowski
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
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16
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Jamal QMS, Ahmad V. Bacterial metabolomics: current applications for human welfare and future aspects. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024:1-24. [PMID: 39078342 DOI: 10.1080/10286020.2024.2385365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 07/31/2024]
Abstract
An imbalanced microbiome is linked to several diseases, such as cancer, inflammatory bowel disease, obesity, and even neurological disorders. Bacteria and their by-products are used for various industrial and clinical purposes. The metabolites under discussion were chosen based on their biological impacts on host and gut microbiota interactions as established by metabolome research. The separation of bacterial metabolites by using statistics and machine learning analysis creates new opportunities for applications of bacteria and their metabolites in the environmental and medical sciences. Thus, the metabolite production strategies, methodologies, and importance of bacterial metabolites for human well-being are discussed in this review.
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Varish Ahmad
- Health Information Technology Department, The Applied College, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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17
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Zhu E, Xie Q, Huang X, Zhang Z. Application of spatial omics in gastric cancer. Pathol Res Pract 2024; 262:155503. [PMID: 39128411 DOI: 10.1016/j.prp.2024.155503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/13/2024]
Abstract
Gastric cancer (GC), a globally prevalent and lethal malignancy, continues to be a key research focus. However, due to its considerable heterogeneity and complex pathogenesis, the treatment and diagnosis of gastric cancer still face significant challenges. With the rapid development of spatial omics technology, which provides insights into the spatial information within tumor tissues, it has emerged as a significant tool in gastric cancer research. This technology affords new insights into the pathology and molecular biology of gastric cancer for scientists. This review discusses recent advances in spatial omics technology for gastric cancer research, highlighting its applications in the tumor microenvironment (TME), tumor heterogeneity, tumor genesis and development mechanisms, and the identification of potential biomarkers and therapeutic targets. Moreover, this article highlights spatial omics' potential in precision medicine and summarizes existing challenges and future directions. It anticipates spatial omics' continuing impact on gastric cancer research, aiming to improve diagnostic and therapeutic approaches for patients. With this review, we aim to offer a comprehensive overview to scientists and clinicians in gastric cancer research, motivating further exploration and utilization of spatial omics technology. Our goal is to improve patient outcomes, including survival rates and quality of life.
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Affiliation(s)
- Erran Zhu
- Department of Clinical Medicine, Grade 20, Hengyang Medical College, University of South China, Hengyang, Hunan, 421001, China
| | - Qi Xie
- Department of Clinical Medicine, Grade 20, Hengyang Medical College, University of South China, Hengyang, Hunan, 421001, China
| | - Xinqi Huang
- Excellent Class, Clinical Medicine, Grade 20, Hengyang Medical College, University of South China, Hengyang, Hunan, 421001, China
| | - Zhiwei Zhang
- Cancer Research Institute of Hengyang Medical College, University of South China; Key Laboratory of Cancer Cellular and Molecular Pathology of Hunan; Department of Pathology, Department of Pathology of Hengyang Medical College, University of South China; The First Affiliated Hospital of University of South China, China.
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18
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Xiong H, Sun S, Zhang W, Zhao D, Liu X, Tian Y, Feng S. Spatial metabolomics method to reveal the differences in chemical composition of raw and honey-fried Stemona tuberosa Lour. by using UPLC-Orbitrap Fusion MS and desorption electrospray ionization mass spectrometry imaging. PHYTOCHEMICAL ANALYSIS : PCA 2024. [PMID: 39072901 DOI: 10.1002/pca.3428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024]
Abstract
INTRODUCTION Stemona tuberosa Lour. (ST) is a significant traditional Chinese medicine (TCM) renowned for its antitussive and insecticidal properties. ST is commonly subjected to processing in clinical practice before being utilized as a medicinal substance. Currently, the customary technique for processing ST is honey-fried. Nevertheless, the specific variations in chemical constituents of ST before and after honey-fried remain unclear. OBJECTIVE This work aimed to analyze the variations in chemical constituents of ST before and after honey-fried and to study the distribution of differential markers in the roots. METHODS UPLC-Orbitrap Fusion MS combined with molecular network analysis was used to analyze the metabolome of ST and honey-fried ST (HST) and to screen the differential metabolites by multivariate statistical analysis. Spatial metabolomics was applied to study the distribution of differential metabolites by desorption electrospray ionization mass spectrometry imaging (DESI-MSI). RESULTS The ST and HST exhibited notable disparities, with 56 and 61 chemical constituents found from each, respectively. After processing, the types of alkaloids decreased, and 12 differential metabolites were screened from the common compounds. The notable component variations were epibisdehydro-tuberostemonine J, neostenine, tuberostemonine, croomine, neotuberostemonine, and so forth. MSI visualized the spatial distribution of differential metabolites. CONCLUSIONS Our research provided a rapid and effective visualization method for the identification and spatial distribution of metabolites in ST. Compared with the traditional method, this method offered more convincing data supporting the processing mechanism investigations of Stemona tuberosa from a macroscopic perspective.
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Affiliation(s)
- Haixuan Xiong
- Henan University of Chinese Medicine, Zhengzhou, China
| | - Shuding Sun
- Henan University of Chinese Medicine, Zhengzhou, China
- Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P. R. China, Zhengzhou, China
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Weiwei Zhang
- Henan University of Chinese Medicine, Zhengzhou, China
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Di Zhao
- Henan University of Chinese Medicine, Zhengzhou, China
- Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P. R. China, Zhengzhou, China
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xuefang Liu
- Henan University of Chinese Medicine, Zhengzhou, China
- Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P. R. China, Zhengzhou, China
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yange Tian
- Henan University of Chinese Medicine, Zhengzhou, China
- Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P. R. China, Zhengzhou, China
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Suxiang Feng
- Henan University of Chinese Medicine, Zhengzhou, China
- Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P. R. China, Zhengzhou, China
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
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19
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Leach FE, Nagornov KO, Kozhinov AN, Tsybin YO. External Data Systems Enable Enhanced (and Sustainable) Fourier Transform Mass Spectrometry Imaging for Legacy Hybrid Linear Ion Trap-Orbitrap Platforms. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39031087 DOI: 10.1021/jasms.4c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2024]
Abstract
Legacy Fourier transform (FT) mass spectrometers provide robust platforms for bioanalytical mass spectrometry (MS) yet lack the most modern performance capabilities. For many laboratories, the routine investment in next generation instrumentation is cost prohibitive. Field-based upgrades provide a direct path to extend the usable lifespan of MS platforms which may be considered antiquated based on performance specifications at the time of manufacture. Here we demonstrate and evaluate the performance of a hybrid linear ion trap (LTQ)-Orbitrap mass spectrometer that has been enhanced via an external high-performance data acquisition and processing system to provide true absorption mode FT processing during an experimental acquisition. For the application to mass spectrometry imaging, several performance metrics have been improved including mass resolving power, mass accuracy, and dynamic range to provide an FTMS system comparable to current platforms. We also demonstrate, perhaps, the unexpected ability of these legacy platforms to detect usable time-domain signals up to 5 s in duration to achieve a mass resolving power 8× higher than the original platform specification.
