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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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Zhang J, Mao Z, Zhang D, Guo L, Zhao H, Miao M. Mass spectrometry imaging as a promising analytical technique for herbal medicines: an updated review. Front Pharmacol 2024; 15:1442870. [PMID: 39148546 PMCID: PMC11324582 DOI: 10.3389/fphar.2024.1442870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/18/2024] [Indexed: 08/17/2024] Open
Abstract
Herbal medicines (HMs) have long played a pivotal role in preventing and treating various human diseases and have been studied widely. However, the complexities present in HM metabolites and their unclear mechanisms of action have posed significant challenges in the modernization of traditional Chinese medicine (TCM). Over the past two decades, mass spectrometry imaging (MSI) has garnered increasing attention as a robust analytical technique that enables the simultaneous execution of qualitative, quantitative, and localization analyses without complex sample pretreatment. With advances in technical solutions, MSI has been extensively applied in the field of HMs. MSI, a label-free ion imaging technique can comprehensively map the spatial distribution of HM metabolites in plant native tissues, thereby facilitating the effective quality control of HMs. Furthermore, the spatial dimension information of small molecule endogenous metabolites within animal tissues provided by MSI can also serve as a supplement to uncover pharmacological and toxicological mechanisms of HMs. In the review, we provide an overview of the three most common MSI techniques. In addition, representative applications in HM are highlighted. Finally, we discuss the current challenges and propose several potential solutions. We hope that the summary of recent findings will contribute to the application of MSI in exploring metabolites and mechanisms of action of HMs.
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Affiliation(s)
- Jinying Zhang
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
- Henan Collaborative Innovation Center for Research and Development on the Whole Industry Chain of Yu-Yao, Zhengzhou, China
| | - Zhiguo Mao
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
- Henan Collaborative Innovation Center for Research and Development on the Whole Industry Chain of Yu-Yao, Zhengzhou, China
| | - Ding Zhang
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
- Henan Collaborative Innovation Center for Research and Development on the Whole Industry Chain of Yu-Yao, Zhengzhou, China
| | - Lin Guo
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
- Henan Collaborative Innovation Center for Research and Development on the Whole Industry Chain of Yu-Yao, Zhengzhou, China
| | - Hui Zhao
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
- Henan Collaborative Innovation Center for Research and Development on the Whole Industry Chain of Yu-Yao, Zhengzhou, China
| | - Mingsan Miao
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
- Henan Collaborative Innovation Center for Research and Development on the Whole Industry Chain of Yu-Yao, Zhengzhou, China
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3
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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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Zhao J, Qin C, Shen Y, Xu C, Yao S, Liang C. A comprehensive review of chloropropanol analytical method in the context of food safety. Food Chem 2024; 446:138776. [PMID: 38417283 DOI: 10.1016/j.foodchem.2024.138776] [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: 10/20/2023] [Revised: 12/29/2023] [Accepted: 02/14/2024] [Indexed: 03/01/2024]
Abstract
Chloropropanols are among the major food contaminants, and quantifying their content in food is a key food-safety issue. In response to the demand for highly sensitive and selective analysis, the scientific community is committed to continuous innovation and optimization of various analytical techniques. This paper comprehensively reviews the latest developments in chloropropanol analysis technologies and systematically compares and analyzes the working principles, application conditions, advantages, and challenges of these methods. Gas chromatography-mass spectrometry is the preferred choice for chloropropanol analysis in complex sample matrices owing to its high resolution, sensitivity, and accuracy. Electrochemical methods provide strong support for the real-time monitoring of chloropropanols because of their high selectivity and sensitivity towards electrochemically active molecules. Other techniques offer innovative solutions for the rapid and accurate analysis of chloropropanol at different levels. Finally, innovative directions for the development of chloropropanol analysis methods for food safety are highlighted.
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Affiliation(s)
- Jinwei Zhao
- Guangxi University College of Light Industry and Food Engineering; Guangxi Key Laboratory of Clean Pulp and Paper and Pollution Control
| | - Chengrong Qin
- Guangxi University College of Light Industry and Food Engineering; Guangxi Key Laboratory of Clean Pulp and Paper and Pollution Control
| | - Yifan Shen
- Guangxi University College of Light Industry and Food Engineering; Guangxi Key Laboratory of Clean Pulp and Paper and Pollution Control
| | - Cheng Xu
- Guangxi University College of Light Industry and Food Engineering; Guangxi Key Laboratory of Clean Pulp and Paper and Pollution Control
| | - Shuangquan Yao
- Guangxi University College of Light Industry and Food Engineering; Guangxi Key Laboratory of Clean Pulp and Paper and Pollution Control
| | - Chen Liang
- Guangxi University College of Light Industry and Food Engineering; Guangxi Key Laboratory of Clean Pulp and Paper and Pollution Control.
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Wang J, Li S, Yang L, Kwan CS, Xie C, Cheung KY, Sun RWY, Chan ASC, Huang Z, Cai Z, Zeng T, Leung KCF. Janus and Amphiphilic MoS 2 2D Sheets for Surface-Directed Orientational Assemblies toward Ex Vivo Dual Substrate Release. SMALL METHODS 2024:e2400533. [PMID: 38874104 DOI: 10.1002/smtd.202400533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/17/2024] [Indexed: 06/15/2024]
Abstract
The two-dimensional (2-D) Janus and amphiphilic molybdenum disulfide (MoS2) nanosheet with opposite optical activities on each side (amphichiral) is synthesized by modifying sandwich-like bulk MoS2 with tannic acid and cholesterol through biphasic emulsion method. This new type of amphichiral Janus MoS2 nanosheet consists of a hydrophilic and positive optical activity tannic acid side as well as a hydrophobic and negative optical activity cholesterol side thereby characterized by circular dichroism. Surface-directed orientational differentiation assemblies are performed for the as-synthesized 2D material and are characterized by contact angle, infrared spectroscopy, X-ray photoelectron, and circular dichroism spectroscopies. The amphiphilic nature of the materials is demonstrated by the pre-organization of the nanosheets on either hydrophobic or hydrophilic surfaces, providing unprecedented properties of circular dichroism signal enhancement and wettability. Selective detachment of the surface organic groups (cholesterol and tannic acid fragments) is realized by matrix-assisted laser desorption/ionisation - time-of-flight (MALDI-TOF) mass spectrometry, and the dual substrate release in tissue is detected by ex vivo mass spectrometry imaging.
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Affiliation(s)
- Jianing Wang
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China
| | - Shuqi Li
- College of Environment, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, Zhejiang, 310014, P. R. China
| | - Lin Yang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, P. R. China
| | - Chak-Shing Kwan
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China
- Department of Chemistry, Great Bay University and Great Bay Institute for Advanced Study, Dongguan, 523000, P. R. China
| | - Chengyi Xie
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China
| | - Kwan Yin Cheung
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China
| | - Raymond Wai-Yin Sun
- Guangzhou Lee & Man Technology Company Limited, 8 Huanshi Avenue, Nansha, Guangzhou, 511458, P. R. China
| | - Albert S C Chan
- Guangzhou Lee & Man Technology Company Limited, 8 Huanshi Avenue, Nansha, Guangzhou, 511458, P. R. China
| | - Zhifeng Huang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, P. R. China
| | - Zongwei Cai
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China
| | - Tao Zeng
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China
- College of Environment, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, Zhejiang, 310014, P. R. China
| | - Ken Cham-Fai Leung
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China
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6
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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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7
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Ikeda T, Kotani M. Thin-section- and matrix-free mass spectrometry imaging: Reproducible sample transfer using novel platinum-coated porous plate formed of glass beads. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9697. [PMID: 38356087 DOI: 10.1002/rcm.9697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/07/2023] [Accepted: 12/12/2023] [Indexed: 02/16/2024]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) typically requires sample preparation such as sectioning and spraying of the matrix. Sample transfer using a Pt-coated porous plate formed of glass beads simplifies preparation and enables reproducible MSI measurements. METHODS The surface of a sintered-glass-bead porous plate was coated with Pt on one side of the plate. Polymer additives and the cross-section of a strawberry were chosen as the sample and transferred to the Pt-coated surface of the plate. This process was completely thin-section- and matrix-free. The prepared plates were analyzed using a commercial MALDI time-of-flight instrument. RESULTS Several constituents of the polymer additives (Irgafos 168 and Irganox 1010) and strawberry metabolites (hexose, citric acid, and sucrose) were detected without organic matrices. These ion images were obtained with a special distribution of the retained constituents. Duplicate prepared plates using the same strawberry cross-section reproduced the ion images. CONCLUSIONS A sample transfer process using a Pt-coated porous plate formed of glass beads was demonstrated as an alternative preparation method for MSI. This process has the potential to simplify MSI preparation and achieve easily reproducible MSI measurements.
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Affiliation(s)
- Takamasa Ikeda
- Hamamatsu Photonics KK, Iwata, Shizuoka, Japan
- The Graduate School for the Creation of New Photonics Industries, Hamamatsu, Shizuoka, Japan
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Knizner KT, Eisenberg SM, Muddiman DC. Prototyping an ionization source for non-engineers. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e4995. [PMID: 38129178 DOI: 10.1002/jms.4995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
Novel mass spectrometry (MS) based analytical platforms have enabled scientists to detect and quantify molecules within biological and environmental samples more accurately. Novel MS instrumentation starts as a prototype and, after years of development, can become a commercial product to be used by the larger MS community. Without the initial prototype, many MS-based instruments today would not be produced. Additionally, biotechnology companies are the main drivers for research, development, and production of novel instruments, but the tools for prototyping instrumentation have never been more accessible. Here, we present a tutorial on prototyping instrumentation through the case study of developing the Next Generation IR-MALDESI source to show that an engineering degree is not required to design and construct a prototype instrument with modern hardware and software. We discuss the prototyping process, the necessary skills required for efficient prototyping, and information about common hardware and software used within initial prototypes.
