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Barrera-Adame DA, Schuster S, Niedermeyer THJ. Mass Spectrometry Imaging of Coniine and Other Hemlock Alkaloids after On-Tissue Derivatization Reveals Distinct Alkaloid Distributions in the Plant. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38904441 DOI: 10.1021/acs.jnatprod.4c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Specialized metabolites play important roles in plants and can, for example, protect plants from predators or pathogens. Alkaloids, due to their pronounced biological activity on higher animals, are one of the most intriguing groups of specialized metabolites, and many of them are known as plant defense compounds. Poison hemlock, Conium maculatum, is well-known for its high content of piperidine alkaloids, of which coniine is the most famous. The distribution, localization, and diversity of these compounds in C. maculatum tissues have not yet been studied in detail. The hemlock alkaloids are low molecular weight compounds with relatively high volatility. They are thus difficult to analyze on-tissue by MALDI mass spectrometry imaging due to delocalization, which occurs even when using an atmospheric pressure ion source. In this manuscript, we describe an on-tissue derivatization method that allows the subsequent determination of the spatial distribution of hemlock alkaloids in different plant tissues by mass spectrometry imaging. Coniferyl aldehyde was found to be a suitable reagent for derivatization of the secondary amine alkaloids. The imaging analysis revealed that even chemically closely related hemlock alkaloids are discretely distributed in different plant tissues. Additionally, we detected a yet undescribed hemlock alkaloid in Conium maculatum seeds.
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Affiliation(s)
- Diana A Barrera-Adame
- Department of Pharmaceutical Biology/Pharmacognosy, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Department of Pharmaceutical Biology, Institute of Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Sabine Schuster
- Department of Pharmaceutical Biology/Pharmacognosy, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Timo H J Niedermeyer
- Department of Pharmaceutical Biology/Pharmacognosy, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Department of Pharmaceutical Biology, Institute of Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
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2
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Pečinka L, Moráň L, Kovačovicová P, Meloni F, Havel J, Pivetta T, Vaňhara P. Intact cell mass spectrometry coupled with machine learning reveals minute changes induced by single gene silencing. Heliyon 2024; 10:e29936. [PMID: 38707401 PMCID: PMC11066331 DOI: 10.1016/j.heliyon.2024.e29936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024] Open
Abstract
Intact (whole) cell MALDI TOF mass spectrometry is a commonly used tool in clinical microbiology for several decades. Recently it was introduced to analysis of eukaryotic cells, including cancer and stem cells. Besides targeted metabolomic and proteomic applications, the intact cell MALDI TOF mass spectrometry provides a sufficient sensitivity and specificity to discriminate cell types, isogenous cell lines or even the metabolic states. This makes the intact cell MALDI TOF mass spectrometry a promising tool for quality control in advanced cell cultures with a potential to reveal batch-to-batch variation, aberrant clones, or unwanted shifts in cell phenotype. However, cellular alterations induced by change in expression of a single gene has not been addressed by intact cell mass spectrometry yet. In this work we used a well-characterized human ovarian cancer cell line SKOV3 with silenced expression of a tumor suppressor candidate 3 gene (TUSC3). TUSC3 is involved in co-translational N-glycosylation of proteins with well-known global impact on cell phenotype. Altogether, this experimental design represents a highly suitable model for optimization of intact cell mass spectrometry and analysis of spectral data. Here we investigated five machine learning algorithms (k-nearest neighbors, decision tree, random forest, partial least squares discrimination, and artificial neural network) and optimized their performance either in pure populations or in two-component mixtures composed of cells with normal or silenced expression of TUSC3. All five algorithms reached accuracy over 90 % and were able to reveal even subtle changes in mass spectra corresponding to alterations of TUSC3 expression. In summary, we demonstrate that spectral fingerprints generated by intact cell MALDI-TOF mass spectrometry coupled to a machine learning classifier can reveal minute changes induced by alteration of a single gene, and therefore contribute to the portfolio of quality control applications in routine cell and tissue cultures.
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Affiliation(s)
- Lukáš Pečinka
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Czech Republic
| | - Lukáš Moráň
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Petra Kovačovicová
- International Clinical Research Center, St. Anne's University Hospital Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Francesca Meloni
- Chemical and Geological Sciences Department, University of Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Josef Havel
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Czech Republic
| | - Tiziana Pivetta
- Chemical and Geological Sciences Department, University of Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Petr Vaňhara
- International Clinical Research Center, St. Anne's University Hospital Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Mutithu DW, Aremu OO, Mokaila D, Bana T, Familusi M, Taylor L, Martin LJ, Heathfield LJ, Kirwan JA, Wiesner L, Adeola HA, Lumngwena EN, Manganyi R, Skatulla S, Naidoo R, Ntusi NAB. A study protocol to characterise pathophysiological and molecular markers of rheumatic heart disease and degenerative aortic stenosis using multiparametric cardiovascular imaging and multiomics techniques. PLoS One 2024; 19:e0303496. [PMID: 38739622 PMCID: PMC11090351 DOI: 10.1371/journal.pone.0303496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
INTRODUCTION Rheumatic heart disease (RHD), degenerative aortic stenosis (AS), and congenital valve diseases are prevalent in sub-Saharan Africa. Many knowledge gaps remain in understanding disease mechanisms, stratifying phenotypes, and prognostication. Therefore, we aimed to characterise patients through clinical profiling, imaging, histology, and molecular biomarkers to improve our understanding of the pathophysiology, diagnosis, and prognosis of RHD and AS. METHODS In this cross-sectional, case-controlled study, we plan to recruit RHD and AS patients and compare them to matched controls. Living participants will undergo clinical assessment, echocardiography, CMR and blood sampling for circulatory biomarker analyses. Tissue samples will be obtained from patients undergoing valve replacement, while healthy tissues will be obtained from cadavers. Immunohistology, proteomics, metabolomics, and transcriptome analyses will be used to analyse circulatory- and tissue-specific biomarkers. Univariate and multivariate statistical analyses will be used for hypothesis testing and identification of important biomarkers. In summary, this study aims to delineate the pathophysiology of RHD and degenerative AS using multiparametric CMR imaging. In addition to discover novel biomarkers and explore the pathomechanisms associated with RHD and AS through high-throughput profiling of the tissue and blood proteome and metabolome and provide a proof of concept of the suitability of using cadaveric tissues as controls for cardiovascular disease studies.