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Affiliation(s)
- Franklin E Leach
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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20
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Guan C, Kong L. Mass spectrometry imaging in pulmonary disorders. Clin Chim Acta 2024; 561:119835. [PMID: 38936534 DOI: 10.1016/j.cca.2024.119835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
Mass Spectrometry Imaging (MSI) represents a novel and advancing technology that offers unparalleled in situ characterization of tissues. It provides comprehensive insights into the chemical structures, relative abundances, and spatial distributions of a vast array of both identified and unidentified endogenous and exogenous compounds, a capability not paralleled by existing analytical methodologies. Recent scholarly endeavors have increasingly explored the utility of MSI in the adjunct diagnosis and biomarker research of pulmonary disorders, including but not limited to lung cancer. Concurrently, MSI has proven instrumental in elucidating the spatiotemporal dynamics of various pharmacological agents. This review concisely delineates the fundamental principles underpinning MSI, its applications in pulmonary disease diagnosis, biomarker discovery, and drug distribution investigations. Additionally, it presents a forward-looking perspective on the prospective trajectories of MSI technological advancements.
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Affiliation(s)
- Chunliu Guan
- Key Laboratory of Environment Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, China
| | - Lu Kong
- Key Laboratory of Environment Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, China.
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21
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Kissman EN, Sosa MB, Millar DC, Koleski EJ, Thevasundaram K, Chang MCY. Expanding chemistry through in vitro and in vivo biocatalysis. Nature 2024; 631:37-48. [PMID: 38961155 DOI: 10.1038/s41586-024-07506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/01/2024] [Indexed: 07/05/2024]
Abstract
Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.
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Affiliation(s)
- Elijah N Kissman
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Max B Sosa
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Douglas C Millar
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Edward J Koleski
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | | | - Michelle C Y Chang
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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22
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Hong H, Habib A, Bi L, Qais DS, Wen L. Hollow Cathode Discharge Ionization Mass Spectrometry: Detection, Quantification and Gas Phase Ion-Molecule Reactions of Explosives and Related Compounds. Crit Rev Anal Chem 2024; 54:148-174. [PMID: 35467991 DOI: 10.1080/10408347.2022.2067467] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Mass spectrometry (MS) has become an essential analytical method in every sector of science and technology. Because of its unique ability to provide direct molecular structure information on analytes, an extra method is rarely required. This review describes fabrication of a variable-pressure hollow cathode discharge (HCD) ion source for MS in detection, quantification and investigation of gas-phase ion molecule reactions of explosives and related compounds using air as a carrier gas. The HCD ion source has been designed in such a way that by altering the ion source pressures, the system can generate both HCD and conventional GD. This design enables for the selective detection and quantification of explosives at trace to ultra-trace levels. The pressure-dependent HCD ion source has also been used to investigate ion-molecule reactions in the gas phase of explosives and related compounds. The mechanism of ion formation in explosive reactions is also discussed.
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Affiliation(s)
- Huanhuan Hong
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Ahsan Habib
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- Department of Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Lei Bi
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | | | - Luhong Wen
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
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23
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Colley ME, Esselman AB, Scott CF, Spraggins JM. High-Specificity Imaging Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:1-24. [PMID: 38594938 DOI: 10.1146/annurev-anchem-083023-024546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Imaging mass spectrometry (IMS) enables highly multiplexed, untargeted tissue mapping for a broad range of molecular classes, facilitating in situ biological discovery. Yet, challenges persist in molecular specificity, which is the ability to discern one molecule from another, and spatial specificity, which is the ability to link untargeted imaging data to specific tissue features. Instrumental developments have dramatically improved IMS spatial resolution, allowing molecular observations to be more readily associated with distinct tissue features across spatial scales, ranging from larger anatomical regions to single cells. High-performance mass analyzers and systems integrating ion mobility technologies are also becoming more prevalent, further improving molecular coverage and the ability to discern chemical identity. This review provides an overview of recent advancements in high-specificity IMS that are providing critical biological context to untargeted molecular imaging, enabling integrated analyses, and addressing advanced biomedical research applications.
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Affiliation(s)
- Madeline E Colley
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Allison B Esselman
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Claire F Scott
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jeffrey M Spraggins
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- 5Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Brorsen LF, McKenzie JS, Pinto FE, Glud M, Hansen HS, Haedersdal M, Takats Z, Janfelt C, Lerche CM. Metabolomic profiling and accurate diagnosis of basal cell carcinoma by MALDI imaging and machine learning. Exp Dermatol 2024; 33:e15141. [PMID: 39036889 DOI: 10.1111/exd.15141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024]
Abstract
Basal cell carcinoma (BCC), the most common keratinocyte cancer, presents a substantial public health challenge due to its high prevalence. Traditional diagnostic methods, which rely on visual examination and histopathological analysis, do not include metabolomic data. This exploratory study aims to molecularly characterize BCC and diagnose tumour tissue by applying matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and machine learning (ML). BCC tumour development was induced in a mouse model and tissue sections containing BCC (n = 12) were analysed. The study design involved three phases: (i) Model training, (ii) Model validation and (iii) Metabolomic analysis. The ML algorithm was trained on MS data extracted and labelled in accordance with histopathology. An overall classification accuracy of 99.0% was reached for the labelled data. Classification of unlabelled tissue areas aligned with the evaluation of a certified Mohs surgeon for 99.9% of the total tissue area, underscoring the model's high sensitivity and specificity in identifying BCC. Tentative metabolite identifications were assigned to 189 signals of importance for the recognition of BCC, each indicating a potential tumour marker of diagnostic value. These findings demonstrate the potential for MALDI-MSI coupled with ML to characterize the metabolomic profile of BCC and to diagnose tumour tissue with high sensitivity and specificity. Further studies are needed to explore the potential of implementing integrated MS and automated analyses in the clinical setting.
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Affiliation(s)
- Lauritz F Brorsen
- Department of Dermatology, Copenhagen University Hospital-Bispebjerg and Frederiksberg, Copenhagen, Denmark
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - James S McKenzie
- Department of Digestion, Metabolism and Reproduction, Imperial College London, London, UK
| | - Fernanda E Pinto
- Department of Dermatology, Copenhagen University Hospital-Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Martin Glud
- Department of Dermatology, Copenhagen University Hospital-Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Harald S Hansen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Merete Haedersdal
- Department of Dermatology, Copenhagen University Hospital-Bispebjerg and Frederiksberg, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Zoltan Takats
- Department of Digestion, Metabolism and Reproduction, Imperial College London, London, UK
| | - Christian Janfelt
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Catharina M Lerche
- Department of Dermatology, Copenhagen University Hospital-Bispebjerg and Frederiksberg, Copenhagen, Denmark
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
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25
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HUANG D, LIU X, XU G. [Research progress of deep learning applications in mass spectrometry imaging data analysis]. Se Pu 2024; 42:669-680. [PMID: 38966975 PMCID: PMC11224939 DOI: 10.3724/sp.j.1123.2023.10035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Indexed: 07/06/2024] Open
Abstract
Mass spectrometry imaging (MSI) is a promising method for characterizing the spatial distribution of compounds. Given the diversified development of acquisition methods and continuous improvements in the sensitivity of this technology, both the total amount of generated data and complexity of analysis have exponentially increased, rendering increasing challenges of data postprocessing, such as large amounts of noise, background signal interferences, as well as image registration deviations caused by sample position changes and scan deviations, and etc. Deep learning (DL) is a powerful tool widely used in data analysis and image reconstruction. This tool enables the automatic feature extraction of data by building and training a neural network model, and achieves comprehensive and in-depth analysis of target data through transfer learning, which has great potential for MSI data analysis. This paper reviews the current research status, application progress and challenges of DL in MSI data analysis, focusing on four core stages: data preprocessing, image reconstruction, cluster analysis, and multimodal fusion. The application of a combination of DL and mass spectrometry imaging in the study of tumor diagnosis and subtype classification is also illustrated. This review also discusses trends of development in the future, aiming to promote a better combination of artificial intelligence and mass spectrometry technology.