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Affiliation(s)
- Kevan T Knizner
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Seth M Eisenberg
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
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Fei AT, Strand DW, Wang J. Registration of hyperspectral images and mass spectrometry data for the correlation of tissue optical spectra and molecular profiles. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2024; 12827:1282708. [PMID: 38827822 PMCID: PMC11141327 DOI: 10.1117/12.3007718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Hyperspectral imaging (HSI) is a label-free imaging modality that is emerging for non-invasive detection of various diseases including cancers. HSI provides high-resolution spatial images where each pixel has a spectral curve with numerous wavelength bands from the visible to infrared ranges. The rich spatial and spectral information can be used to discriminate various types of tissues and pathophysiological conditions. However, it can be difficult to explain spectral data with respect to the underline cellular and molecular mechanism. In this study, we developed an approach that registers hyperspectral images and mass spectrometry (MS) data where MS provides tissue molecular profiles. Human prostate tissues that were obtained after prostatectomy were used in the experiments. The whole prostate was first sliced every six mm. A customized hyperspectral surgical microscope was used to acquire HSI data from the sliced tissue. For MS data analysis, the sliced tissue of the prostate was divided into 51 small regions and then processed separately for each region. The immediately adjacent tissue was sliced and processed histologically for H&E staining. The MS molecular profiles were correlated with the hyperspectral images in this study.
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Affiliation(s)
| | - Douglas W Strand
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jing Wang
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, Texas
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10
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Joignant AN, Knizner KT, Xi Y, Muddiman DC. Evaluating the optimal tissue thickness for mass spectrometry imaging using infrared matrix-assisted laser desorption electrospray ionization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9638. [PMID: 37817341 PMCID: PMC10881192 DOI: 10.1002/rcm.9638] [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: 06/02/2023] [Revised: 08/26/2023] [Accepted: 08/26/2023] [Indexed: 10/12/2023]
Abstract
RATIONALE Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) utilizes a 2970 nm mid-IR laser to desorb samples with depth resolutions (Z) on the order of micrometers. Conventionally, 5-20 μm thick tissue sections are used to characterize different applications of the IR-MALDESI source, but an optimal thickness has not been systematically investigated. METHODS Mouse liver was sectioned to various thicknesses and analyzed using IR-MALDESI mass spectrometry imaging (MSI). Height profiles of tissue sections of various cryosectioned thicknesses were acquired to affirm tissue thickness. Tissue sections of each thickness were measured using a Keyence microscope. Paraffin wax was cryosectioned, mounted on microscope slides, and measured using a chromatic confocal sensor system to determine the cryostat sectioning accuracy. RESULTS Analyzing sectioned tissues at higher thickness (>10 μm) leads to lower ion abundance, a decrease in signal over long analysis times, and more frequent instrument cleaning. Additionally, increasing tissue thickness above the optimum (7 μm) does not result in a significant increase in lipid annotations. CONCLUSIONS This work defines an optimal sample thickness for IR-MALDESI-MSI and demonstrates the utility of optimizing tissue thickness for MSI platforms of comparable Z resolution.
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Affiliation(s)
- Alena N. Joignant
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Kevan T. Knizner
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Ying Xi
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - David C. Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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Behera RN, Bisht VS, Giri K, Ambatipudi K. Realm of proteomics in breast cancer management and drug repurposing to alleviate intricacies of treatment. Proteomics Clin Appl 2023; 17:e2300016. [PMID: 37259687 DOI: 10.1002/prca.202300016] [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: 02/16/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023]
Abstract
Breast cancer, a multi-networking heterogeneous disease, has emerged as a serious impediment to progress in clinical oncology. Although technological advancements and emerging cancer research studies have mitigated breast cancer lethality, a precision cancer-oriented solution has not been achieved. Thus, this review will persuade the acquiescence of proteomics-based diagnostic and therapeutic options in breast cancer management. Recently, the evidence of breast cancer health surveillance through imaging proteomics, single-cell proteomics, interactomics, and post-translational modification (PTM) tracking, to construct proteome maps and proteotyping for stage-specific and sample-specific cancer subtyping have outperformed conventional ways of dealing with breast cancer by increasing diagnostic efficiency, prognostic value, and predictive response. Additionally, the paradigm shift in applied proteomics for designing a chemotherapy regimen to identify novel drug targets with minor adverse effects has been elaborated. Finally, the potential of proteomics in alleviating the occurrence of chemoresistance and enhancing reprofiled drugs' effectiveness to combat therapeutic obstacles has been discussed. Owing to the enormous potential of proteomics techniques, the clinical recognition of proteomics in breast cancer management can be achievable and therapeutic intricacies can be surmountable.
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Affiliation(s)
- Rama N Behera
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Vinod S Bisht
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kuldeep Giri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kiran Ambatipudi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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12
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Eisenberg SM, Knizner KT, Muddiman DC. Metabolite Annotation Confidence Score (MACS): A Novel MSI Identification Scoring Tool. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2222-2231. [PMID: 37606933 DOI: 10.1021/jasms.3c00178] [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: 08/23/2023]
Abstract
Mass spectrometry imaging (MSI) is an analytical technique capable of measuring and visualizing the spatial distribution of thousands of ions across a sample. Measured ions can be putatively identified and annotated by comparing their mass-to-charge ratio (m/z) to a database of known compounds. For high-resolution, accurate mass (HRAM) imaging data sets, this is commonly performed by the annotation platform METASPACE. Annotations are reported with a metabolite-signal-match (MSM) score as a measure of the annotation's confidence level. However, the MSM scores reported by METASPACE often do not reflect a reasonable confidence level of an annotation and are not assigned consistently. The metabolite annotation confidence score (MACS) is an alternative scoring system based on fundamental mass spectrometry imaging metrics (mass measurement accuracy, spectral accuracy, and spatial distribution) to generate values that reflect the confidence of a specific annotation in HRAM-MSI data sets. Herein, the MACS system is characterized and compared to MSM scores from ions annotated by METASPACE.
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Affiliation(s)
- Seth M Eisenberg
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Kevan T Knizner
- FTMS Laboratory for Human Health Research, Department of Chemistry, 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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Kumar BS. Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) in disease diagnosis: an overview. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:3768-3784. [PMID: 37503728 DOI: 10.1039/d3ay00867c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tissue analysis, which is essential to histology and is considered the benchmark for the diagnosis and prognosis of many illnesses, including cancer, is significant. During surgery, the surgical margin of the tumor is assessed using the labor-intensive, challenging, and commonly subjective technique known as frozen section histopathology. In the biopsy section, large numbers of molecules can now be visualized at once (ion images) following recent developments in [MSI] mass spectrometry imaging under atmospheric conditions. This is vastly superior to and different from the single optical tissue image processing used in traditional histopathology. This review article will focus on the advancement of desorption electrospray ionization mass spectrometry imaging [DESI-MSI] technique, which is label-free and requires little to no sample preparation. Since the proportion of molecular species in normal and abnormal tissues is different, DESI-MSI can capture ion images of the distributions of lipids and metabolites on biopsy sections, which can provide rich diagnostic information. This is not a systematic review but a summary of well-known, cutting-edge and recent DESI-MSI applications in cancer research between 2018 and 2023.
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Affiliation(s)
- Bharath Sampath Kumar
- Independent Researcher, 21, B2, 27th Street, Nanganallur, Chennai 61, TamilNadu, India.
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14
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Lin J, Yun K, Sun Q, Xiang P, Wu L, Yang S, Dun J, Fu S, Chen H. How to sample a seizure plant: the role of the visualization spatial distribution analysis of Lophophora williamsii as an example. Forensic Sci Res 2023; 8:140-151. [PMID: 37621449 PMCID: PMC10445667 DOI: 10.1093/fsr/owad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/16/2023] [Indexed: 08/26/2023] Open
Abstract
Natural compounds in plants are often unevenly distributed, and determining the best sampling locations to obtain the most representative results is technically challenging. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can provide the basis for formulating sampling guideline. For a succulent plant sample, ensuring the authenticity and in situ nature of the spatial distribution analysis results during MSI analysis also needs to be thoroughly considered. In this study, we developed a well-established and reliable MALDI-MSI method based on preservation methods, slice conditions, auxiliary matrices, and MALDI parameters to detect and visualize the spatial distribution of mescaline in situ in Lophophora williamsii. The MALDI-MSI results were validated using liquid chromatography-tandem mass spectrometry. Low-temperature storage at -80°C and drying of "bookmarks" were the appropriate storage methods for succulent plant samples and their flower samples, and cutting into 40 μm thick sections at -20°C using gelatin as the embedding medium is the appropriate sectioning method. The use of DCTB (trans-2-[3-(4-tert-butylphenyl)-2-methyl-2-propenylidene]malononitrile) as an auxiliary matrix and a laser intensity of 45 are favourable MALDI parameter conditions for mescaline analysis. The region of interest semi-quantitative analysis revealed that mescaline is concentrated in the epidermal tissues of L. williamsii as well as in the meristematic tissues of the crown. The study findings not only help to provide a basis for determining the best sampling locations for mescaline in L. williamsii, but they also provide a reference for the optimization of storage and preparation conditions for raw plant organs before MALDI detection. Key Points An accurate in situ MSI method for fresh water-rich succulent plants was obtained based on multi-parameter comparative experiments.Spatial imaging analysis of mescaline in Lophophora williamsii was performed using the above method.Based on the above results and previous results, a sampling proposal for forensic medicine practice is tentatively proposed.