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Affiliation(s)
- Daniel W. Mutithu
- Department of Medicine, Cape Heart Institute, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases, South African Medical Research Council, Cape Town, South Africa
| | - Olukayode O. Aremu
- Department of Medicine, Cape Heart Institute, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases, South African Medical Research Council, Cape Town, South Africa
| | - Dipolelo Mokaila
- Department of Medicine, Cape Heart Institute, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases, South African Medical Research Council, Cape Town, South Africa
| | - Tasnim Bana
- Department of Medicine, Cape Heart Institute, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases, South African Medical Research Council, Cape Town, South Africa
| | - Mary Familusi
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Department of Civil Engineering, University of Cape Town, Cape Town, South Africa
| | - Laura Taylor
- Division of Forensic Medicine and Toxicology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Lorna J. Martin
- Division of Forensic Medicine and Toxicology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Laura J. Heathfield
- Division of Forensic Medicine and Toxicology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Jennifer A. Kirwan
- Metabolomics Platform, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center (MDC) for Molecular Medicine, Helmholtz Association, Berlin, Germany
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Henry A. Adeola
- Division of Dermatology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Evelyn N. Lumngwena
- Department of Medicine, Cape Heart Institute, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases, South African Medical Research Council, Cape Town, South Africa
- School of Clinical Medicine, University of the Witwatersrand, Johannesburg, South Africa
| | - Rodgers Manganyi
- Chris Barnard Division of Cardiothoracic Surgery, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Sebastian Skatulla
- Department of Civil Engineering, University of Cape Town, Cape Town, South Africa
| | - Richard Naidoo
- Division of Anatomical Pathology, Department of Pathology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
| | - Ntobeko A. B. Ntusi
- Department of Medicine, Cape Heart Institute, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases, South African Medical Research Council, Cape Town, South Africa
- Cape Universities Body Imaging Centre, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research, University of Cape Town, Cape Town, South Africa
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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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5
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Paulson AE, Larson EA, Lee YJ. Mobilized Electrospray Device for On-Tissue Chemical Derivatization in MALDI-MS Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:205-213. [PMID: 38147682 DOI: 10.1021/jasms.3c00290] [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: 12/28/2023]
Abstract
Applying solutions of a matrix or derivatization agent via microdroplets is a common sample preparation technique for matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) experiments. Mobilized nebulizer sprayers are commonly used to create a homogeneous matrix or reagent layer across large surfaces. Electrospray devices have also been used to produce microdroplets for the same purpose but are rarely used for large tissues due to their immobility. Herein, we present a movable electrospray device that can be used for large tissue sample preparation through a simple modification to an automatic commercial nebulizer device. As demonstrated for on-tissue chemical derivatization (OTCD) with Girard's reagent T using a mimetic tissue model, the sprayer has the additional benefit of being able to investigate reaction acceleration in OTCD when comparing electrostatically charged spray to electrostatically neutral spray. Finally, MALDI-MSI of fatty aldehydes is successfully demonstrated in rat brain tissues using this device for both OTCD and matrix application.
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Affiliation(s)
- Andrew E Paulson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Evan A Larson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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6
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Pečinka L, Vlachová M, Moráň L, Gregorová J, Porokh V, Kovačovicová P, Almáši M, Pour L, Štork M, Havel J, Ševčíková S, Vaňhara P. Improved Screening of Monoclonal Gammopathy Patients by MALDI-TOF Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2646-2653. [PMID: 37994781 DOI: 10.1021/jasms.3c00166] [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: 11/24/2023]
Abstract
Monoclonal gammopathies are a group of blood diseases characterized by presence of abnormal immunoglobulins in peripheral blood and/or urine of patients. Multiple myeloma and plasma cell leukemia are monoclonal gammopathies with unclear etiology, caused by malignant transformation of bone marrow plasma cells. Mass spectrometry with matrix-assisted laser desorption/ionization and time-of-flight detection is commonly used for investigation of the peptidome and small proteome of blood plasma with high accuracy, robustness, and cost-effectivity. In addition, mass spectrometry coupled with advanced statistics can be used for molecular profiling, classification, and diagnosis of liquid biopsies and tissue specimens in various malignancies. Despite the fact there have been fully optimized protocols for mass spectrometry of normal blood plasma available for decades, in monoclonal gammopathy patients, the massive alterations of biophysical and biochemical parameters of peripheral blood plasma often limit the mass spectrometry measurements. In this paper, we present a new two-step extraction protocol and demonstrated the enhanced resolution and intensity (>50×) of mass spectra obtained from extracts of peripheral blood plasma from monoclonal gammopathy patients. When coupled with advanced statistics and machine learning, the mass spectra profiles enabled the direct identification, classification, and discrimination of multiple myeloma and plasma cell leukemia patients with high accuracy and precision. A model based on PLS-DA achieved the best performance with 71.5% accuracy (95% confidence interval, CI = 57.1-83.3%) when the 10× repeated 5-fold CV was performed. In summary, the two-step extraction protocol improved the analysis of monoclonal gammopathy peripheral blood plasma samples by mass spectrometry and provided a tool for addressing the complex molecular etiology of monoclonal gammopathies.