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26
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Hu S, Habib A, Xiong W, Chen L, Bi L, Wen L. Mass Spectrometry Imaging Techniques: Non-Ambient and Ambient Ionization Approaches. Crit Rev Anal Chem 2024:1-54. [PMID: 38889072 DOI: 10.1080/10408347.2024.2362703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Molecular information can be acquired from sample surfaces in real time using a revolutionary molecular imaging technique called mass spectrometry imaging (MSI). The technique can concurrently provide high spatial resolution information on the spatial distribution and relative proportion of many different compounds. Thus, many scientists have been drawn to the innovative capabilities of the MSI approach, leading to significant focus in various fields during the past few decades. This review describes the sampling protocol, working principle and applications of a few non-ambient and ambient ionization mass spectrometry imaging techniques. The non-ambient techniques include secondary ionization mass spectrometry and matrix-assisted laser desorption ionization, while the ambient techniques include desorption electrospray ionization, laser ablation electrospray ionization, probe electro-spray ionization, desorption atmospheric pressure photo-ionization and femtosecond laser desorption ionization. The review additionally addresses the advantages and disadvantages of ambient and non-ambient MSI techniques in relation to their suitability, particularly for biological samples used in tissue diagnostics. Last but not least, suggestions and conclusions are made regarding the challenges and future prospects of MSI.
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Affiliation(s)
- Shundi Hu
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Ahsan Habib
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- Department of Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Wei Xiong
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - La Chen
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Lei Bi
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Luhong Wen
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
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Ashbacher SM, Mills Q, Sohn AL, Xie DY, Muddiman DC. Incorporation of Three Different Optical Trains into the IR-MALDESI Mass Spectrometry Imaging Platform to Characterize Artemisia annua. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1245-1252. [PMID: 38686539 DOI: 10.1021/jasms.4c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Artemisinin is the leading medication for the treatment of malaria and is only produced naturally in Artemisia annua. The localization of artemisinin in both the glandular and non-glandular trichomes of the plant makes it an ideal candidate for mass spectrometry imaging (MSI) as a model system for method development. Infrared matrix-assisted laser desorption electrospray ionization MSI (IR-MALDESI-MSI) has the capability to detect hundreds to thousands of analytes simultaneously, providing abundance information in conjunction with species localization throughout a sample. The development of several new optical trains and their application to the IR-MALDESI-MSI platform has improved data quality in previous proof-of-concept experiments but has not yet been applied to analysis of native biological samples, especially the MSI analysis of plants. This study aimed to develop a workflow and optimize MSI parameters, specifically the laser optical train, for the analysis of Artemisia annua with the NextGen IR-MALDESI platform coupled to an Orbitrap Exploris 240 mass spectrometer. Two laser optics were compared to the conventional set up, of which include a Schwarzschild-like reflective objective and a diffractive optical element (DOE). These optics, respectively, enhance the spatial resolution of imaging experiments or create a square spot shape for top-hat imaging. Ultimately, we incorporated and characterized three different optical trains into our analysis of Artemisia annua to study metabolites in the artemisinin pathway. These improvements in our workflow, resulted in high spatial resolution and improved ion abundance from previous work, which will allow us to address many different questions in plant biology beyond this model system.
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28
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Ross DH, Bhotika H, Zheng X, Smith RD, Burnum-Johnson KE, Bilbao A. Computational tools and algorithms for ion mobility spectrometry-mass spectrometry. Proteomics 2024; 24:e2200436. [PMID: 38438732 DOI: 10.1002/pmic.202200436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/06/2024]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.
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Affiliation(s)
- Dylan H Ross
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Harsh Bhotika
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aivett Bilbao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
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29
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Ozdemir A, Lin JL, Gulfen M, Chen CH. Advancing mass spectrometry-based chemical imaging: A noncontact continuous flow surface probe in mass spectrometry for enhanced signal detection and spatial resolution. Talanta 2024; 273:125858. [PMID: 38442563 DOI: 10.1016/j.talanta.2024.125858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
A new method has been developed for mass spectrometric imaging of small molecules and proteins on tissue or in thinly sliced materials. A laser desorption Venturi electrospray ionization-mass spectrometer was developed for molecular imaging. This method combines laser desorption (LD) and electrospray ionization (ESI) systems before a mass spectrometer (MS). To carry out laser desorption, samples are excited with a laser from the back side of a glass substrate. The desorbed molecules or particles are then captured by a solvent flow. In the ESI system, these desorbed particles and molecules are ionized. The spray part of the solvent system consists of two capillaries: one delivers solvent to the sample plate sides to capture desorbed molecules and particles, and the other carries the solution to the mass spectrometry side using the Venturi effect. A 2D stage facilitates sampling. The system is designed to minimize the sample size after desorption using a 355 nm diode laser, and it is optimized for molecules of various sizes, including organic molecules, amino acids, and proteins. Despite challenging atmospheric conditions for protein desorption, this specialized design enables the collection of protein spectra. The amino acids and other small molecules showed high sensitivity in the MSI measurements. This innovative MS imaging system can be directly applied to real tissue systems and other plant samples to visualize the molecular level distributions.
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Affiliation(s)
- Abdil Ozdemir
- Department of Chemistry, Faculty of Science, Sakarya University, 54187, Esentepe, Sakarya, Turkey.
| | - Jung-Lee Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Mustafa Gulfen
- Department of Chemistry, Faculty of Science, Sakarya University, 54187, Esentepe, Sakarya, Turkey
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30
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Ghafari N, Sleno L. Challenges and recent advances in quantitative mass spectrometry-based metabolomics. ANALYTICAL SCIENCE ADVANCES 2024; 5:e2400007. [PMID: 38948317 PMCID: PMC11210748 DOI: 10.1002/ansa.202400007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 06/03/2024] [Accepted: 06/08/2024] [Indexed: 07/02/2024]
Abstract
The field of metabolomics has gained tremendous interest in recent years. Whether the goal is to discover biomarkers related to certain pathologies or to better understand the impact of a drug or contaminant, numerous studies have demonstrated how crucial it is to understand variations in metabolism. Detailed knowledge of metabolic variabilities can lead to more effective treatments, as well as faster or less invasive diagnostics. Exploratory approaches are often employed in metabolomics, using relative quantitation to look at perturbations between groups of samples. Most metabolomics studies have been based on metabolite profiling using relative quantitation, with very few studies using an approach for absolute quantitation. Using accurate quantitation facilitates the comparison between different studies, as well as enabling longitudinal studies. In this review, we discuss the most widely used techniques for quantitative metabolomics using mass spectrometry (MS). Various aspects will be addressed, such as the use of external and/or internal standards, derivatization techniques, in vivo isotopic labelling, or quantitative MS imaging. The principles, as well as the associated limitations and challenges, will be described for each approach.