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Affiliation(s)
- Jiaman Lin
- School of Forensic Medicine, Shanxi Medical University, Key Laboratory of Forensic Medicine in Shanxi Province, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Jinzhong, China
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, Key Laboratory of Forensic Medicine in Shanxi Province, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Jinzhong, China
| | - Qiran Sun
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Ping Xiang
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Lina Wu
- School of Forensic Medicine, Shanxi Medical University, Key Laboratory of Forensic Medicine in Shanxi Province, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Jinzhong, China
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Shuo Yang
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | | | - Shanlin Fu
- School of Forensic Medicine, Shanxi Medical University, Key Laboratory of Forensic Medicine in Shanxi Province, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Jinzhong, China
| | - Hang Chen
- Department of Forensic Toxicology, Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
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15
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Guo X, Wang X, Tian C, Dai J, Zhao Z, Duan Y. Development of mass spectrometry imaging techniques and its latest applications. Talanta 2023; 264:124721. [PMID: 37271004 DOI: 10.1016/j.talanta.2023.124721] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023]
Abstract
Mass spectrometry imaging (MSI) is a novel molecular imaging technology that collects molecular information from the surface of samples in situ. The spatial distribution and relative content of various compounds can be visualized simultaneously with high spatial resolution. The prominent advantages of MSI promote the active development of ionization technology and its broader applications in diverse fields. This article first gives a brief introduction to the vital parts of the processes during MSI. On this basis, provides a comprehensive overview of the most relevant MS-based imaging techniques from their mechanisms, pros and cons, and applications. In addition, a critical issue in MSI, matrix effects is also discussed. Then, the representative applications of MSI in biological, forensic, and environmental fields in the past 5 years have been summarized, with a focus on various types of analytes (e.g., proteins, lipids, polymers, etc.) Finally, the challenges and further perspectives of MSI are proposed and concluded.
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Affiliation(s)
- Xing Guo
- College of Chemistry and Material Science, Northwest University, Xi'an, 710069, PR China
| | - Xin Wang
- College of Chemistry and Material Science, Northwest University, Xi'an, 710069, PR China
| | - Caiyan Tian
- College of Life Science, Sichuan University, Chengdu, 610064, PR China
| | - Jianxiong Dai
- Aliben Science and Technology Company Limited, Chengdu, 610064, PR China
| | | | - Yixiang Duan
- College of Chemistry and Material Science, Northwest University, Xi'an, 710069, PR China; Research Center of Analytical Instrumentation, Sichuan University, Chengdu, 610064, PR China.
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16
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Sharman K, Patterson NH, Weiss A, Neumann EK, Guiberson ER, Ryan DJ, Gutierrez DB, Spraggins JM, Van de Plas R, Skaar EP, Caprioli RM. Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue. J Proteome Res 2023; 22:1394-1405. [PMID: 35849531 PMCID: PMC9845430 DOI: 10.1021/acs.jproteome.2c00206] [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: 01/21/2023]
Abstract
Spatially targeted proteomics analyzes the proteome of specific cell types and functional regions within tissue. While spatial context is often essential to understanding biological processes, interpreting sub-region-specific protein profiles can pose a challenge due to the high-dimensional nature of the data. Here, we develop a multivariate approach for rapid exploration of differential protein profiles acquired from distinct tissue regions and apply it to analyze a published spatially targeted proteomics data set collected from Staphylococcus aureus-infected murine kidney, 4 and 10 days postinfection. The data analysis process rapidly filters high-dimensional proteomic data to reveal relevant differentiating species among hundreds to thousands of measured molecules. We employ principal component analysis (PCA) for dimensionality reduction of protein profiles measured by microliquid extraction surface analysis mass spectrometry. Subsequently, k-means clustering of the PCA-processed data groups samples by chemical similarity. Cluster center interpretation revealed a subset of proteins that differentiate between spatial regions of infection over two time points. These proteins appear involved in tricarboxylic acid metabolomic pathways, calcium-dependent processes, and cytoskeletal organization. Gene ontology analysis further uncovered relationships to tissue damage/repair and calcium-related defense mechanisms. Applying our analysis in infectious disease highlighted differential proteomic changes across abscess regions over time, reflecting the dynamic nature of host-pathogen interactions.
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Affiliation(s)
- Kavya Sharman
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Program in Chemical & Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Emma R Guiberson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Daniel J Ryan
- Pfizer Inc., Chesterfield, Missouri 63017, United States
| | - Danielle B Gutierrez
- Mass Spectrometry Research Center, 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 37232, 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
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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17
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Brožová K, Hantusch B, Kenner L, Kratochwill K. Spatial Proteomics for the Molecular Characterization of Breast Cancer. Proteomes 2023; 11:17. [PMID: 37218922 PMCID: PMC10204503 DOI: 10.3390/proteomes11020017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/30/2023] [Accepted: 04/23/2023] [Indexed: 05/24/2023] Open
Abstract
Breast cancer (BC) is a major global health issue, affecting a significant proportion of the female population and contributing to high rates of mortality. One of the primary challenges in the treatment of BC is the disease's heterogeneity, which can lead to ineffective therapies and poor patient outcomes. Spatial proteomics, which involves the study of protein localization within cells, offers a promising approach for understanding the biological processes that contribute to cellular heterogeneity within BC tissue. To fully leverage the potential of spatial proteomics, it is critical to identify early diagnostic biomarkers and therapeutic targets, and to understand protein expression levels and modifications. The subcellular localization of proteins is a key factor in their physiological function, making the study of subcellular localization a major challenge in cell biology. Achieving high resolution at the cellular and subcellular level is essential for obtaining an accurate spatial distribution of proteins, which in turn can enable the application of proteomics in clinical research. In this review, we present a comparison of current methods of spatial proteomics in BC, including untargeted and targeted strategies. Untargeted strategies enable the detection and analysis of proteins and peptides without a predetermined molecular focus, whereas targeted strategies allow the investigation of a predefined set of proteins or peptides of interest, overcoming the limitations associated with the stochastic nature of untargeted proteomics. By directly comparing these methods, we aim to provide insights into their strengths and limitations and their potential applications in BC research.
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Affiliation(s)
- Klára Brožová
- Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
- Division of Molecular and Structural Preclinical Imaging, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1210 Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria
| | - Brigitte Hantusch
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria
- CBmed GmbH—Center for Biomarker Research in Medicine, 8010 Graz, Austria
- Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, 1090 Vienna, Austria
| | - Klaus Kratochwill
- Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
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18
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Savarino P, Demeyer M, Decroo C, Colson E, Gerbaux P. Mass spectrometry analysis of saponins. MASS SPECTROMETRY REVIEWS 2023; 42:954-983. [PMID: 34431118 DOI: 10.1002/mas.21728] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/13/2021] [Accepted: 08/09/2021] [Indexed: 05/26/2023]
Abstract
Saponins are amphiphilic molecules of pharmaceutical interest and most of their biological activities (i.e., cytotoxic, hemolytic, fungicide, etc.) are associated to their membranolytic properties. These molecules are secondary metabolites present in numerous plants and in some marine animals, such as sea cucumbers and starfishes. Structurally, all saponins correspond to the combination of a hydrophilic glycan, consisting of sugar chain(s), linked to a hydrophobic triterpenoidic or steroidic aglycone, named the sapogenin. Saponins present a high structural diversity and their structural characterization remains extremely challenging. Ideally, saponin structures are best established using nuclear magnetic resonance experiments conducted on isolated molecules. However, the extreme structural diversity of saponins makes them challenging from a structural analysis point of view since, most of the time, saponin extracts consist in a huge number of congeners presenting only subtle structural differences. In the present review, we wish to offer an overview of the literature related to the development of mass spectrometry for the study of saponins. This review will demonstrate that most of the past and current mass spectrometry methods, including electron, electrospray and matrix-assisted laser desorption/ionization ionizations, gas/liquid chromatography coupled to (tandem) mass spectrometry, collision-induced dissociation including MS3 experiments, multiple reaction monitoring based quantification, ion mobility experiments, and so forth, have been used for saponin investigations with great success on enriched extracts but also directly on tissues using imaging methods.
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Affiliation(s)
- Philippe Savarino
- Organic Synthesis and Mass Spectrometry Laboratory, Biosciences Research Institute, University of Mons-UMONS, Mons, Belgium
| | - Marie Demeyer
- Organic Synthesis and Mass Spectrometry Laboratory, Biosciences Research Institute, University of Mons-UMONS, Mons, Belgium
| | - Corentin Decroo
- Organic Synthesis and Mass Spectrometry Laboratory, Biosciences Research Institute, University of Mons-UMONS, Mons, Belgium
| | - Emmanuel Colson
- Organic Synthesis and Mass Spectrometry Laboratory, Biosciences Research Institute, University of Mons-UMONS, Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Biosciences Research Institute, University of Mons-UMONS, Mons, Belgium
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19
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Dekker J, Larson T, Tzvetkov J, Harvey VL, Dowle A, Hagan R, Genever P, Schrader S, Soressi M, Hendy J. Spatial analysis of the ancient proteome of archeological teeth using mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9486. [PMID: 36735645 DOI: 10.1002/rcm.9486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
RATIONALE Proteins extracted from archaeological bone and teeth are utilised for investigating the phylogeny of extinct and extant species, the biological sex and age of past individuals, as well as ancient health and physiology. However, variable preservation of proteins in archaeological materials represents a major challenge. METHODS To better understand the spatial distribution of ancient proteins preserved within teeth, we applied matrix assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for the first time to bioarchaeological samples to visualise the intensity of proteins in archaeological teeth thin sections. We specifically explored the spatial distribution of four proteins (collagen type I, of which the chains alpha-1 and alpha-2, alpha-2-HS-glycoprotein, haemoglobin subunit alpha and myosin light polypeptide 6). RESULTS We successfully identified ancient proteins in archaeological teeth thin sections using mass spectrometry imaging. The data are available via ProteomeXchange with identifier PXD038114. However, we observed that peptides did not always follow our hypotheses for their spatial distribution, with distinct differences observed in the spatial distribution of several proteins, and occasionally between peptides of the same protein. CONCLUSIONS While it remains unclear what causes these differences in protein intensity distribution within teeth, as revealed by MALDI-MSI in this study, we have demonstrated that MALDI-MSI can be successfully applied to mineralised bioarchaeological tissues to detect ancient peptides. In future applications, this technique could be particularly fruitful not just for understanding the preservation of proteins in a range of archaeological materials, but making informed decisions on sampling strategies and the targeting of key proteins of archaeological and biological interest.