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Affiliation(s)
- Lukáš Pečinka
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
| | - Monika Vlachová
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - Lukáš Moráň
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Žlutý kopec 7, 602 00 Brno, Czech Republic
| | - Jana Gregorová
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - Volodymyr Porokh
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - Petra Kovačovicová
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - Martina Almáši
- Department of Clinical Hematology, University Hospital Brno, Jihlavská 20, 625 00 Brno, Czech Republic
| | - Luděk Pour
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Jihlavská 20, 625 00 Brno, Czech Republic
| | - Martin Štork
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Jihlavská 20, 625 00 Brno, Czech Republic
| | - Josef Havel
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
| | - Sabina Ševčíková
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
- Department of Clinical Hematology, University Hospital Brno, Jihlavská 20, 625 00 Brno, Czech Republic
| | - Petr Vaňhara
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
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Zemaitis KJ, Lin VS, Ahkami AH, Winkler TE, Anderton CR, Veličković D. Expanded Coverage of Phytocompounds by Mass Spectrometry Imaging Using On-Tissue Chemical Derivatization by 4-APEBA. Anal Chem 2023; 95:12701-12709. [PMID: 37594382 DOI: 10.1021/acs.analchem.3c01345] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Probing the entirety of any species metabolome is an analytical grand challenge, especially on a cellular scale. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a common spatial metabolomics assay, but this technique has limited molecular coverage for several reasons. To expand the application space of spatial metabolomics, we developed an on-tissue chemical derivatization (OTCD) workflow using 4-APEBA for the confident identification of several dozen elusive phytocompounds. Overall, this new OTCD method enabled the annotation of roughly 280 metabolites, with only a 10% overlap in metabolic coverage when compared to analog negative ion mode MALDI-MSI on serial sections. We demonstrate that 4-APEBA outperforms other derivatization agents by providing: (1) broad specificity toward carbonyls, (2) low background, and (3) introduction of bromine isotopes. Notably, the latter two attributes also facilitate more confidence in our bioinformatics for data processing. The workflow detailed here trailblazes a path toward spatial hormonomics within plant samples, enhancing the detection of carboxylates, aldehydes, and plausibly other carbonyls. As such, several phytohormones, which have various roles within stress responses and cellular communication, can now be spatially profiled, as demonstrated in poplar root and soybean root nodule.
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Affiliation(s)
- Kevin J Zemaitis
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vivian S Lin
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Amir H Ahkami
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tanya E Winkler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christopher R Anderton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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8
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Borisjuk L, Horn P, Chapman K, Jakob PM, Gündel A, Rolletschek H. Seeing plants as never before. THE NEW PHYTOLOGIST 2023; 238:1775-1794. [PMID: 36895109 DOI: 10.1111/nph.18871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/06/2023] [Indexed: 05/04/2023]
Abstract
Imaging has long supported our ability to understand the inner life of plants, their development, and response to a dynamic environment. While optical microscopy remains the core tool for imaging, a suite of novel technologies is now beginning to make a significant contribution to visualize plant metabolism. The purpose of this review was to provide the scientific community with an overview of current imaging methods, which rely variously on either nuclear magnetic resonance (NMR), mass spectrometry (MS) or infrared (IR) spectroscopy, and to present some examples of their application in order to illustrate their utility. In addition to providing a description of the basic principles underlying these technologies, the review discusses their various advantages and limitations, reveals the current state of the art, and suggests their potential application to experimental practice. Finally, a view is presented as to how the technologies will likely develop, how these developments may encourage the formulation of novel experimental strategies, and how the enormous potential of these technologies can contribute to progress in plant science.
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Affiliation(s)
- Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Patrick Horn
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Kent Chapman
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Peter M Jakob
- Institute of Experimental Physics 5, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Andre Gündel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
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9
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Forsman TT, Paulson AE, Larson EA, Looft T, Lee YJ. On-tissue chemical derivatization of volatile metabolites for matrix-assisted laser desorption/ionization mass spectrometry imaging. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4918. [PMID: 37045444 DOI: 10.1002/jms.4918] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/14/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Mass spectrometry imaging (MSI) of volatile metabolites is challenging, especially in matrix-assisted laser desorption/ionization (MALDI). Most MALDI ion sources operate in vacuum, which leads to the vaporization of volatile metabolites during analysis. In addition, tissue samples are often dried during sample preparation, leading to the loss of volatile metabolites even for other MSI techniques. On-tissue chemical derivatization can dramatically reduce the volatility of analytes. Herein, a derivatization method is proposed utilizing N,N,N-trimethyl-2-(piperazin-1-yl)ethan-1-aminium iodide to chemically modify short-chain fatty acids in chicken cecum, ileum, and jejunum tissue sections before sample preparation for MSI visualization.
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Affiliation(s)
- Trevor T Forsman
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011, USA
| | - Andrew E Paulson
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011, USA
| | - Evan A Larson
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011, USA
| | - Torey Looft
- National Animal Disease Center, Agricultural Research Services, United States Department of Agriculture, Ames, Iowa, 50010, USA
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011, USA
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Wittek O, Römpp A. Autofocusing MALDI MS imaging of processed food exemplified by the contaminant acrylamide in German gingerbread. Sci Rep 2023; 13:5400. [PMID: 37012286 PMCID: PMC10070467 DOI: 10.1038/s41598-023-32004-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
Acrylamide is a toxic reaction product occurring in dry-heated food such as bakery products. To meet the requirements laid down in recent international legal norms calling for reduction strategies in food prone to acrylamide formation, efficient chromatography-based quantification methods are available. However, for an efficient mitigation of acrylamide levels, not only the quantity, but also the contaminant's distributions are of interest especially in inhomogeneous food consisting of multiple ingredients. A promising tool to investigate the spatial distribution of analytes in food matrices is mass spectrometry imaging (MS imaging). In this study, an autofocusing MALDI MS imaging method was developed for German gingerbread as an example for highly processed and instable food with uneven surfaces. Next to endogenous food constituents, the process contaminant acrylamide was identified and visualized keeping a constant laser focus throughout the measurement. Statistical analyses based on relative acrylamide intensities suggest a higher contamination of nut fragments compared to the dough. In a proof-of-concept experiment, a newly developed in-situ chemical derivatization protocol is described using thiosalicylic acid for highly selective detection of acrylamide. This study presents autofocusing MS imaging as a suitable complementary method for the investigation of analytes' distributions in complex and highly processed food.