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Affiliation(s)
- Nathan Ghafari
- Chemistry Department/CERMO‐FCUniversity of Quebec in Montreal (UQAM)MontrealCanada
| | - Lekha Sleno
- Chemistry Department/CERMO‐FCUniversity of Quebec in Montreal (UQAM)MontrealCanada
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31
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Strnad Š, Vrkoslav V, Mengr A, Fabián O, Rybáček J, Kubánek M, Melenovský V, Maletínská L, Cvačka J. Thermal evaporation as sample preparation for silver-assisted laser desorption/ionization mass spectrometry imaging of cholesterol in amyloid tissues. Analyst 2024; 149:3152-3160. [PMID: 38630503 DOI: 10.1039/d4an00181h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Cholesterol plays an important biological role in the body, and its disruption in homeostasis and synthesis has been implicated in several diseases. Mapping the locations of cholesterol is crucial for gaining a better understanding of these conditions. Silver deposition has proven to be an effective method for analyzing cholesterol using mass spectrometry imaging (MSI). We optimized and evaluated thermal evaporation as an alternative deposition technique to sputtering for silver deposition in MSI of cholesterol. A silver layer with a thickness of 6 nm provided an optimal combination of cholesterol signal intensity and mass resolution. The deposition of an ultrathin nanofilm of silver enabled high-resolution MSI with a pixel size of 10 μm. We used this optimized method to visualize the distribution of cholesterol in the senile plaques in the brains of APP/PS1 mice, a model that resembles Alzheimer's disease pathology. We found that cholesterol was evenly distributed across the frontal cortex tissue, with no evidence of plaque-like accumulation. Additionally, we investigated the presence and distribution of cholesterol in myocardial sections of a human heart affected by wild-type ATTR amyloidosis. We identified the presence of cholesterol in areas with amyloid deposition, but complete colocalization was not observed.
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Affiliation(s)
- Štěpán Strnad
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10, Prague, Czech Republic.
| | - Vladimír Vrkoslav
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10, Prague, Czech Republic.
| | - Anna Mengr
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10, Prague, Czech Republic.
| | - Ondřej Fabián
- Institute for Clinical and Experimental Medicine, 140 21, Prague, Czech Republic
- Department of Pathology and Molecular Medicine, Third Faculty of Medicine, Charles University and Thomayer Hospital, 140 59, Prague, Czech Republic
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10, Prague, Czech Republic.
| | - Miloš Kubánek
- Institute for Clinical and Experimental Medicine, 140 21, Prague, Czech Republic
| | - Vojtěch Melenovský
- Institute for Clinical and Experimental Medicine, 140 21, Prague, Czech Republic
| | - Lenka Maletínská
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10, Prague, Czech Republic.
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10, Prague, Czech Republic.
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32
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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33
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Song Y, Xiao F, Aa J, Wang G. Desorption Electrospray Ionization Mass Spectrometry Imaging Techniques Depict a Reprogramming of Energy and Purine Metabolism in the Core Brain Regions of Chronic Social Defeat Stress Mice. Metabolites 2024; 14:284. [PMID: 38786761 PMCID: PMC11123228 DOI: 10.3390/metabo14050284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Depression is associated with pathological changes and metabolic abnormalities in multiple brain regions. The simultaneous comprehensive and in situ detection of endogenous molecules in all brain regions is essential for a comprehensive understanding of depression pathology, which is described in this paper. A method based on desorption electrospray ionization mass spectrometry imaging (DESI-MSI) technology was developed to classify mouse brain regions using characteristic lipid molecules and to detect the metabolites in mouse brain tissue samples simultaneously. The results showed that characteristic lipid molecules can be used to clearly distinguish each subdivision of the mouse brain, and the accuracy of this method is higher than that of the conventional staining method. The cerebellar cortex, medial prefrontal cortex, hippocampus, striatum, nucleus accumbens-core, and nucleus accumbens-shell exhibited the most significant differences in the chronic social defeat stress model. An analysis of metabolic pathways revealed that 13 kinds of molecules related to energy metabolism and purine metabolism exhibited significant changes. A DESI-MSI method was developed for the detection of pathological brain sections. We found, for the first time, that there are characteristic changes in the energy metabolism in the cortex and purine metabolism in the striatum, which is highly important for obtaining a deeper and more comprehensive understanding of the pathology of depression and discovering regulatory targets.
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Affiliation(s)
| | | | - Jiye Aa
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing 210009, China; (Y.S.); (F.X.)
| | - Guangji Wang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing 210009, China; (Y.S.); (F.X.)
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34
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Chakraborty A, Kamat SS. Lysophosphatidylserine: A Signaling Lipid with Implications in Human Diseases. Chem Rev 2024; 124:5470-5504. [PMID: 38607675 DOI: 10.1021/acs.chemrev.3c00701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Lysophosphatidylserine (lyso-PS) has emerged as yet another important signaling lysophospholipid in mammals, and deregulation in its metabolism has been directly linked to an array of human autoimmune and neurological disorders. It has an indispensable role in several biological processes in humans, and therefore, cellular concentrations of lyso-PS are tightly regulated to ensure optimal signaling and functioning in physiological settings. Given its biological importance, the past two decades have seen an explosion in the available literature toward our understanding of diverse aspects of lyso-PS metabolism and signaling and its association with human diseases. In this Review, we aim to comprehensively summarize different aspects of lyso-PS, such as its structure, biodistribution, chemical synthesis, and SAR studies with some synthetic analogs. From a biochemical perspective, we provide an exhaustive coverage of the diverse biological activities modulated by lyso-PSs, such as its metabolism and the receptors that respond to them in humans. We also briefly discuss the human diseases associated with aberrant lyso-PS metabolism and signaling and posit some future directions that may advance our understanding of lyso-PS-mediated mammalian physiology.
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Affiliation(s)
- Arnab Chakraborty
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Siddhesh S Kamat
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
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35
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Shin M, Seo M, Lee K, Yoon K. Super-resolution techniques for biomedical applications and challenges. Biomed Eng Lett 2024; 14:465-496. [PMID: 38645589 PMCID: PMC11026337 DOI: 10.1007/s13534-024-00365-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 04/23/2024] Open
Abstract
Super-resolution (SR) techniques have revolutionized the field of biomedical applications by detailing the structures at resolutions beyond the limits of imaging or measuring tools. These techniques have been applied in various biomedical applications, including microscopy, magnetic resonance imaging (MRI), computed tomography (CT), X-ray, electroencephalogram (EEG), ultrasound, etc. SR methods are categorized into two main types: traditional non-learning-based methods and modern learning-based approaches. In both applications, SR methodologies have been effectively utilized on biomedical images, enhancing the visualization of complex biological structures. Additionally, these methods have been employed on biomedical data, leading to improvements in computational precision and efficiency for biomedical simulations. The use of SR techniques has resulted in more detailed and accurate analyses in diagnostics and research, essential for early disease detection and treatment planning. However, challenges such as computational demands, data interpretation complexities, and the lack of unified high-quality data persist. The article emphasizes these issues, underscoring the need for ongoing development in SR technologies to further improve biomedical research and patient care outcomes.