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Affiliation(s)
- Joannes Dekker
- BioArCh, Department of Archaeology, University of York, York, UK
- Section for GeoBiology, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Faculty of Archaeology, Leiden University, Leiden, the Netherlands
| | - Tony Larson
- Metabolomics & Proteomics Laboratory, Bioscience Technology Facility, Department of Biology, University of York, York, UK
| | | | - Virginia L Harvey
- BioArCh, Department of Archaeology, University of York, York, UK
- Department of Biological Sciences, University of Chester, Chester, UK
| | - Adam Dowle
- Metabolomics & Proteomics Laboratory, Bioscience Technology Facility, Department of Biology, University of York, York, UK
| | - Richard Hagan
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Paul Genever
- Department of Biology, University of York, York, UK
| | - Sarah Schrader
- Faculty of Archaeology, Leiden University, Leiden, the Netherlands
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, Leiden, the Netherlands
| | - Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
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20
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Ma W, Luo L, Liang K, Liu T, Su J, Wang Y, Li J, Zhou SK, Shyh-Chang N. XAI-enabled neural network analysis of metabolite spatial distributions. Anal Bioanal Chem 2023; 415:2819-2830. [PMID: 37083759 DOI: 10.1007/s00216-023-04694-8] [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: 01/16/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/22/2023]
Abstract
We used deep neural networks to process the mass spectrometry imaging (MSI) data of mouse muscle (young vs aged) and human cancer (tumor vs normal adjacent) tissues, with the aim of using explainable artificial intelligence (XAI) methods to rapidly identify biomarkers that can distinguish different classes of tissues, from several thousands of metabolite features. We also modified classic neural network architectures to construct a deep convolutional neural network that is more suitable for processing high-dimensional MSI data directly, instead of using dimension reduction techniques, and compared it to seven other machine learning analysis methods' performance in classification accuracy. After ascertaining the superiority of Channel-ResNet10, we used a novel channel selection-based XAI method to identify the key metabolite features that were responsible for its learning accuracy. These key metabolite biomarkers were then processed using MetaboAnalyst for pathway enrichment mapping. We found that Channel-ResNet10 was superior to seven other machine learning methods for MSI analysis, reaching > 98% accuracy in muscle aging and colorectal cancer datasets. We also used a novel channel selection-based XAI method to find that in young and aged muscle tissues, the differentially distributed metabolite biomarkers were especially enriched in the propanoate metabolism pathway, suggesting it as a novel target pathway for anti-aging therapy.
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Affiliation(s)
- Wenwu Ma
- Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Lanfang Luo
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Kun Liang
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Taoyan Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jiali Su
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Yuefan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jun Li
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- Center for Medical Imaging Robotics, Analytic Computing & Learning (MIRACLE), School of Biomedical Engineering &, Suzhou Institute for Advance Research, University of Science and Technology of China, Suzhou, China
| | - S Kevin Zhou
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- Center for Medical Imaging Robotics, Analytic Computing & Learning (MIRACLE), School of Biomedical Engineering &, Suzhou Institute for Advance Research, University of Science and Technology of China, Suzhou, China
| | - Ng Shyh-Chang
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
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21
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Krijnen K, Keelor JD, Böhm S, Ellis SR, Köster C, Höhndorf J, Heeren RMA, Anthony IGM. A Multimodal SIMS/MALDI Mass Spectrometry Imaging Source with Secondary Electron Imaging Capabilities for Use with timsTOF Instruments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:720-727. [PMID: 36891615 PMCID: PMC10080675 DOI: 10.1021/jasms.2c00381] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Mass spectrometry imaging (MSI) is a surface analysis technique that produces chemical images and is commonly used for biological and biomedical research. Multimodal imaging combines multiple imaging modes in order to get a more comprehensive view of a sample. Multimodal MSI images are often acquired using multiple MSI instruments, which leads to issues regarding image registration and increases the chance of sample damage or degradation during sample transfer. These problems can be solved by using a single instrument that can image in multiple modes. In order to improve the efficiency of multimodal imaging and investigate complementary modes of MSI, we have modified a prototype Bruker timsTOF fleX by adding secondary ion mass spectrometry (SIMS) and secondary electron (SE) imaging capabilities while preserving the ability to perform matrix-assisted laser desorption/ionization (MALDI). We show multimodal images collected on this instrument that required only trivial registration and were acquired without sample transfer between imaging trials. Furthermore, we characterize the performance of SIMS, SE, and MALDI imaging and compare the performance of the modified instrument to a commercial timsTOF fleX.
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Affiliation(s)
- Kasper Krijnen
- Maastricht
MultiModal Molecular Imaging (M4i) Institute, Division of Imaging
Mass Spectrometry, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Joel D. Keelor
- Maastricht
MultiModal Molecular Imaging (M4i) Institute, Division of Imaging
Mass Spectrometry, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Sebastian Böhm
- Bruker
Daltonics GmbH & Co KG, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Shane R. Ellis
- Maastricht
MultiModal Molecular Imaging (M4i) Institute, Division of Imaging
Mass Spectrometry, Maastricht University, 6229 ER Maastricht, The Netherlands
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Claus Köster
- Bruker
Daltonics GmbH & Co KG, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Jens Höhndorf
- Bruker
Daltonics GmbH & Co KG, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Ron M. A. Heeren
- Maastricht
MultiModal Molecular Imaging (M4i) Institute, Division of Imaging
Mass Spectrometry, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ian G. M. Anthony
- Maastricht
MultiModal Molecular Imaging (M4i) Institute, Division of Imaging
Mass Spectrometry, Maastricht University, 6229 ER Maastricht, The Netherlands
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22
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Analysis of Metabolite Distribution in Rat Liver of High-Fat Model by Mass Spectrometry Imaging. Metabolites 2023; 13:metabo13030411. [PMID: 36984851 PMCID: PMC10057431 DOI: 10.3390/metabo13030411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Hyperlipidemia is a medical condition characterized by elevated levels of blood lipids, especially triglycerides (TG). However, it remains unclear whether TG levels remain consistently elevated throughout the entire developmental stage of the high-lipid state. In our animal experiment, we found that TG levels were significantly higher in the early stage of the high-lipid model but significantly decreased at the 14th week of the late stage, reaching levels similar to those of the control group. This suggests that TG levels in the high-lipid model are not always higher than those of the control group. To determine the reason for this observation, we used in situ mass spectrometry imaging (MSI) to detect the distribution of metabolites in the liver of rats. The metabolite distribution of the control rats at different stages was significantly different from that of the model rats, and the high-lipid model differed significantly from the control rats. We identified nine functional metabolites that showed differences throughout the period, namely, PA(20:3-OH/i-21:0), PA(20:4-OH/22:6), PG(20:5-OH/i-16:0), PG(22:6-2OH/i-13:0), PG(O-18:0/20:4), PGP(18:3-OH/i-12:0), PGP(PGJ2/i-15:0), SM(d18:0/18:1-2OH), and TG(14:0/14:0/16:0), among which TG was most significantly correlated with hyperlipidemia and high lipid. This study is unique in that it used MSI to reveal the changes in metabolites in situ, showing the distribution of different metabolites or the same metabolite in liver tissue. The findings highlight the importance of considering the animal’s age when using TG as a biomarker for hyperlipidemia. Additionally, the MSI images of the liver in the high-lipid model clearly indicated the distribution and differences of more significant metabolites, providing valuable data for further research into new biomarkers and mechanisms of hyperlipidemia. This new pathway of in situ, visualized, and data-rich metabolomics research provides a more comprehensive understanding of the characteristics of high lipid and its implications for disease prevention and treatment.
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Deschamps E, Calabrese V, Schmitz I, Hubert-Roux M, Castagnos D, Afonso C. Advances in Ultra-High-Resolution Mass Spectrometry for Pharmaceutical Analysis. Molecules 2023; 28:molecules28052061. [PMID: 36903305 PMCID: PMC10003995 DOI: 10.3390/molecules28052061] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
Pharmaceutical analysis refers to an area of analytical chemistry that deals with active compounds either by themselves (drug substance) or when formulated with excipients (drug product). In a less simplistic way, it can be defined as a complex science involving various disciplines, e.g., drug development, pharmacokinetics, drug metabolism, tissue distribution studies, and environmental contamination analyses. As such, the pharmaceutical analysis covers drug development to its impact on health and the environment. Moreover, due to the need for safe and effective medications, the pharmaceutical industry is one of the most heavily regulated sectors of the global economy. For this reason, powerful analytical instrumentation and efficient methods are required. In the last decades, mass spectrometry has been increasingly used in pharmaceutical analysis both for research aims and routine quality controls. Among different instrumental setups, ultra-high-resolution mass spectrometry with Fourier transform instruments, i.e., Fourier transform ion cyclotron resonance (FTICR) and Orbitrap, gives access to valuable molecular information for pharmaceutical analysis. In fact, thanks to their high resolving power, mass accuracy, and dynamic range, reliable molecular formula assignments or trace analysis in complex mixtures can be obtained. This review summarizes the principles of the two main types of Fourier transform mass spectrometers, and it highlights applications, developments, and future perspectives in pharmaceutical analysis.
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Affiliation(s)
- Estelle Deschamps
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
- ORIL Industrie, Servier Group, 13 r Auguste Desgenétais, 76210 Bolbec, France
| | - Valentina Calabrese
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100 Villeurbanne, France
| | - Isabelle Schmitz
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
| | - Marie Hubert-Roux
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
| | - Denis Castagnos
- ORIL Industrie, Servier Group, 13 r Auguste Desgenétais, 76210 Bolbec, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
- Correspondence:
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Grgic A, Krestensen KK, Heeren RMA. Optimized protocol for MALDI MSI of N-glycans using an on-tissue digestion in fresh frozen tissue sections. Sci Rep 2023; 13:2776. [PMID: 36797298 PMCID: PMC9935634 DOI: 10.1038/s41598-023-29560-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Glycans play an important role in biology with multiple cellular functions ranging from cell signaling, mobility and growth to protein folding and localization. The N-glycosylation state within a tissue has been found to vary greatly between healthy and diseased patients and has proven to have an important clinical diagnostic value. Matrix assisted laser-desorption ionization (MALDI) mass spectrometry imaging (MSI) allows for untargeted analysis of biomolecules, including N-glycans, on a tissue section and provides a spatial context of the analyte. Until now, N-glycans have been predominantly analyzed using MALDI MSI on formalin-fixed paraffin embedded (FFPE) tissue sections, however this greatly reduces the clinical applicability, as the FFPE embedding process alters the biological environment of the tissue. Here we developed a protocol that allows for MALDI MSI of N-glycans from fresh frozen tissue that matches the current standard of FFPE analysis. By optimizing several steps in the sample preparation, we see orders of magnitude increase in signal intensity. Furthermore, this method limits delocalization of released N-glycans, thus improving the effective spatial resolution of the label-free molecular images. This protocol provides a novel perspective towards clinical application of MALDI MSI and capitalizes on the diagnostic value of N-glycan analysis.