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Affiliation(s)
- Oliver Wittek
- Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitaetsstrasse 30, 95447, Bayreuth, Germany
| | - Andreas Römpp
- Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitaetsstrasse 30, 95447, Bayreuth, Germany.
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11
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Liu H, Feng C, Yang T, Zhang Z, Wei X, Sun Y, Zhang L, Li W, Yu D. Combined metabolomics and gut microbiome to investigate the effects and mechanisms of Yuquan Pill on type 2 diabetes in rats. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1222:123713. [PMID: 37059008 DOI: 10.1016/j.jchromb.2023.123713] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/16/2023] [Accepted: 04/03/2023] [Indexed: 04/09/2023]
Abstract
Yuquan Pill (YQP) is a traditional Chinese medicine (TCM) for the treatment of type 2 diabetes (T2DM) in China for many years, and has a beneficial clinical effect. In this study, the antidiabetic mechanism of YQP was investigated for the first time from the perspective of metabolomics and intestinal microbiota. After 28 days of high-fat feeding, rats were injected intraperitoneally with streptozotocin (STZ, 35 mg/kg) followed by a single oral administration of YQP 2.16 g/kg and metformin 200 mg/kg for 5 weeks. The results showed that YQP was effectively improved insulin resistance and alleviated hyperglycemia and hyperlipidemia associated with T2DM. YQP was found to regulate metabolism and gut microbiota in T2DM rats using untargeted metabolomics and gut microbiota integration. Forty-one metabolites and five metabolic pathways were identified, including Ascorbate and aldarate metabolism, Nicotinate and nicotinamide metabolism, Galactose metabolism, Pentose phosphate pathway and Tyrosine metabolism. YQP can regulate T2DM-induced dysbacteriosis by modulating the abundance of Firmicutes, Bacteroidetes, Ruminococcus, Lactobacillus. The restorative effects of YQP in rats with T2DM have been confirmed and provide a scientific basis for the clinical treatment of diabetic patients.
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12
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Elhanani O, Ben-Uri R, Keren L. Spatial profiling technologies illuminate the tumor microenvironment. Cancer Cell 2023; 41:404-420. [PMID: 36800999 DOI: 10.1016/j.ccell.2023.01.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/01/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023]
Abstract
The tumor microenvironment (TME) is composed of many different cellular and acellular components that together drive tumor growth, invasion, metastasis, and response to therapies. Increasing realization of the significance of the TME in cancer biology has shifted cancer research from a cancer-centric model to one that considers the TME as a whole. Recent technological advancements in spatial profiling methodologies provide a systematic view and illuminate the physical localization of the components of the TME. In this review, we provide an overview of major spatial profiling technologies. We present the types of information that can be extracted from these data and describe their applications, findings and challenges in cancer research. Finally, we provide a future perspective of how spatial profiling could be integrated into cancer research to improve patient diagnosis, prognosis, stratification to treatment and development of novel therapeutics.
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Affiliation(s)
- Ofer Elhanani
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Raz Ben-Uri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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13
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Pena-Rodríguez E, García-Berrocoso T, Vázquez Fernández E, Otero-Espinar FJ, Abian J, Fernández-Campos F. Monitoring dexamethasone skin biodistribution with ex vivo MALDI-TOF mass spectrometry imaging and confocal Raman microscopy. Int J Pharm 2023; 636:122808. [PMID: 36889415 DOI: 10.1016/j.ijpharm.2023.122808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
Abstract
Two of the most promising techniques in terms of ex vivo skin imaging and quantifying are confocal Raman microscopy and MALDI-TOF mass spectrometry imaging (MALDI-TOF MSI). Both techniques were set up, and the semiquantitative skin biodistribution of previously developed dexamethasone (DEX) loaded lipomers was compared using Benzalkonium chloride (BAK) as a tracer of the nanoparticles. In MALDI-TOF MSI, DEX was derivatised with GirT (DEX-GirT) and the semiquantitative biodistribution of both DEX-GirT and BAK was successfully obtained. The amount of DEX measured by confocal Raman microscopy was higher than that measured by MALDI-TOF MSI, but MALDI-TOF MSI proved to be a more suitable technique for tracing BAK. An absorption-promoting tendency of DEX loaded in lipomers versus a free-DEX solution was observed in confocal Raman microscopy. The higher spatial resolution of confocal Raman microscopy (350 nm) with respect to MALDI-TOF MSI (50 μm) allowed to observe specific skin structures like hair follicles. Nevertheless, the faster sampling rate of MALDI-TOF-MSI, permitted the analysis of larger tissue regions. In conclusion, both techniques allowed to simultaneously analyze semiquantitative data together with qualitative images of biodistribution, which is a very helpful tool when designing nanoparticles that accumulate in specific anatomical regions.