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Affiliation(s)
- Minwoo Shin
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
| | - Minjee Seo
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
| | - Kyunghyun Lee
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
| | - Kyungho Yoon
- School of Mathematics and Computing (Computational Science and Engineering), Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722 Republic of Korea
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36
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Bottomley H, Phillips J, Hart P. Improved Detection of Tryptic Peptides from Tissue Sections Using Desorption Electrospray Ionization Mass Spectrometry Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:922-934. [PMID: 38602416 PMCID: PMC11066963 DOI: 10.1021/jasms.4c00006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/08/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024]
Abstract
DESI-MSI is an ambient ionization technique used frequently for the detection of lipids, small molecules, and drug targets. Until recently, DESI had only limited use for the detection of proteins and peptides due to the setup and needs around deconvolution of data resulting in a small number of species being detected at lower spatial resolution. There are known differences in the ion species detected using DESI and MALDI for nonpeptide molecules, and here, we identify that this extends to proteomic species. DESI MS images were obtained for tissue sections of mouse and rat brain using a precommercial heated inlet (approximately 450 °C) to the mass spectrometer. Ion mobility separation resolved spectral overlap of peptide ions and significantly improved the detection of multiply charged species. The images acquired were of pixel size 100 μm (rat brain) and 50 μm (mouse brain), respectively. Observed tryptic peptides were filtered against proteomic target lists, generated by LC-MS, enabling tentative protein assignment for each peptide ion image. Precise localizations of peptide ions identified by DESI and MALDI were found to be comparable. Some spatially localized peptides ions were observed in DESI that were not found in the MALDI replicates, typically, multiply charged species with a low mass to charge ratio. This method demonstrates the potential of DESI-MSI to detect large numbers of tryptic peptides from tissue sections with enhanced spatial resolution when compared to previous DESI-MSI studies.
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Affiliation(s)
- Heather Bottomley
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
| | - Jonathan Phillips
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
| | - Philippa Hart
- Medicines
Discovery Catapult, Alderley Park, Block 35, Mereside, Macclesfield SK10 4ZF, U.K.
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Santos AA, Delgado TC, Marques V, Ramirez-Moncayo C, Alonso C, Vidal-Puig A, Hall Z, Martínez-Chantar ML, Rodrigues CM. Spatial metabolomics and its application in the liver. Hepatology 2024; 79:1158-1179. [PMID: 36811413 PMCID: PMC11020039 DOI: 10.1097/hep.0000000000000341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/05/2023] [Indexed: 02/24/2023]
Abstract
Hepatocytes work in highly structured, repetitive hepatic lobules. Blood flow across the radial axis of the lobule generates oxygen, nutrient, and hormone gradients, which result in zoned spatial variability and functional diversity. This large heterogeneity suggests that hepatocytes in different lobule zones may have distinct gene expression profiles, metabolic features, regenerative capacity, and susceptibility to damage. Here, we describe the principles of liver zonation, introduce metabolomic approaches to study the spatial heterogeneity of the liver, and highlight the possibility of exploring the spatial metabolic profile, leading to a deeper understanding of the tissue metabolic organization. Spatial metabolomics can also reveal intercellular heterogeneity and its contribution to liver disease. These approaches facilitate the global characterization of liver metabolic function with high spatial resolution along physiological and pathological time scales. This review summarizes the state of the art for spatially resolved metabolomic analysis and the challenges that hinder the achievement of metabolome coverage at the single-cell level. We also discuss several major contributions to the understanding of liver spatial metabolism and conclude with our opinion on the future developments and applications of these exciting new technologies.
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Affiliation(s)
- André A. Santos
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa C. Delgado
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Bizkaia, Spain
- Congenital Metabolic Disorders, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Vanda Marques
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Carmen Ramirez-Moncayo
- Institute of Clinical Sciences, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | | | - Antonio Vidal-Puig
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Centro Investigation Principe Felipe, Valencia, Spain
| | - Zoe Hall
- Division of Systems Medicine, Imperial College London, London, UK
| | - María Luz Martínez-Chantar
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain
| | - Cecilia M.P. Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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38
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Prentice BM. Imaging with mass spectrometry: Which ionization technique is best? JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5016. [PMID: 38625003 DOI: 10.1002/jms.5016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 04/17/2024]
Abstract
The use of mass spectrometry (MS) to acquire molecular images of biological tissues and other substrates has developed into an indispensable analytical tool over the past 25 years. Imaging mass spectrometry technologies are widely used today to study the in situ spatial distributions for a variety of analytes. Early MS images were acquired using secondary ion mass spectrometry and matrix-assisted laser desorption/ionization. Researchers have also designed and developed other ionization techniques in recent years to probe surfaces and generate MS images, including desorption electrospray ionization (DESI), nanoDESI, laser ablation electrospray ionization, and infrared matrix-assisted laser desorption electrospray ionization. Investigators now have a plethora of ionization techniques to select from when performing imaging mass spectrometry experiments. This brief perspective will highlight the utility and relative figures of merit of these techniques within the context of their use in imaging mass spectrometry.
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Affiliation(s)
- Boone M Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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39
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Zhang S, Fang T, He Y, Feng W, Yu Z, Zheng Y, Zhang C, Hu S, Liu Z, Liu J, Yu J, Zhang H, He A, Gong Y, He Z, Yang K, Xi Z, Yu W, Zhou L, Yao L, Yue S. VHL mutation drives human clear cell renal cell carcinoma progression through PI3K/AKT-dependent cholesteryl ester accumulation. EBioMedicine 2024; 103:105070. [PMID: 38564827 PMCID: PMC10999658 DOI: 10.1016/j.ebiom.2024.105070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Cholesteryl ester (CE) accumulation in intracellular lipid droplets (LDs) is an essential signature of clear cell renal cell carcinoma (ccRCC), but its molecular mechanism and pathological significance remain elusive. METHODS Enabled by the label-free Raman spectromicroscopy, which integrated stimulated Raman scattering microscopy with confocal Raman spectroscopy on the same platform, we quantitatively analyzed LD distribution and composition at the single cell level in intact ccRCC cell and tissue specimens in situ without any processing or exogenous labeling. Since we found that commonly used ccRCC cell lines actually did not show the CE-rich signature, primary cancer cells were isolated from human tissues to retain the lipid signature of ccRCC with CE level as high as the original tissue, which offers a preferable cell model for the study of cholesterol metabolism in ccRCC. Moreover, we established a patient-derived xenograft (PDX) mouse model that retained the CE-rich phenotype of human ccRCC. FINDINGS Surprisingly, our results revealed that CE accumulation was induced by tumor suppressor VHL mutation, the most common mutation of ccRCC. Moreover, VHL mutation was found to promote CE accumulation by upregulating HIFα and subsequent PI3K/AKT/mTOR/SREBPs pathway. Inspiringly, inhibition of cholesterol esterification remarkably suppressed ccRCC aggressiveness in vitro and in vivo with negligible toxicity, through the reduced membrane cholesterol-mediated downregulations of integrin and MAPK signaling pathways. INTERPRETATION Collectively, our study improves current understanding of the role of CE accumulation in ccRCC and opens up new opportunities for treatment. FUNDING This work was supported by National Natural Science Foundation of China (No. U23B2046 and No. 62027824), National Key R&D Program of China (No. 2023YFC2415500), Fundamental Research Funds for the Central Universities (No. YWF-22-L-547), PKU-Baidu Fund (No. 2020BD033), Peking University First Hospital Scientific and Technological Achievement Transformation Incubation Guidance Fund (No. 2022CX02), and Beijing Municipal Health Commission (No. 2020-2Z-40713).