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Affiliation(s)
- Andrej Grgic
- grid.5012.60000 0001 0481 6099The Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Kasper K. Krestensen
- grid.5012.60000 0001 0481 6099The Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ron M. A. Heeren
- grid.5012.60000 0001 0481 6099The Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
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25
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Russo C, Clench MR. Spatially Resolved Quantitation of Drug in Skin Equivalents Using Mass Spectrometry Imaging (MSI). Methods Mol Biol 2023; 2688:27-40. [PMID: 37410281 DOI: 10.1007/978-1-0716-3319-9_3] [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] [Indexed: 07/07/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has seen a growing interest as a leading technique in the pharmaceutical industry for mapping label-free exogenous and endogenous species in biological tissues. However, the use of MALDI-MSI to perform spatially resolved absolute quantitation of species directly in tissues is still challenging, and robust quantitative mass spectrometry imaging (QMSI) methods need to be developed. In this study, we describe the microspotting technique for analytical and internal standard deposition, matrix sublimation, powerful QMSI software, and mass spectrometry imaging setup to obtain absolute quantitation of drug distribution in 3D skin models.
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Affiliation(s)
- Cristina Russo
- Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK.
- Department of Natural Sciences, Middlesex University, London, UK.
| | - Malcolm R Clench
- Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
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26
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Chao HC, McLuckey SA. Recent Advances in Gas-phase Ion/Ion Chemistry for Lipid Analysis. Trends Analyt Chem 2023; 158:116852. [PMID: 36583222 PMCID: PMC9794197 DOI: 10.1016/j.trac.2022.116852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Gas-phase ion/ion reactions can be used to alter analyte ion-types for subsequent dissociation both quickly and efficiently without the need for altering analyte ionization conditions. This capability can be particularly useful when the ion-type that is most efficiently generated by the ionization method at hand does not provide the structural information of interest using available dissociation methods. This situation often arises in the analysis of lipids, which constitute a diverse array of chemical species with many possibilities for isomers. Gas-phase ion/ion reactions have been demonstrated to be capable of enhancing the ability of tandem mass spectrometry to characterize the structures of various lipid classes. This review summarizes progress to date in the application of gas-phase ion/ion reactions to lipid structural characterization.
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Affiliation(s)
- Hsi-Chun Chao
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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27
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Knizner KT, Kibbe RR, Garrard KP, Nuñez JR, Anderton CR, Muddiman DC. On the importance of color in mass spectrometry imaging. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4898. [PMID: 36463891 PMCID: PMC9944061 DOI: 10.1002/jms.4898] [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: 09/27/2022] [Revised: 11/07/2022] [Accepted: 11/17/2022] [Indexed: 05/12/2023]
Abstract
Mass spectrometry imaging (MSI) data visualization relies on heatmaps to show the spatial distribution and measured abundances of molecules within a sample. Nonuniform color gradients such as jet are still commonly used to visualize MSI data, increasing the probability of data misinterpretation and false conclusions. Also, the use of nonuniform color gradients and the combination of hues used in common colormaps make it challenging for people with color vision deficiencies (CVDs) to visualize and accurately interpret data. Here we present best practices for choosing a colormap to accurately display MSI data, improve readability, and accommodate all CVDs. We also provide other resources on the misuse of color in the scientific field and resources on scientifically derived colormaps presented herein.
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Affiliation(s)
- Kevan T. Knizner
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Russell R. Kibbe
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Kenneth P. Garrard
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Molecular Education, Technology and Research Innovation Center (METRIC)North Carolina State UniversityRaleighNorth CarolinaUSA
- Precision Engineering ConsortiumNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Jamie R. Nuñez
- Earth and Biological Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Christopher R. Anderton
- Earth and Biological Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA
| | - David C. Muddiman
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Molecular Education, Technology and Research Innovation Center (METRIC)North Carolina State UniversityRaleighNorth CarolinaUSA
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28
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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29
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Wang X, Hebert DD, Runsewe DO, Pohlman GE, Hoffmann WD, Irvin JA. Electroactive Polymer-Based Spray Ionization for Direct Mass Spectrometric Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1840-1849. [PMID: 36149251 DOI: 10.1021/jasms.2c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Electrochemically deposited electroactive polymer (EAP) films were investigated for their potential to enhance the performance of ambient ionization mass spectrometry (MS). Several EAPs of varying hydrophobicity were evaluated, including the superhydrophobic polymer poly[3,4-(2-dodecylethylenedioxy)thiophene] (PEDOT-C12). The EAPs were electropolymerized onto indium tin oxide-coated glass, placed in front of the inlet of a mass spectrometer, and charged to 3.5-4.5 kV. Analyte solutions were then applied to the surface, initiating ionization events. Analytes including peptides and small molecule pharmaceuticals were studied in 0.1% formic acid in methanol/water ("spray solvent") as well as in synthetic biological fluid matrices, using both EAP spray ionization (EAPSI) and paper spray ionization (PSI). Each EAPSI analysis required as little as 0.1 μL of solution, and the resulting sprays were stable and reproducible. The sensitivity, limit of detection (LOD), and limit of quantification (LOQ) were evaluated using bradykinin, cannabinol, and cannabidiol, which were prepared in pure solvents, artificial urine, and artificial saliva. The limits of detection and quantitation for EAPSI were improved relative to PSI by 1-2 orders of magnitude for analytes prepared in methanol/water and on the same order of magnitude as PSI for analytes prepared in artificial saliva and urine. This EAP-based spray ionization technique offers possibilities for rapid MS analysis with small sample sizes, high accuracy, and miniaturization of MS instruments.
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Affiliation(s)
- Xu Wang
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
| | - David D Hebert
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
| | - Damilola O Runsewe
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
| | - Gabriel E Pohlman
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
| | - William D Hoffmann
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
| | - Jennifer A Irvin
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
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30
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Zhao D, Yu P, Han B, Qiao F. Study on the Distribution of Low Molecular Weight Metabolites in Mango Fruit by Air Flow-Assisted Ionization Mass Spectrometry Imaging. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27185873. [PMID: 36144608 PMCID: PMC9505047 DOI: 10.3390/molecules27185873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022]
Abstract
Mass spectrometry imaging is a novel molecular imaging technique that has been developing rapidly in recent years. Air flow-assisted ionization mass spectrometry imaging (AFAI-MSI) has received wide attention in the biomedical field because of its features such as not needing a pretreatment sample, having high sensitivity, and wide coverage of metabolite detection. In this study, we set up a mass spectrometry imaging method for analyzing low molecular metabolites in mango fruits by the AFAI-MSI method. Compounds such as organic acids, vitamin C, and phenols were detected from mango tissue by mass spectrometry under the negative ion scanning mode, and their spatial distribution was analyzed. As a result, all the target compounds showed different distributions. Citric acid was mainly distributed in the pulp. Malic acid, quinic acid, and vitamin C universally existed in the pulp and peel. However, galloylglucose isomer and 5-galloylquinic acid were predominantly found in the peel. These results show that AFAI-MSI can be used for the analysis of mango fruit endogenous metabolites conveniently and directly, which will facilitate the rapid identification and in situ characterization of plant endogenous substances.
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Affiliation(s)
- Deqing Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture/Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ping Yu
- Yunyang County Agricultural Technology Service Center of Chongqing, Chongqing 404500, China
| | - Bingjun Han
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Fei Qiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture/Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: ; Tel.: +86-089866961395
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31
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Next Generation Digital Pathology: Emerging Trends and Measurement Challenges for Molecular Pathology. JOURNAL OF MOLECULAR PATHOLOGY 2022. [DOI: 10.3390/jmp3030014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Digital pathology is revolutionising the analysis of histological features and is becoming more and more widespread in both the clinic and research. Molecular pathology extends the tissue morphology information provided by conventional histopathology by providing spatially resolved molecular information to complement the structural information provided by histopathology. The multidimensional nature of the molecular data poses significant challenge for data processing, mining, and analysis. One of the key challenges faced by new and existing pathology practitioners is how to choose the most suitable molecular pathology technique for a given diagnosis. By providing a comparison of different methods, this narrative review aims to introduce the field of molecular pathology, providing a high-level overview of many different methods. Since each pixel of an image contains a wealth of molecular information, data processing in molecular pathology is more complex. The key data processing steps and variables, and their effect on the data, are also discussed.
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32
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Khalil SM, Sprenger RR, Hermansson M, Ejsing CS. DDA-imaging with structural identification of lipid molecules on an Orbitrap Velos Pro mass spectrometer. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4882. [PMID: 36055222 PMCID: PMC9541402 DOI: 10.1002/jms.4882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/05/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) is a useful technique for visualizing the spatial distribution of lipid molecules in tissues. Nevertheless, the use of MSI to investigate local lipid metabolic hallmarks has until recently been hampered by a lack of adequate technology that supports confident lipid identification. This limitation was recently mitigated by the development of DDA-imaging technology where high-resolution MSI is combined with parallel acquisition of lipid tandem MS2 spectra on a hybrid ion trap-Orbitrap Elite mass spectrometer featuring a resolving power of 240,000 and a scan time of 1 s. Here, we report the key tenets related to successful transfer of the DDA-imaging technology onto an Orbitrap Velos Pro instrument featuring a resolving power of 120,000 and a scan time of 2 s. Through meticulous performance assessments and method optimization, we tuned the DDA-imaging method to be able to confidently identify 73 molecular lipid species in mouse brain sections and demonstrate that the performance of the technology is comparable with DDA-imaging on the Orbitrap Elite. Altogether, our work shows that DDA-imaging on the Orbitrap Velos Pro instrument can serve as a robust workhorse for lipid imaging in routine applications.