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Affiliation(s)
- Eloy Pena-Rodríguez
- Laboratory Reig Jofre, R&D Department, 08970, Sant Joan Despí, Barcelona, Spain.
| | - Teresa García-Berrocoso
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (IIBB-CSIC), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Laboratorio de Proteómica CSIC/Universitat Autònoma de Barcelona (UAB), IIBB-CSIC, Barcelona, Spain
| | - Ezequiel Vázquez Fernández
- Pharmacology, Pharmacy and Pharmaceutical Technology Department, Faculty of Pharmacy, University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Francisco J Otero-Espinar
- Pharmacology, Pharmacy and Pharmaceutical Technology Department, Faculty of Pharmacy, University of Santiago de Compostela (USC), Santiago de Compostela, Spain; Parqueasil Group, Health Research Institute of Santiago de Compostela (FIDIS), Santiago de Compostela, Spain; Institute of Materials (iMATUS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain.
| | - Joaquin Abian
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (IIBB-CSIC), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Laboratorio de Proteómica CSIC/Universitat Autònoma de Barcelona (UAB), IIBB-CSIC, Barcelona, Spain
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14
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Hu R, Li Y, Yang Y, Liu M. Mass spectrometry-based strategies for single-cell metabolomics. MASS SPECTROMETRY REVIEWS 2023; 42:67-94. [PMID: 34028064 DOI: 10.1002/mas.21704] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
Single cell analysis has drawn increasing interest from the research community due to its capability to interrogate cellular heterogeneity, allowing refined tissue classification and facilitating novel biomarker discovery. With the advancement of relevant instruments and techniques, it is now possible to perform multiple omics including genomics, transcriptomics, metabolomics or even proteomics at single cell level. In comparison with other omics studies, single-cell metabolomics (SCM) represents a significant challenge since it involves many types of dynamically changing compounds with a wide range of concentrations. In addition, metabolites cannot be amplified. Although difficult, considerable progress has been made over the past decade in mass spectrometry (MS)-based SCM in terms of processing technologies and biochemical applications. In this review, we will summarize recent progress in the development of promising MS platforms, sample preparation methods and SCM analysis of various cell types (including plant cell, cancer cell, neuron, embryo cell, and yeast cell). Current limitations and future research directions in the field of SCM will also be discussed.
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Affiliation(s)
- Rui Hu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunhuang Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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15
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Sohn AL, Ping L, Glass JD, Seyfried NT, Hector EC, Muddiman DC. Interrogating the Metabolomic Profile of Amyotrophic Lateral Sclerosis in the Post-Mortem Human Brain by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization (IR-MALDESI) Mass Spectrometry Imaging (MSI). Metabolites 2022; 12:1096. [PMID: 36355179 PMCID: PMC9696666 DOI: 10.3390/metabo12111096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 01/03/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an idiopathic, fatal neurodegenerative disease characterized by progressive loss of motor function with an average survival time of 2-5 years after diagnosis. Due to the lack of signature biomarkers and heterogenous disease phenotypes, a definitive diagnosis of ALS can be challenging. Comprehensive investigation of this disease is imperative to discovering unique features to expedite the diagnostic process and improve diagnostic accuracy. Here, we present untargeted metabolomics by mass spectrometry imaging (MSI) for comparing sporadic ALS (sALS) and C9orf72 positive (C9Pos) post-mortem frontal cortex human brain tissues against a control cohort. The spatial distribution and relative abundance of metabolites were measured by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) MSI for association to biological pathways. Proteomic studies on the same patients were completed via LC-MS/MS in a previous study, and results were integrated with imaging metabolomics results to enhance the breadth of molecular coverage. Utilizing METASPACE annotation platform and MSiPeakfinder, nearly 300 metabolites were identified across the sixteen samples, where 25 were identified as dysregulated between disease cohorts. The dysregulated metabolites were further examined for their relevance to alanine, aspartate, and glutamate metabolism, glutathione metabolism, and arginine and proline metabolism. The dysregulated pathways discussed are consistent with reports from other ALS studies. To our knowledge, this work is the first of its kind, reporting on the investigation of ALS post-mortem human brain tissue analyzed by multiomic MSI.
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Affiliation(s)
- Alexandria L. Sohn
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Lingyan Ping
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jonathan D. Glass
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicholas T. Seyfried
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Emily C. Hector
- Department of Statistics, 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
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC 27695, USA
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16
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Harkin C, Smith KW, Cruickshank FL, Logan Mackay C, Flinders B, Heeren RMA, Moore T, Brockbank S, Cobice DF. On-tissue chemical derivatization in mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2022; 41:662-694. [PMID: 33433028 PMCID: PMC9545000 DOI: 10.1002/mas.21680] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/03/2020] [Accepted: 12/15/2020] [Indexed: 05/04/2023]
Abstract
Mass spectrometry imaging (MSI) combines molecular and spatial information in a valuable tool for a wide range of applications. Matrix-assisted laser desorption/ionization (MALDI) is at the forefront of MSI ionization due to its wide availability and increasing improvement in spatial resolution and analysis speed. However, ionization suppression, low concentrations, and endogenous and methodological interferences cause visualization problems for certain molecules. Chemical derivatization (CD) has proven a viable solution to these issues when applied in mass spectrometry platforms. Chemical tagging of target analytes with larger, precharged moieties aids ionization efficiency and removes analytes from areas of potential isobaric interferences. Here, we address the application of CD on tissue samples for MSI analysis, termed on-tissue chemical derivatization (OTCD). MALDI MSI will remain the focus platform due to its popularity, however, alternative ionization techniques such as liquid extraction surface analysis and desorption electrospray ionization will also be recognized. OTCD reagent selection, application, and optimization methods will be discussed in detail. MSI with OTCD is a powerful tool to study the spatial distribution of poorly ionizable molecules within tissues. Most importantly, the use of OTCD-MSI facilitates the analysis of previously inaccessible biologically relevant molecules through the adaptation of existing CD methods. Though further experimental optimization steps are necessary, the benefits of this technique are extensive.