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Affiliation(s)
- Shuo Zhang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Tinghe Fang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Yexuan He
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Weichen Feng
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Zhuoyang Yu
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Yaoyao Zheng
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Chi Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Shuai Hu
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Zhuojun Liu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Jia Liu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Jian Yu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Han Zhang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Anbang He
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Zhisong He
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Kaiwei Yang
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Zhijun Xi
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Wei Yu
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.
| | - Shuhua Yue
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China.
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40
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Xu G, Gan S, Guo B, Yang L. Application of clustering strategy for automatic segmentation of tissue regions in mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9717. [PMID: 38389435 DOI: 10.1002/rcm.9717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/24/2024]
Abstract
RATIONALE Mass spectrometry imaging (MSI) has been widely used in biomedical research fields. Each pixel in MSI consists of a mass spectrum that reflects the molecule feature of the tissue spot. Because MSI contains high-dimensional datasets, it is highly desired to develop computational methods for data mining and constructing tissue segmentation maps. METHODS To visualize different tissue regions based on mass spectrum features and improve the efficiency in processing enormous data, we proposed a computational strategy that consists of four procedures including preprocessing, data reduction, clustering, and quantitative validation. RESULTS In this study, we examined the combination of t-distributed stochastic neighbor embedding (t-SNE) and hierarchical clustering (HC) for MSI data analysis. Using publicly available MSI datasets, one dataset of mouse urinary bladder, and one dataset of human colorectal cancer, we demonstrated that the generated tissue segmentation maps from this combination were superior to other data reduction and clustering algorithms. Using the staining image as a reference, we assessed the performance of clustering algorithms with external and internal clustering validation measures, including purity, adjusted Rand index (ARI), Davies-Bouldin index (DBI), and spatial aggregation index (SAI). The result indicated that SAI delivered excellent performance for automatic segmentation of tissue regions in MSI. CONCLUSIONS We used a clustering algorithm to construct tissue automatic segmentation in MSI datasets. The performance was evaluated by comparing it with the stained image and calculating clustering validation indexes. The results indicated that SAI is important for automatic tissue segmentation in MSI, different from traditional clustering validation measures. Compared to the reports that used internal clustering validation measures such as DBI, our method offers more effective evaluation of clustering results for MSI segmentation. We envision that the proposed automatic image segmentation strategy can facilitate deep learning in molecular feature extraction and biomarker discovery for the biomedical applications of MSI.
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Affiliation(s)
- Guang Xu
- College of Computer, Hubei University of Education, Wuhan, China
| | - Shengfeng Gan
- College of Computer, Hubei University of Education, Wuhan, China
| | - Bo Guo
- College of Computer, Hubei University of Education, Wuhan, China
| | - Li Yang
- College of Computer, Hubei University of Education, Wuhan, China
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41
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Shi Q, Wan Z, Lu S, Fang C, Yan C, Zhang X. Investigating the effects of PFOA accumulation and depuration on specific phospholipids in zebrafish through imaging mass spectrometry. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2024; 26:700-709. [PMID: 38376352 DOI: 10.1039/d3em00413a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Perfluorooctanoic acid (PFOA) is an emerging persistent organic pollutant. Exposure to PFOA was observed to have a correlation with the expression levels of phospholipids. However, there are currently no studies that directly visualize the effects of PFOA on phospholipids. To this end, matrix-assisted laser desorption/ionization time of flight imaging mass spectrometry (MALDI-TOF-IMS) was used to visualize changes in phospholipids in the different tissues of zebrafish following exposure to PFOA. This study found that the major perturbed phospholipids were phosphatidylcholine (PC), diacylglycerol (DG), phosphatidic acid (PA), phosphatidylglycerol (PG), sphingomyelin (SM), and triacylglycerol (TG). These perturbed phospholipids caused by PFOA were reversible in some tissues (liver, gill, and brain) and irreversible in others (such as the highly exposed intestine). Moreover, the spatial distribution of perturbed phospholipids was mainly located around the edge or center of the tissues, implying that these tissue regions need special attention. This study provides novel insight into the biological toxicity and toxicity mechanisms induced by emerging environmental pollutants.
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Affiliation(s)
- Qiuyue Shi
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, National Environmental Protection Dongting Lake Scientific Observation and Research Station, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Zhengfen Wan
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, National Environmental Protection Dongting Lake Scientific Observation and Research Station, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Shaoyong Lu
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, National Environmental Protection Dongting Lake Scientific Observation and Research Station, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Cheng Fang
- Global Centre for Environmental Remediation, University of Newcastle, Callaghan, NSW 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Changzhou Yan
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xian Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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Lin J, Li M, Pei Z, Zhang Y, Yu Q, Zhong J, Han L, Zhang D, Huang H. Study on the white frost formation mechanism during storage of Phyllanthus emblica Linn. fruit based on component analysis and spatial metabolomics. J Pharm Biomed Anal 2024; 241:115960. [PMID: 38237545 DOI: 10.1016/j.jpba.2023.115960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/29/2023] [Accepted: 12/31/2023] [Indexed: 02/21/2024]
Abstract
The Phyllanthus emblica Linn. fruit (PEF) is a well-known medicinal and food homologous item in tropical Southeast Asian. During the drying and storing processes, some PEF will grow white frost on its surface, which is typically taken as a sign of greater quality. However, the material basis and formation mechanism of white frost on PEF surfaces are currently unclear, and there is no sufficient evidence to support the correlation between white frost on PEF surfaces and their quality. In this paper, high-performance liquid chromatography (HPLC) was used to study the differences in active ingredient content of PEF medicinal materials with and without frost. The microstructure and elemental composition of white frost were studied using scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS). The Fourier transform infrared spectroscopy (FT-IR) was used to analysis the main functional groups in white frost. The ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS) combined with UNIFI database, EDS and FT-IR results, and reference materials were used to identify the chemical composition of white frost. The exocarp of PEF before and after drying and storage was analyzed by spatial metabolomics using desorption electrospray ionization (DESI) mass spectrometry imaging system to reveal the formation mechanism of white frost on the surface of PEF. The results found that the PEF with frost have higher levels of active ingredients than those without frost. EDS and FT-IR results show that white frost is mainly composed of C, O, K elements, and contains a large number of phenolic hydroxyl, carboxyl etc. UPLC-Q-TOF-MS/MS results found that the main components of white frost were organic acids, fatty acids, and tannins, including quality markers such as gallic acid and ellagic acid etc. Spatial metabolomics research found that the white frost formation mechanism mainly involved in the ascorbate and aldarate metabolism, cutin, suberin and wax biosynthesis, citrate cycle (TCA cycle) and biosynthesis of unsaturated fatty acid. This study reveals the material basis, formation mechanism, and relationship between the surface white frost of PEF and the quality of medicinal materials, providing valuable information for the quality evaluation of PEF.