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Affiliation(s)
- Saleh M. Khalil
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Richard R. Sprenger
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Martin Hermansson
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Christer S. Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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Jing F, Wang L, Yang M, Wu C, Li J, Shi L, Feng S, Li F. Visualizing the spatial distribution of functional metabolites in Forsythia suspensa at different harvest stages by MALDI mass spectrometry imaging. Fitoterapia 2022; 162:105285. [PMID: 36041592 DOI: 10.1016/j.fitote.2022.105285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/22/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022]
Abstract
As a traditional Chinese medicine, Forsythia suspensa (F. suspensa) has attracted much attention due to its significant pharmacological activity. Revealing the spatial distribution of metabolites during F. suspensa development is important for understanding its biosynthesis rules and improving the quality of medicinal materials. However, there is currently a lack of information on the spatial distribution of F. suspensa metabolites. In this work, the spatial distribution and growth metabolism patterns of important metabolites of F. suspensa were studied for the first time using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Using 2,5-dimethylnaphthalene (DAN) as the matrix and detecting in negative ion mode, the spatial distribution and growth patterns of 11 metabolites obtained from longitudinal sections of F. suspensa included pinoresinol, phillygenin, forsythoside A, forsythoside E, rutin, caffeic acid, malic acid, citric acid, stearic acid, oleic acid, and linoleic acid. These results showed the mesocarp and endosperm tissues of F. suspensa were important for storing important functional metabolites. Changes in mesocarp and endosperm growth and development tissues caused large changes in the content of important functional metabolites in F. suspensa. These results provide a basis for understanding the spatial distribution of metabolites in F. suspensa tissues and the significant changes that occur during growth and development, exploring the mechanism of important synthesis of metabolites, regulating the harvest of F. suspensa, and improving the quality of medicinal herbs.
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Affiliation(s)
- Fengtang Jing
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Lei Wang
- Yantai Food and Drug Inspection Center, Yantai, Shandong 264000, China
| | - Min Yang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Chao Wu
- Shandong Drug and Food Vocational College, Weihai 264210, China
| | - Jian Li
- Department of Pharmacy, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250000, China
| | - Lei Shi
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Shuai Feng
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; Shandong Provincial Collaborative Innovation Center for Quality Control and Construction of the Whole Industrial Chain of Traditional Chinese Medicine, Jinan 250355, China..
| | - Feng Li
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
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Baquer G, Sementé L, Mahamdi T, Correig X, Ràfols P, García-Altares M. What are we imaging? Software tools and experimental strategies for annotation and identification of small molecules in mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2022:e21794. [PMID: 35822576 DOI: 10.1002/mas.21794] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) has become a widespread analytical technique to perform nonlabeled spatial molecular identification. The Achilles' heel of MSI is the annotation and identification of molecular species due to intrinsic limitations of the technique (lack of chromatographic separation and the difficulty to apply tandem MS). Successful strategies to perform annotation and identification combine extra analytical steps, like using orthogonal analytical techniques to identify compounds; with algorithms that integrate the spectral and spatial information. In this review, we discuss different experimental strategies and bioinformatics tools to annotate and identify compounds in MSI experiments. We target strategies and tools for small molecule applications, such as lipidomics and metabolomics. First, we explain how sample preparation and the acquisition process influences annotation and identification, from sample preservation to the use of orthogonal techniques. Then, we review twelve software tools for annotation and identification in MSI. Finally, we offer perspectives on two current needs of the MSI community: the adaptation of guidelines for communicating confidence levels in identifications; and the creation of a standard format to store and exchange annotations and identifications in MSI.
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Affiliation(s)
- Gerard Baquer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Lluc Sementé
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Toufik Mahamdi
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Xavier Correig
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - Pere Ràfols
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - María García-Altares
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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Mass spectral imaging showing the plant growth-promoting rhizobacteria's effect on the Brachypodium awn. Biointerphases 2022; 17:031006. [PMID: 35738921 DOI: 10.1116/6.0001949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The plant growth-promoting rhizobacteria (PGPR) on the host plant surface play a key role in biological control and pathogenic response in plant functions and growth. However, it is difficult to elucidate the PGPR effect on plants. Such information is important in biomass production and conversion. Brachypodium distachyon (Brachypodium), a genomics model for bioenergy and native grasses, was selected as a C3 plant model; and the Gram-negative Pseudomonas fluorescens SBW25 (P.) and Gram-positive Arthrobacter chlorophenolicus A6 (A.) were chosen as representative PGPR strains. The PGPRs were introduced to the Brachypodium seed's awn prior to germination, and their possible effects on the seeding and growth were studied using different modes of time-of-flight secondary ion mass spectrometry (ToF-SIMS) measurements, including a high mass-resolution spectral collection and delayed image extraction. We observed key plant metabolic products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and auxin indole-3-acetic acid in the Brachypodium awns. Furthermore, principal component analysis and two-dimensional imaging analysis reveal that the Brachypodium awns are sensitive to the PGPR, leading to chemical composition and morphology changes on the awn surface. Our results show that ToF-SIMS can be an effective tool to probe cell-to-cell interactions at the biointerface. This work provides a new approach to studying the PGPR effects on awn and shows its potential for the research of plant growth in the future.
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Mass Spectrometry-Based Analysis of Lipid Involvement in Alzheimer’s Disease Pathology—A Review. Metabolites 2022; 12:metabo12060510. [PMID: 35736443 PMCID: PMC9228715 DOI: 10.3390/metabo12060510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 01/27/2023] Open
Abstract
Irregularities in lipid metabolism have been linked to numerous neurodegenerative diseases. The roles of abnormal brain, plasma, and cerebrospinal fluid (CSF) lipid levels in Alzheimer’s disease (AD) onset and progression specifically have been described to a great extent in the literature. Apparent hallmarks of AD include, but are not limited to, genetic predisposition involving the APOE Ɛ4 allele, oxidative stress, and inflammation. A common culprit tied to many of these hallmarks is disruption in brain lipid homeostasis. Therefore, it is important to understand the roles of lipids, under normal and abnormal conditions, in each process. Lipid influences in processes such as inflammation and blood–brain barrier (BBB) disturbance have been primarily studied via biochemical-based methods. There is a need, however, for studies focused on uncovering the relationship between lipid irregularities and AD by molecular-based quantitative analysis in transgenic animal models and human samples alike. In this review, mass spectrometry as it has been used as an analytical tool to address the convoluted relationships mentioned above is discussed. Additionally, molecular-based mass spectrometry strategies that should be used going forward to further relate structure and function relationships of lipid irregularities and hallmark AD pathology are outlined.
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37
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Mikolasch TA, Oballa E, Vahdati-Bolouri M, Jarvis E, Cui Y, Cahn A, Terry RL, Sahota J, Thakrar R, Marshall P, Porter JC. Mass spectrometry detection of inhaled drug in distal fibrotic lung. Respir Res 2022; 23:118. [PMID: 35546672 PMCID: PMC9092847 DOI: 10.1186/s12931-022-02026-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 04/14/2022] [Indexed: 12/04/2022] Open
Abstract
Background Currently the only available therapies for fibrotic Interstitial Lung Disease are administered systemically, often causing significant side effects. Inhaled therapy could avoid these but to date there is no evidence that drug can be effectively delivered to distal, fibrosed lung. We set out to combine mass spectrometry and histopathology with rapid sample acquisition using transbronchial cryobiopsy to determine whether an inhaled drug can be delivered to fibrotic, distal lung parenchyma in participants with Interstitial Lung Disease. Methods Patients with radiologically and multidisciplinary team confirmed fibrotic Interstitial Lung Disease were eligible for this study. Transbronchial cryobiopsies and endobronchial biopsies were taken from five participants, with Interstitial Lung Disease, within 70 min of administration of a single dose of nebulised ipratropium bromide. Thin tissue cryosections were analysed by Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry imaging and correlated with histopathology. The remainder of the cryobiopsies were homogenised and analysed by Liquid Chromatography—tandem Mass Spectrometry. Results Drug was detected in proximal and distal lung samples from all participants. Fibrotic regions were identified in research samples of four of the five participants. Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry imaging showed co-location of ipratropium with fibrotic regions in samples from three participants. Conclusions In this proof of concept study, using mass spectrometry, we demonstrate for the first-time that an inhaled drug can deposit in distal fibrotic lung parenchyma in patients with Interstitial Lung Disease. This suggests that drugs to treat pulmonary fibrosis could potentially be administered by the inhaled route. Trial registration A prospective clinical study approved by London Camden and Kings Cross Research Ethics Committee and registered on clinicaltrials.gov (NCT03136120) Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02026-5.