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Affiliation(s)
- Carla Harkin
- Mass Spectrometry Centre, Biomedical Sciences Research Institute (BMSRI), School of Biomedical SciencesUlster UniversityColeraineNorthern IrelandUK
| | - Karl W. Smith
- National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility (ICR)Florida State UniversityTallahasseeFloridaUSA
| | - Faye L. Cruickshank
- Scottish Instrumentation and Research Centre for Advanced Mass Spectrometry (SIRCAMS), EaStCHEM School of ChemistryUniversity of EdinburghScotlandUK
| | - C. Logan Mackay
- Scottish Instrumentation and Research Centre for Advanced Mass Spectrometry (SIRCAMS), EaStCHEM School of ChemistryUniversity of EdinburghScotlandUK
| | - Bryn Flinders
- Screening Division, Mass Spectrometry, Hair DiagnostixDutch Screening GroupMaastrichtThe Netherlands
| | - Ron M. A. Heeren
- Maastricht Multimodal Molecular Imaging Institute (M4I)University of MaastrichtMaastrichtThe Netherlands
| | - Tara Moore
- Genomic Medicine, Biomedical Sciences Research Institute (BMSRI), School of Biomedical SciencesUlster UniversityColeraineNorthern IrelandUK
| | | | - Diego F. Cobice
- Mass Spectrometry Centre, Biomedical Sciences Research Institute (BMSRI), School of Biomedical SciencesUlster UniversityColeraineNorthern IrelandUK
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17
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Harkin C, Smith KW, MacKay CL, Moore T, Brockbank S, Ruddock M, Cobice DF. Spatial localization of β-unsaturated aldehyde markers in murine diabetic kidney tissue by mass spectrometry imaging. Anal Bioanal Chem 2022; 414:6657-6670. [PMID: 35881173 PMCID: PMC9411223 DOI: 10.1007/s00216-022-04229-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/04/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2022]
Abstract
Diabetic nephropathy (DN) is the leading cause of end-stage renal disease. Limitations in current diagnosis and screening methods have sparked a search for more specific and conclusive biomarkers. Hyperglycemic conditions generate a plethora of harmful molecules in circulation and within tissues. Oxidative stress generates reactive α-dicarbonyls and β-unsaturated hydroxyhexenals, which react with proteins to form advanced glycation end products. Mass spectrometry imaging (MSI) enables the detection and spatial localization of molecules in biological tissue sections. Here, for the first time, the localization and semiquantitative analysis of “reactive aldehydes” (RAs) 4-hydroxyhexenal (4-HHE), 4-hydroxynonenal (4-HNE), and 4-oxo-2-nonenal (4-ONE) in the kidney tissues of a diabetic mouse model is presented. Ionization efficiency was enhanced through on-tissue chemical derivatization (OTCD) using Girard’s reagent T (GT), forming positively charged hydrazone derivatives. MSI analysis was performed using matrix-assisted laser desorption ionization (MALDI) coupled with Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR). RA levels were elevated in diabetic kidney tissues compared to lean controls and localized throughout the kidney sections at a spatial resolution of 100 µm. This was confirmed by liquid extraction surface analysis–MSI (LESA-MSI) and liquid chromatography–mass spectrometry (LC–MS). This method identified β-unsaturated aldehydes as “potential” biomarkers of DN and demonstrated the capability of OTCD-MSI for detection and localization of poorly ionizable molecules by adapting existing chemical derivatization methods. Untargeted exploratory distribution analysis of some precursor lipids was also assessed using MALDI-FT-ICR-MSI.
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Affiliation(s)
- Carla Harkin
- Mass Spectrometry Centre, Biomedical Sciences Research Institute (BMSRI), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | - Karl W Smith
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32310-4005, USA.,Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - C Logan MacKay
- Scottish Instrumentation and Research Centre for Advanced Mass Spectrometry (SIRCAMS), EastChem School of Chemistry, University of Edinburgh, Edinburgh, Scotland, UK
| | - Tara Moore
- Genomic Medicine, Biomedical Sciences Research Institute (BMSRI), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | | | - Mark Ruddock
- Randox Laboratories Ltd, 55 The Diamond Rd, Crumlin, UK
| | - Diego F Cobice
- Mass Spectrometry Centre, Biomedical Sciences Research Institute (BMSRI), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK.
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18
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Bourceau P, Michellod D, Geier B, Liebeke M. Spatial metabolomics shows contrasting phosphonolipid distributions in tissues of marine bivalves. PEERJ ANALYTICAL CHEMISTRY 2022. [DOI: 10.7717/peerj-achem.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lipids are an integral part of cellular membranes that allow cells to alter stiffness, permeability, and curvature. Among the diversity of lipids, phosphonolipids uniquely contain a phosphonate bond between carbon and phosphorous. Despite this distinctive biochemical characteristic, few studies have explored the biological role of phosphonolipids, although a protective function has been inferred based on chemical and biological stability. We analyzed two species of marine mollusks, the blue mussel Mytilus edulis and pacific oyster Crassostrea gigas, and determined the diversity of phosphonolipids and their distribution in different organs. High-resolution spatial metabolomics revealed that the lipidome varies significantly between tissues within one organ. Despite their chemical similarity, we observed a high heterogeneity of phosphonolipid distributions that originated from minor structural differences. Some phosphonolipids are ubiquitously distributed, while others are present almost exclusively in the layer of ciliated epithelial cells. This distinct localization of certain phosphonolipids in tissues exposed to the environment could support the hypothesis of a protective function in mollusks. This study highlights that the tissue specific distribution of an individual metabolite can be a valuable tool for inferring its function and guiding functional analyses.