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Affiliation(s)
- Junzhi Lin
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China
| | - Mengqi Li
- Pharmacy department, Sichuan Nursing Vocational College, Chengdu 610100, China
| | - Zhaoqing Pei
- Tianfu TCM Innovation Harbour, Chengdu University of Traditional Chinese Medicine, Pengzhou 611930, China
| | - Yifan Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qiang Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jingping Zhong
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Li Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Dingkun Zhang
- Tianfu TCM Innovation Harbour, Chengdu University of Traditional Chinese Medicine, Pengzhou 611930, China; State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Haozhou Huang
- Innovative Institute of Chinese Medicine and Pharmacy and Meishan Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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Chen LC, Lee C, Hsu CC. Towards developing a matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) compatible tissue expansion protocol. Anal Chim Acta 2024; 1297:342345. [PMID: 38438227 DOI: 10.1016/j.aca.2024.342345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/05/2024] [Accepted: 02/04/2024] [Indexed: 03/06/2024]
Abstract
Mass spectrometry imaging (MSI) visualizes spatial distribution of molecules in a biological tissue. However, compared with traditional microscopy-based imaging, conventional MSI is limited to its spatial resolution, resulting in difficulties in identifying detailed tissue morphological characters, such as lesion boundary or nanoscale structures. On the other hand, expansion microscopy, a tissue expansion method widely used in optical imaging to improve morphological details, has great potential to solve insufficient spatial resolution in mass spectrometry imaging (MSI). However, expansion microscopy was not originally designed for MSI, resulting in problems while combining expansion microscopy and MSI such as expanded sample fragility, vacuum stability and molecule loss during sample preparation. In this research we developed a MALDI MSI compatible expansion protocol by adjusting sample preparation methods during tissue expansion, successfully combining expansion microscopy with MSI. After tissue expansion the expanded sample can be readily applied to MALDI MSI sample preparation and further data acquisition. The MALDI MSI compatible expansion protocol has great potential to be widely applied in MALDI MSI sample preparation to facilitate improvement of MSI spatial resolution.
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Affiliation(s)
- Li-Cyun Chen
- Department of Chemistry, National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei City, 106319, Taiwan.
| | - Chuping Lee
- Department of Chemistry, National Chung Hsing University, No.145, Xingda Rd., South Dist., Taichung City, 40227, Taiwan.
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei City, 106319, Taiwan.
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Yuan X, Bowling A, Gemperline E, Mannam V, Howard S. Real-time, depth-resolved, in vivo multiphoton fluorescence lifetime imaging microscopy of agricultural herbicide treatments in plants. OPTICS EXPRESS 2024; 32:13733-13745. [PMID: 38859335 DOI: 10.1364/oe.507002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/13/2024] [Indexed: 06/12/2024]
Abstract
The development of effective and safe agricultural treatments requires sub-cellular insight of the biochemical effects of treatments in living tissue in real-time. Industry-standard mass spectroscopic imaging lacks real-time in vivo capability. As an alternative, multiphoton fluorescence lifetime imaging microscopy (MPM-FLIM) allows for 3D sub-cellular quantitative metabolic imaging but is often limited to low frame rates. To resolve relatively fast effects (e.g., photosynthesis inhibiting treatments), high-frame-rate MPM-FLIM is needed. In this paper, we demonstrate and evaluate a high-speed MPM-FLIM system, "Instant FLIM", as a time-resolved 3D sub-cellular molecular imaging system in highly scattering, living plant tissues. We demonstrate simultaneous imaging of cellular autofluorescence and crystalline agrochemical crystals within plant tissues. We further quantitatively investigate the herbicidal effects of two classes of agricultural herbicide treatments, photosystem II inhibiting herbicide (Basagran) and auxin-based herbicide (Arylex), and successfully demonstrate the capability of the MPM-FLIM system to measure biological changes over a short time with enhanced imaging speed. Results indicate that high-frame-rate 3D MPM-FLIM achieves the required fluorescence lifetime resolution, temporal resolution, and spatial resolution to be a useful tool in basic plant cellular biology research and agricultural treatment development.
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45
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Fowowe M, Yu A, Wang J, Onigbinde S, Nwaiwu J, Bennett AI, Mechref Y. Suppressing the background of LC-ESI-MS analysis of permethylated glycans using the active background ion reduction device. Electrophoresis 2024. [PMID: 38573014 DOI: 10.1002/elps.202300301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Mass spectrometry (MS) has revolutionized analytical chemistry, enabling precise identification and quantification of chemical species, which is pivotal for biomarker discovery and understanding complex biological systems. Despite its versatility, the presence of background ions in MS analysis hinders the sensitive detection of low-abundance analytes. Therefore, studies aimed at lowering background ion levels have become increasingly important. Here, we utilized the commercially available Active Background Ion Reduction Device (ABIRD) to suppress background ions and assess its effect on the liquid chromatography-electrospray ionization (LC-ESI)-MS analyses of N-glycans on the Q Exactive HF mass spectrometer. We also investigated the effect of different solvent vapors in the ESI source on N-glycan analysis by MS. ABIRD generally had no effect on high-mannose and neutral structures but reduced the intensity of some structures that contained sialic acid, fucose, or both when methanol vapor filled the ESI source. Based on our findings on the highest number of identified N-glycans from human serum, methanol vapor in the ion source compartment may enhance N-glycan LC-ESI-MS analyses by improving the desolvation of droplets formed during the ESI process due to its high volatility. This protocol may be further validated and extended to advanced bottom-up proteomic/glycoproteomic studies for the analysis of peptide/glycopeptide ions by MS.
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Affiliation(s)
- Mojibola Fowowe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Judith Nwaiwu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Andrew I Bennett
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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46
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Klein D, Rivera ES, Caprioli RM, Spraggins JM. Imaging Mass Spectrometry of Isotopically Resolved Intact Proteins on a Trapped Ion-Mobility Quadrupole Time-of-Flight Mass Spectrometer. Anal Chem 2024; 96:5065-5070. [PMID: 38517028 PMCID: PMC10993197 DOI: 10.1021/acs.analchem.3c05252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
In this work, we demonstrate rapid, high spatial, and high spectral resolution imaging of intact proteins by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) on a hybrid quadrupole-reflectron time-of-flight (qTOF) mass spectrometer equipped with trapped ion mobility spectrometry (TIMS). Historically, untargeted MALDI IMS of proteins has been performed on TOF mass spectrometers. While advances in TOF instrumentation have enabled rapid, high spatial resolution IMS of intact proteins, TOF mass spectrometers generate relatively low-resolution mass spectra with limited mass accuracy. Conversely, the implementation of MALDI sources on high-resolving power Fourier transform (FT) mass spectrometers has allowed IMS experiments to be conducted with high spectral resolution with the caveat of increasingly long data acquisition times. As illustrated here, qTOF mass spectrometers enable protein imaging with the combined advantages of TOF and FT mass spectrometers. Protein isotope distributions were resolved for both a protein standard mixture and proteins detected from a whole-body mouse pup tissue section. Rapid (∼10 pixels/s) 10 μm lateral spatial resolution IMS was performed on a rat brain tissue section while maintaining isotopic spectral resolution. Lastly, proof-of-concept MALDI-TIMS data was acquired from a protein mixture to demonstrate the ability to differentiate charge states by ion mobility. These experiments highlight the advantages of qTOF and timsTOF platforms for resolving and interpreting complex protein spectra generated from tissue by IMS.