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Affiliation(s)
- Theresia A Mikolasch
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK. .,University College London Hospitals NHS Foundation Trust, London, UK.
| | - Eunice Oballa
- Discovery Medicine, Clinical Pharmacology and Experimental Medicine, GSK Research and Development, Stevenage, UK
| | | | - Emily Jarvis
- Development Biostatistics, GSK Development, Stevenage, UK
| | - Yi Cui
- Safety and Medical Governance, Pharma Safety, GSK Development, Stevenage, UK
| | - Anthony Cahn
- Discovery Medicine, Clinical Pharmacology and Experimental Medicine, GSK Research and Development, Stevenage, UK
| | - Rebecca L Terry
- Pathology, In Vitro/In Vivo Translation, GSK Research, Stevenage, UK
| | - Jagdeep Sahota
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK.,University College London Hospitals NHS Foundation Trust, London, UK
| | - Ricky Thakrar
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Peter Marshall
- Bioimaging, In Vitro/In Vivo Translation, GSK Research, Stevenage, UK
| | - Joanna C Porter
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK.,University College London Hospitals NHS Foundation Trust, London, UK
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Angerer TB, Bour J, Biagi JL, Moskovets E, Frache G. Evaluation of 6 MALDI-Matrices for 10 μm Lipid Imaging and On-Tissue MSn with AP-MALDI-Orbitrap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:760-771. [PMID: 35358390 PMCID: PMC9074099 DOI: 10.1021/jasms.1c00327] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Mass spectrometry imaging is a technique uniquely suited to localize and identify lipids in a tissue sample. Using an atmospheric pressure (AP-) matrix-assisted laser desorption ionization (MALDI) source coupled to an Orbitrap Elite, numerous lipid locations and structures can be determined in high mass resolution spectra and at cellular spatial resolution, but careful sample preparation is necessary. We tested 11 protocols on serial brain sections for the commonly used MALDI matrices CHCA, norharmane, DHB, DHAP, THAP, and DAN in combination with tissue washing and matrix additives to determine the lipid coverage, signal intensity, and spatial resolution achievable with AP-MALDI. In positive-ion mode, the most lipids could be detected with CHCA and THAP, while THAP and DAN without additional treatment offered the best signal intensities. In negative-ion mode, DAN showed the best lipid coverage and DHAP performed superiorly for gangliosides. DHB produced intense cholesterol signals in the white matter. One hundred fifty-five lipids were assigned in positive-ion mode (THAP) and 137 in negative-ion mode (DAN), and 76 peaks were identified using on-tissue tandem-MS. The spatial resolution achievable with DAN was 10 μm, confirmed with on tissue line-scans. This enabled the association of lipid species to single neurons in AP-MALDI images. The results show that the performance of AP-MALDI is comparable to vacuum MALDI techniques for lipid imaging.
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Affiliation(s)
- Tina B. Angerer
- Luxembourg
Institute of Science and Technology (LIST), Advanced Characterization platform, Materials Research
and Technology, 41, rue
du Brill, L-4422 Belvaux, Luxembourg
| | - Jerome Bour
- Luxembourg
Institute of Science and Technology (LIST), Advanced Characterization platform, Materials Research
and Technology, 41, rue
du Brill, L-4422 Belvaux, Luxembourg
| | - Jean-Luc Biagi
- Luxembourg
Institute of Science and Technology (LIST), Advanced Characterization platform, Materials Research
and Technology, 41, rue
du Brill, L-4422 Belvaux, Luxembourg
| | | | - Gilles Frache
- Luxembourg
Institute of Science and Technology (LIST), Advanced Characterization platform, Materials Research
and Technology, 41, rue
du Brill, L-4422 Belvaux, Luxembourg
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Müller WH, Verdin A, De Pauw E, Malherbe C, Eppe G. Surface-assisted laser desorption/ionization mass spectrometry imaging: A review. MASS SPECTROMETRY REVIEWS 2022; 41:373-420. [PMID: 33174287 PMCID: PMC9292874 DOI: 10.1002/mas.21670] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 05/04/2023]
Abstract
In the last decades, surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) has attracted increasing interest due to its unique capabilities, achievable through the nanostructured substrates used to promote the analyte desorption/ionization. While the most widely recognized asset of SALDI-MS is the untargeted analysis of small molecules, this technique also offers the possibility of targeted approaches. In particular, the implementation of SALDI-MS imaging (SALDI-MSI), which is the focus of this review, opens up new opportunities. After a brief discussion of the nomenclature and the fundamental mechanisms associated with this technique, which are still highly controversial, the analytical strategies to perform SALDI-MSI are extensively discussed. Emphasis is placed on the sample preparation but also on the selection of the nanosubstrate (in terms of chemical composition and morphology) as well as its functionalization possibilities for the selective analysis of specific compounds in targeted approaches. Subsequently, some selected applications of SALDI-MSI in various fields (i.e., biomedical, biological, environmental, and forensic) are presented. The strengths and the remaining limitations of SALDI-MSI are finally summarized in the conclusion and some perspectives of this technique, which has a bright future, are proposed in this section.
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Affiliation(s)
- Wendy H. Müller
- Mass Spectrometry Laboratory, MolSys Research Unit, Chemistry DepartmentUniversity of LiègeLiègeBelgium
| | - Alexandre Verdin
- Mass Spectrometry Laboratory, MolSys Research Unit, Chemistry DepartmentUniversity of LiègeLiègeBelgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, Chemistry DepartmentUniversity of LiègeLiègeBelgium
| | - Cedric Malherbe
- Mass Spectrometry Laboratory, MolSys Research Unit, Chemistry DepartmentUniversity of LiègeLiègeBelgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, Chemistry DepartmentUniversity of LiègeLiègeBelgium
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40
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Technical steps towards enhanced localization of proteins in cultural heritage samples by immunofluorescence microscopy and micro-reflectance imaging spectroscopy. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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41
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Versatile Mass Spectrometry-Based Intraoperative Diagnosis of Liver Tumor in a Multiethnic Cohort. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Currently used techniques for intraoperative assessment of tumor resection margins are time-consuming and laborious and, more importantly, lack specificity. Moreover, pathological diagnosis during surgery does not often give a clear outcome. Recent advances in mass spectrometry (MS) and instrumentation have made it possible to obtain detailed molecular information from tissue specimens in real-time, with minimal sample pre-treatment. Probe Electro Spray Ionization MS (PESI-MS), combined with artificial intelligence (AI), has demonstrated its effectiveness in distinguishing liver cancer tissues from healthy tissues in a large Italian population group. As the MS profile can reflect the patient’s ethnicity, dietary habits, or particular operating room procedures, the AI algorithm must be well trained to distinguish different groups. We used a large dataset composed of liver tumor and healthy specimens, from the Italian and Japanese populations, to develop a versatile algorithm free from ethnic bias. The system can classify tissues with discrepancies <5% from the pathologist’s diagnosis. These results demonstrate the potential of the PESI-MS system to distinguish tumor from surrounding non-tumor tissues in patients, with minimal bias from race/ethnicity or etiological characteristics or operating room procedures.
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42
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Petrov PB, Awoniyi LO, Šuštar V, Balci MÖ, Mattila PK. AutoCoEv—A High-Throughput In Silico Pipeline for Predicting Inter-Protein Coevolution. Int J Mol Sci 2022; 23:ijms23063351. [PMID: 35328772 PMCID: PMC8952222 DOI: 10.3390/ijms23063351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
Protein–protein interactions govern cellular processes via complex regulatory networks, which are still far from being understood. Thus, identifying and understanding connections between proteins can significantly facilitate our comprehension of the mechanistic principles of protein functions. Coevolution between proteins is a sign of functional communication and, as such, provides a powerful approach to search for novel direct or indirect molecular partners. However, an evolutionary analysis of large arrays of proteins in silico is a highly time-consuming effort that has limited the usage of this method for protein pairs or small protein groups. Here, we developed AutoCoEv, a user-friendly, open source, computational pipeline for the search of coevolution between a large number of proteins. By driving 15 individual programs, culminating in CAPS2 as the software for detecting coevolution, AutoCoEv achieves a seamless automation and parallelization of the workflow. Importantly, we provide a patch to the CAPS2 source code to strengthen its statistical output, allowing for multiple comparison corrections and an enhanced analysis of the results. We apply the pipeline to inspect coevolution among 324 proteins identified to be located at the vicinity of the lipid rafts of B lymphocytes. We successfully detected multiple coevolutionary relations between the proteins, predicting many novel partners and previously unidentified clusters of functionally related molecules. We conclude that AutoCoEv, can be used to predict functional interactions from large datasets in a time- and cost-efficient manner.
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Affiliation(s)
- Petar B. Petrov
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- Correspondence: (P.B.P.); (P.K.M.)
| | - Luqman O. Awoniyi
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Vid Šuštar
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
| | - M. Özge Balci
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Pieta K. Mattila
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- Correspondence: (P.B.P.); (P.K.M.)
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43
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Huang L, Nie L, Dai Z, Dong J, Jia X, Yang X, Yao L, Ma SC. The application of mass spectrometry imaging in traditional Chinese medicine: a review. Chin Med 2022; 17:35. [PMID: 35248086 PMCID: PMC8898510 DOI: 10.1186/s13020-022-00586-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/22/2022] [Indexed: 08/26/2023] Open
Abstract
AbstractMass spectrometry imaging is a frontier technique which connects classical mass spectrometry with ion imaging. Various types of chemicals could be visualized in their native tissues using mass spectrometry imaging. Up to now, the most commonly applied mass spectrometry imaging techniques are matrix assisted laser desorption ionization mass spectrometry imaging, desorption electrospray ionization mass spectrometry imaging and secondary ion mass spectrometry imaging. This review gives an introduction to the principles, development and applications of commonly applied mass spectrometry imaging techniques, and then illustrates the application of mass spectrometry imaging in the investigation of traditional Chinese medicine. Recently, mass spectrometry imaging has been adopted to explore the spatial distribution of endogenous metabolites in traditional Chinese medicine. Data collected from mass spectrometry imaging can be further utilized to search for marker components of traditional Chinese medicine, discover new compounds from traditional herbs, and differentiate between medicinal plants that are similar in botanical features. Moreover, mass spectrometry imaging also plays a role in revealing the pharmacological and toxicological mechanisms of traditional Chinese medicine.
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Abstract
Mass spectrometry imaging (MSI) is a technique for obtaining information on the distribution of various molecules by performing mass spectrometry directly on the sample surface. The applications range from small molecules such as lipids to large molecules such as proteins. It is also possible to detect pharmaceuticals and elemental isotopes in interstellar matter. This review will introduce various applications of MSI with examples.