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Affiliation(s)
- Patric Bourceau
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM—Center for Marine Environmental Sciences of the University of Bremen, Bremen, Germany
| | - Dolma Michellod
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Benedikt Geier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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19
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Larson EA, Forsman TT, Stuart L, Alexandrov T, Lee YJ. Rapid and Automatic Annotation of Multiple On-Tissue Chemical Modifications in Mass Spectrometry Imaging with Metaspace. Anal Chem 2022; 94:8983-8991. [PMID: 35708227 DOI: 10.1021/acs.analchem.2c00979] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On-tissue chemical derivatization is a valuable tool for expanding compound coverage in untargeted metabolomic studies with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Applying multiple derivatization agents in parallel increases metabolite coverage even further but results in large and more complex datasets that can be challenging to analyze. In this work, we present a pipeline to provide rigorous annotations for on-tissue derivatized MSI data using Metaspace. To test and validate the pipeline, maize roots were used as a model system to obtain MSI datasets after chemical derivatization with four different reagents, Girard's T and P for carbonyl groups, coniferyl aldehyde for primary amines, and 2-picolylamine for carboxylic acids. Using this pipeline helped us annotate 631 unique metabolites from the CornCyc/BraChem database compared to 256 in the underivatized dataset, yet, at the same time, shortening the processing time compared to manual processing and providing robust and systematic scoring and annotation. We have also developed a method to remove false derivatized annotations, which can clean 5-25% of false derivatized annotations from the derivatized data, depending on the reagent. Taken together, our pipeline facilitates the use of broadly targeted spatial metabolomics using multiple derivatization reagents.
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Affiliation(s)
- Evan A Larson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Trevor T Forsman
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Lachlan Stuart
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany.,Molecular Medicine Partnership Unit, EMBL, Heidelberg 69117, Germany
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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20
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Dong Y, Aharoni A. Image to insight: exploring natural products through mass spectrometry imaging. Nat Prod Rep 2022; 39:1510-1530. [PMID: 35735199 DOI: 10.1039/d2np00011c] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 2017 to 2022Mass spectrometry imaging (MSI) has become a mature molecular imaging technique that is well-matched for natural product (NP) discovery. Here we present a brief overview of MSI, followed by a thorough discussion of different MSI applications in NP research. This review will mainly focus on the recent progress of MSI in plants and microorganisms as they are the main producers of NPs. Specifically, the opportunity and potential of combining MSI with other imaging modalities and stable isotope labeling are discussed. Throughout, we focus on both the strengths and weaknesses of MSI, with an eye on future improvements that are necessary for the progression of MSI toward routine NP studies. Finally, we discuss new areas of research, future perspectives, and the overall direction that the field may take in the years to come.
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Affiliation(s)
- Yonghui Dong
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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21
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Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology. Int J Mol Sci 2022; 23:ijms23136985. [PMID: 35805979 PMCID: PMC9266571 DOI: 10.3390/ijms23136985] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.
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22
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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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23
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Kubicki M, Giannakopoulos G, Lamshöft M, Dittgen J. Spatially Resolved Investigation of Herbicide-Safener Interaction in Maize ( Zea mays L.) by MALDI-Imaging Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6368-6376. [PMID: 35583469 DOI: 10.1021/acs.jafc.2c00768] [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: 06/15/2023]
Abstract
Monitoring agrochemical distribution within plant tissues delivers significant insights into the adsorption, distribution, metabolism, and elimination of agrochemicals. Detection and imaging of the safener cyprosulfamide (CSA) and the herbicide thiencarbazone-methyl (TCM) after micro-droplet application on the surface of maize leaves (Zea mays L.) have been achieved using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI). The agrochemicals were deposited onto the adaxial surface of maize leaves on growing plants, and their uptake, distribution, and metabolism were investigated at four timepoints (3 h, 24 h, 4 days, and 7 days) to assess the influence of CSA treatment on TCM metabolism. MALDI MSI visualized significant changes for the metabolism of TCM after 24 h. Although TCM metabolism was detected neither in the control without the safener nor in the approach with CSA on the second leaf, the co-application on the same leaf showed significant metabolism of the herbicide by detecting the metabolite N-demethylated TCM. These findings suggest that safener protection against herbicide injury is a rapid process in which CSA and TCM need to be present in the same tissues. This study showcases the use of MALDI MSI to visualize and analyze indirect interactions of two substances in planta.
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Affiliation(s)
- Michael Kubicki
- Crop Science Division, Environmental Safety─Metabolism & Kinetics, Bayer AG, 40789 Monheim am Rhein, Germany
| | - George Giannakopoulos
- Crop Protection Group, School of Natural and Environmental Sciences, Newcastle University, NE1 7RU Newcastle Upon Tyne, U.K
| | - Marc Lamshöft
- Crop Science Division, Environmental Safety─Metabolism & Kinetics, Bayer AG, 40789 Monheim am Rhein, Germany
| | - Jan Dittgen
- Crop Science Division, Weed Control Research, Bayer AG, 65926 Frankfurt, Germany
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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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25
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DeLaney K, Phetsanthad A, Li L. ADVANCES IN HIGH-RESOLUTION MALDI MASS SPECTROMETRY FOR NEUROBIOLOGY. MASS SPECTROMETRY REVIEWS 2022; 41:194-214. [PMID: 33165982 PMCID: PMC8106695 DOI: 10.1002/mas.21661] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/13/2020] [Indexed: 05/08/2023]
Abstract
Research in the field of neurobiology and neurochemistry has seen a rapid expansion in the last several years due to advances in technologies and instrumentation, facilitating the detection of biomolecules critical to the complex signaling of neurons. Part of this growth has been due to the development and implementation of high-resolution Fourier transform (FT) mass spectrometry (MS), as is offered by FT ion cyclotron resonance (FTICR) and Orbitrap mass analyzers, which improves the accuracy of measurements and helps resolve the complex biological mixtures often analyzed in the nervous system. The coupling of matrix-assisted laser desorption/ionization (MALDI) with high-resolution MS has drastically expanded the information that can be obtained with these complex samples. This review discusses notable technical developments in MALDI-FTICR and MALDI-Orbitrap platforms and their applications toward molecules in the nervous system, including sequence elucidation and profiling with de novo sequencing, analysis of post-translational modifications, in situ analysis, key advances in sample preparation and handling, quantitation, and imaging. Notable novel applications are also discussed to highlight key developments critical to advancing our understanding of neurobiology and providing insight into the exciting future of this field. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
- To whom correspondence should be addressed. , Phone: (608) 265-8491, Fax: (608) 262-5345., Mailing Address: 5125 Rennebohm Hall, 777 Highland Avenue, Madison, WI 53706
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26
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O'Neill KC, Dueñas ME, Larson E, Forsman TT, Lee YJ. Enhancing Metabolite Coverage for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Through Multiple On-Tissue Chemical Derivatizations. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2437:197-213. [PMID: 34902150 DOI: 10.1007/978-1-0716-2030-4_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ability to study and visualize metabolites on a cellular and sub-cellular level is important for gaining insights into biological pathways and metabolism of multicellular organisms. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is a powerful analytical tool for metabolomics experiments due to its high sensitivity and small sampling size. The spatial resolution in MALDI-MSI is mainly limited by the number of molecules available in a small sampling size. When the sampling size is low enough to achieve cellular or subcellular spatial resolution, signal intensity is sacrificed making poorly ionized metabolites difficult to detect. To overcome this limitation, on-tissue chemical derivatization reactions have been used to enhance the desorption/ionization efficiency of selected classes of compounds by adding a functional group with a permanent positive charge or one that can be easily ionized. By utilizing several chemical derivatizations in parallel, metabolite coverage can be drastically improved. This chapter outlines methodology for sample preparation and data analysis for on-tissue chemical derivatization using various derivatization reagents.