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Affiliation(s)
- Dustin
R. Klein
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Emilio S. Rivera
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Richard M. Caprioli
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Medicine, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M. Spraggins
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
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Zhou Y, Wu Q, Zhao Z, Wang Y, Lu H. Photocatalytic degradation-based ambient mass spectrometry imaging for enhancing detection coverage of poorly-ionizable lipidomes. Talanta 2024; 270:125564. [PMID: 38159350 DOI: 10.1016/j.talanta.2023.125564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/03/2024]
Abstract
Localization of lipidomes and tracking their spatial changes in tissues by mass spectrometry imaging (MSI) plays an important role in unveiling the mechanisms of living processes, diseases and therapeutic treatments. However, it is always challenging to achieve direct MSI of poorly-ionizable lipids, such as glycolipids and glycerolipids, due to the strong ion suppression and isobaric peaks interference from high-abundance phosphatidylcholines (PCs) in tissues. Here we developed a photocatalytic degradation-based ambient liquid extraction MSI method to largely enhance the detection coverage of poorly-ionizable lipids by rapid online removal of PCs in MSI. Phospholipids were found to be selectively photodegraded on TiO2 surface in acidic conditions in the presence of water under UV irradiation, while other poorly-ionizable lipids remained. Sulfate ion could largely improve the degradation efficiencies. Anatase nanoparticles-embedded TiO2 monolith was in-situ synthesized in the capillary of ambient liquid extraction system, and rapid online photodegradation of PCs was achieved during MSI with efficiency >80 %, largely reducing ion suppression. The pathway analysis showed that PC was oxidatively degraded starting from hydroxylation of C=C bonds. With intense UV irradiation, PCs were completely degraded into small molecules<200 Da without interference on the detection of endogenous lipids. With the new MSI method, detection coverage to cerebrosides, ceramides and diglycerides was enhanced by 2-9 times comparing with traditional MSI. Clearer localizations were observed for poorly-ionizable lipids via the new method than traditional method. Thus, this work provided a complementary MSI method for traditional MSI to address the issues on direct imaging of poorly ionizable lipids in ambient conditions.
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Affiliation(s)
- Yongchang Zhou
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha, 410083, PR China
| | - Qian Wu
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha, 410083, PR China.
| | - Zhihao Zhao
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha, 410083, PR China
| | - Yang Wang
- Laboratory of Ethnopharmacology, Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Hunan, Changsha, 410008, PR China
| | - Hongmei Lu
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha, 410083, PR China
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Pegoraro C, Domingo-Ortí I, Conejos-Sánchez I, Vicent MJ. Unlocking the Mitochondria for Nanomedicine-based Treatments: Overcoming Biological Barriers, Improving Designs, and Selecting Verification Techniques. Adv Drug Deliv Rev 2024; 207:115195. [PMID: 38325562 DOI: 10.1016/j.addr.2024.115195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/13/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Enhanced targeting approaches will support the treatment of diseases associated with dysfunctional mitochondria, which play critical roles in energy generation and cell survival. Obstacles to mitochondria-specific targeting include the presence of distinct biological barriers and the need to pass through (or avoid) various cell internalization mechanisms. A range of studies have reported the design of mitochondrially-targeted nanomedicines that navigate the complex routes required to influence mitochondrial function; nonetheless, a significant journey lies ahead before mitochondrially-targeted nanomedicines become suitable for clinical use. Moving swiftly forward will require safety studies, in vivo assays confirming effectiveness, and methodologies to validate mitochondria-targeted nanomedicines' subcellular location/activity. From a nanomedicine standpoint, we describe the biological routes involved (from administration to arrival within the mitochondria), the features influencing rational design, and the techniques used to identify/validate successful targeting. Overall, rationally-designed mitochondria-targeted-based nanomedicines hold great promise for precise subcellular therapeutic delivery.
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Affiliation(s)
- Camilla Pegoraro
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inés Domingo-Ortí
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inmaculada Conejos-Sánchez
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - María J Vicent
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
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Parmar D, Rosado-Rosa JM, Shrout JD, Sweedler JV. Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms. Methods 2024; 224:21-34. [PMID: 38295894 PMCID: PMC11149699 DOI: 10.1016/j.ymeth.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/17/2023] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence. Mass spectrometry imaging (MSI) bridges the gap by generating spatial chemical information with unmatched chemical detail, making it an irreplaceable analytical platform in the multi-modal imaging of biofilms. In the last two decades, over 30 species of biofilm-forming bacteria have been studied using MSI in different environments. The literature conveys both analytical advancements and an improved understanding of the effects of environmental variables such as host surface characteristics, antibiotics, and other species of microorganisms on biofilms. This review summarizes the insights from frequently studied model microorganisms. We share a detailed list of organism-wide metabolites, commonly observed mass spectral adducts, culture conditions, strains of bacteria, substrate, broad problem definition, and details of the MS instrumentation, such as ionization sources and matrix, to facilitate future studies. We also compared the spatial characteristics of the secretome under different study designs to highlight changes because of various environmental influences. In addition, we highlight the current limitations of MSI in relation to biofilm characterization to enable cross-comparison between experiments. Overall, MSI has emerged to become an important approach for the spatial/chemical characterization of bacterial biofilms and its use will continue to grow as MSI becomes more accessible.
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Affiliation(s)
- Dharmeshkumar Parmar
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joenisse M Rosado-Rosa
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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50
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Xu J, Chen H, Wang C, Ma Y, Song Y. Raman Flow Cytometry and Its Biomedical Applications. BIOSENSORS 2024; 14:171. [PMID: 38667164 PMCID: PMC11048678 DOI: 10.3390/bios14040171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024]
Abstract
Raman flow cytometry (RFC) uniquely integrates the "label-free" capability of Raman spectroscopy with the "high-throughput" attribute of traditional flow cytometry (FCM), offering exceptional performance in cell characterization and sorting. Unlike conventional FCM, RFC stands out for its elimination of the dependency on fluorescent labels, thereby reducing interference with the natural state of cells. Furthermore, it significantly enhances the detection information, providing a more comprehensive chemical fingerprint of cells. This review thoroughly discusses the fundamental principles and technological advantages of RFC and elaborates on its various applications in the biomedical field, from identifying and characterizing cancer cells for in vivo cancer detection and surveillance to sorting stem cells, paving the way for cell therapy, and identifying metabolic products of microbial cells, enabling the differentiation of microbial subgroups. Moreover, we delve into the current challenges and future directions regarding the improvement in sensitivity and throughput. This holds significant implications for the field of cell analysis, especially for the advancement of metabolomics.
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Affiliation(s)
- Jiayang Xu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Hangzhou 310058, China;
- Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Hongyi Chen
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, China
| | - Ce Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yuting Ma
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, China
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