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Affiliation(s)
- Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University
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45
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Mugume Y, Ding G, Dueñas ME, Liu M, Lee YJ, Nikolau BJ, Bassham DC. Complex Changes in Membrane Lipids Associated with the Modification of Autophagy in Arabidopsis. Metabolites 2022; 12:metabo12020190. [PMID: 35208263 PMCID: PMC8876039 DOI: 10.3390/metabo12020190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/26/2022] [Accepted: 02/11/2022] [Indexed: 12/28/2022] Open
Abstract
Autophagy is a conserved mechanism among eukaryotes that degrades and recycles cytoplasmic components. Autophagy is known to influence the plant metabolome, including lipid content; however, its impact on the plant lipidome is not fully understood, and most studies have analyzed a single or few mutants defective in autophagy. To gain more insight into the effect of autophagy on lipid concentrations and composition, we quantitatively profiled glycerolipids from multiple Arabidopsis thaliana mutants altered in autophagy and compared them with wild-type seedlings under nitrogen replete (+N; normal growth) and nitrogen starvation (−N; autophagy inducing) conditions. Mutants include those in genes of the core autophagy pathway, together with other genes that have been reported to affect autophagy. Using Matrix-Assisted Laser Desorption/Ionization—Mass Spectrometry (MALDI-MS), we imaged the cellular distribution of specific lipids in situ and demonstrated that autophagy and nitrogen treatment did not affect their spatial distribution within Arabidopsis seedling leaves. We observed changes, both increases and decreases, in the relative amounts of different lipid species in the mutants compared to WT both in +N and −N conditions, although more changes were seen in −N conditions. The relative amounts of polyunsaturated and very long chain lipids were significantly reduced in autophagy-disrupted mutants compared to WT plants. Collectively, our results provide additional evidence that autophagy affects plant lipid content and that autophagy likely affects lipid properties such as chain length and unsaturation.
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Affiliation(s)
- Yosia Mugume
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA;
| | - Geng Ding
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (G.D.); (B.J.N.)
| | - Maria Emilia Dueñas
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA; (M.E.D.); (Y.-J.L.)
| | - Meiling Liu
- Department of Statistics, Iowa State University, Ames, IA 50011, USA;
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Young-Jin Lee
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA; (M.E.D.); (Y.-J.L.)
| | - Basil J. Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (G.D.); (B.J.N.)
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Diane C. Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA;
- Correspondence: ; Tel.: +1-515-294-7461
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46
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Potthoff A, Minte O, Dreisewerd K, Soltwisch J. Effect of the Laser Pulse Width in MALDI-2: A Comparative Study of Picosecond versus Nanosecond Wide Pulses for Laser Postionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:315-321. [PMID: 35015547 DOI: 10.1021/jasms.1c00308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
MALDI-2 is a recently introduced technique for postionization (PI) in matrix-assisted laser desorption/ionization (MALDI). It is based on an initial photoionization of neutrally desorbed matrix molecules and subsequent charge-transfer reactions in a fine vacuum or atmospheric pressure ion source. MALDI-2 significantly increases the ion yields for numerous classes of analytes, including lipids, glycans, and a range of pharmaceuticals. To obtain insights into the ionization mechanisms underlying the primary step of PI in MALDI-2, we here conducted a set of experiments with two lasers at 266 nm wavelength and pulse durations of 28 ps and 6 ns, respectively, on a modified orthogonal-extracting time-of-flight mass spectrometer (QTOF, Synapt). 2,5-Dihydroxybenzoic acid (DHB) and 2,5-dihydroxyacetophenone (DHAP) were investigated as MALDI matrices in the positive-ion mode with standardized lipid samples. Analyte- and matrix-derived ion signals were recorded as a function of PI laser pulse energies. The ion signal intensity displays a quadratic dependency on PI-laser pulse energy for low to moderate intensities of up to ∼107 W/cm2. This behavior suggests the involvement of resonance enhanced two-photon ionization (REMPI) of neutral matrix molecules in the ionization pathways. Comparing nanosecond and picosecond pulses at the same PI laser pulse energy, higher photon density produced by the shorter pulses generally produced sizably higher ion signal intensities, also corroborating an involvement of REMPI-like processes. Based on a theoretical description of the MALDI-2 process derived from prevalent REMPI theory, comparative measurements allow us to determine the lifetime of the excited states of the employed matrices. Resulting values for both matrices are in good agreement with the literature and corroborate the REMPI-based approach.
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Affiliation(s)
| | - Olaf Minte
- Institute of Hygiene, University of Münster, Münster 48149, Germany
| | - Klaus Dreisewerd
- Institute of Hygiene, University of Münster, Münster 48149, Germany
| | - Jens Soltwisch
- Institute of Hygiene, University of Münster, Münster 48149, Germany
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47
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Houdelet C, Arafah K, Bocquet M, Bulet P. Molecular histoproteomy by MALDI mass spectrometry imaging to uncover markers of the impact of Nosema on Apis mellifera. Proteomics 2022; 22:e2100224. [PMID: 34997678 DOI: 10.1002/pmic.202100224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful technology used to investigate the spatio-temporal distribution of a huge number of molecules throughout a body/tissue section. In this paper, we report the use of MALDI IMS to follow the molecular impact of an experimental infection of Apis mellifera with the microsporidia Nosema ceranae. We performed representative molecular mass fingerprints of selected tissues obtained by dissection. This was followed by MALDI IMS workflows optimization including specimen embedding and positioning as well as washing and matrix application. We recorded the local distribution of peptides/proteins within different tissues from experimentally infected versus non infected honeybees. As expected, a distinction in these molecular profiles between the two conditions was recorded from different anatomical sections of the gut tissue. More importantly, we observed differences in the molecular profiles in the brain, thoracic ganglia, hypopharyngeal glands, and hemolymph. We introduced MALDI IMS as an effective approach to monitor the impact of N. ceranae infection on A. mellifera. This opens perspectives for the discovery of molecular changes in peptides/proteins markers that could contribute to a better understanding of the impact of stressors and toxicity on different tissues of a bee in a single experiment.
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Affiliation(s)
- Camille Houdelet
- CR Université Grenoble Alpes, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Grenoble, France.,Saint Julien-en Genevois, Plateforme BioPark d'Archamps, France
| | - Karim Arafah
- Saint Julien-en Genevois, Plateforme BioPark d'Archamps, France
| | | | - Philippe Bulet
- CR Université Grenoble Alpes, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Grenoble, France.,Saint Julien-en Genevois, Plateforme BioPark d'Archamps, France
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Tian X, Zou Z, Yang Z. Extract Metabolomic Information from Mass Spectrometry Images Using Advanced Data Analysis. Methods Mol Biol 2022; 2437:253-272. [PMID: 34902154 DOI: 10.1007/978-1-0716-2030-4_18] [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: 06/14/2023]
Abstract
Mass spectrometry imaging (MSI) data generally contains large sizes and high-dimensional structures due to their inherent complex chemical and spatial information. A variety of data analysis methods have been developed to comprehensively analyze the MSI experimental results and extract essential information. Here, we describe the protocols of data preprocessing and emerging methods for data analyses, including multivariate analysis, machine learning, and image fusion, that have been applied to the data generated from the Single-probe MSI technique. These strategies and methods can be potentially applied to handling data produced from other MSI techniques.
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Affiliation(s)
- Xiang Tian
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Dynamic Omics, Center of Genomics Research (CGR), R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Zhu Zou
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
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49
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Wang Y, Hummon AB. MS imaging of multicellular tumor spheroids and organoids as an emerging tool for personalized medicine and drug discovery. J Biol Chem 2021; 297:101139. [PMID: 34461098 PMCID: PMC8463860 DOI: 10.1016/j.jbc.2021.101139] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
MS imaging (MSI) is a powerful tool in drug discovery because of its ability to interrogate a wide range of endogenous and exogenous molecules in a broad variety of samples. The impressive versatility of the approach, where almost any ionizable biomolecule can be analyzed, including peptides, proteins, lipids, carbohydrates, and nucleic acids, has been applied to numerous types of complex biological samples. While originally demonstrated with harvested organs from animal models and biopsies from humans, these models are time consuming and expensive, which makes it necessary to extend the approach to 3D cell culture systems. These systems, which include spheroid models, prepared from immortalized cell lines, and organoid cultures, grown from patient biopsies, can provide insight on the intersection of molecular information on a spatial scale. In particular, the investigation of drug compounds, their metabolism, and the subsequent distribution of their metabolites in 3D cell culture systems by MSI has been a promising area of study. This review summarizes the different ionization methods, sample preparation steps, and data analysis methods of MSI and focuses on several of the latest applications of MALDI-MSI for drug studies in spheroids and organoids. Finally, the application of this approach in patient-derived organoids to evaluate personalized medicine options is discussed.
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Affiliation(s)
- Yijia Wang
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA.
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Zhang Y, Komorek R, Son J, Riechers S, Zhu Z, Jansson J, Jansson C, Yu XY. Molecular imaging of plant-microbe interactions on the Brachypodium seed surface. Analyst 2021; 146:5855-5865. [PMID: 34378550 DOI: 10.1039/d1an00205h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) play a crucial role in biological control and pathogenic defense on and within plant tissues, however the mechanisms by which plants associate with PGPR to elicit such beneficial effects need further study. Here, we present time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging of Brachypodium distachyon (Brachypodium) seeds with and without exposure to two model PGPR, i.e., Gram-negative Pseudomonas fluorescens SBW25 (P.) and Gram-positive Arthrobacter chlorophenolicus A6 (A.). Delayed image extraction was used to image PGPR-treated seed sections to reveal morphological changes. ToF-SIMS spectral comparison, principal component analysis (PCA), and two-dimensional (2D) imaging show that the selected PGPR have different effects on the host seed surface, resulting in changes in chemical composition and morphology. Metabolite products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and indole-3-acetic acid (IAA), were identified on the PGPR-treated seed surfaces. These compounds have different distributions on the Brachypodium seed surface for the two PGPR, indicating that the different bacteria elicit distinct responses from the host. Our results illustrate that ToF-SIMS is an effective tool to study plant-microbe interactions and to provide insightful information with submicrometer lateral resolution of the chemical distributions associated with morphological features, potentially offering a new way to study the mechanisms underlying beneficial roles of PGPR.
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Affiliation(s)
- Yuchen Zhang
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Rachel Komorek
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Jiyoung Son
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Shawn Riechers
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Zihua Zhu
- Environmental and Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Janet Jansson
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Christer Jansson
- Environmental and Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Xiao-Ying Yu
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
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