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Affiliation(s)
- Kelly C O'Neill
- Department of Chemistry, Iowa State University, Ames, IA, USA
| | | | - Evan Larson
- Department of Chemistry, Iowa State University, Ames, IA, USA
| | | | - Young-Jin Lee
- Department of Chemistry, Iowa State University, Ames, IA, USA.
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Lohse M, Haag R, Lippold E, Vetterlein D, Reemtsma T, Lechtenfeld OJ. Direct Imaging of Plant Metabolites in the Rhizosphere Using Laser Desorption Ionization Ultra-High Resolution Mass Spectrometry. FRONTIERS IN PLANT SCIENCE 2021; 12:753812. [PMID: 34925405 PMCID: PMC8678481 DOI: 10.3389/fpls.2021.753812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
The interplay of rhizosphere components such as root exudates, microbes, and minerals results in small-scale gradients of organic molecules in the soil around roots. The current methods for the direct chemical imaging of plant metabolites in the rhizosphere often lack molecular information or require labeling with fluorescent tags or isotopes. Here, we present a novel workflow using laser desorption ionization (LDI) combined with mass spectrometric imaging (MSI) to directly analyze plant metabolites in a complex soil matrix. Undisturbed samples of the roots and the surrounding soil of Zea mays L. plants from either field- or laboratory-scale experiments were embedded and cryosectioned to 100 μm thin sections. The target metabolites were detected with a spatial resolution of 25 μm in the root and the surrounding soil based on accurate masses using ultra-high mass resolution laser desorption ionization Fourier-transform ion cyclotron resonance mass spectrometry (LDI-FT-ICR-MS). Using this workflow, we could determine the rhizosphere gradients of a dihexose (e.g., sucrose) and other plant metabolites (e.g., coumaric acid, vanillic acid). The molecular gradients for the dihexose showed a high abundance of this metabolite in the root and a strong depletion of the signal intensity within 150 μm from the root surface. Analyzing several sections from the same undisturbed soil sample allowed us to follow molecular gradients along the root axis. Benefiting from the ultra-high mass resolution, isotopologues of the dihexose could be readily resolved to enable the detection of stable isotope labels on the compound level. Overall, the direct molecular imaging via LDI-FT-ICR-MS allows for the first time a non-targeted or targeted analysis of plant metabolites in undisturbed soil samples, paving the way to study the turnover of root-derived organic carbon in the rhizosphere with high chemical and spatial resolution.
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Affiliation(s)
- Martin Lohse
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Rebecca Haag
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- Ansbach University of Applied Sciences, Ansbach, Germany
| | - Eva Lippold
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
- Soil Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Thorsten Reemtsma
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- Institute of Analytical Chemistry, University of Leipzig, Leipzig, Germany
| | - Oliver J. Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- ProVIS – Centre for Chemical Microscopy, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
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28
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Unravel the Local Complexity of Biological Environments by MALDI Mass Spectrometry Imaging. Int J Mol Sci 2021; 22:ijms222212393. [PMID: 34830273 PMCID: PMC8623934 DOI: 10.3390/ijms222212393] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/07/2021] [Accepted: 11/14/2021] [Indexed: 11/30/2022] Open
Abstract
Classic metabolomic methods have proven to be very useful to study functional biology and variation in the chemical composition of different tissues. However, they do not provide any information in terms of spatial localization within fine structures. Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) does and reaches at best a spatial resolution of 0.25 μm depending on the laser setup, making it a very powerful tool to analyze the local complexity of biological samples at the cellular level. Here, we intend to give an overview of the diversity of the molecules and localizations analyzed using this method as well as to update on the latest adaptations made to circumvent the complexity of samples. MALDI MSI has been widely used in medical sciences and is now developing in research areas as diverse as entomology, microbiology, plant biology, and plant–microbe interactions, the rhizobia symbiosis being the most exhaustively described so far. Those are the fields of interest on which we will focus to demonstrate MALDI MSI strengths in characterizing the spatial distributions of metabolites, lipids, and peptides in relation to biological questions.
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29
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Merdas M, Lagarrigue M, Vanbellingen Q, Umbdenstock T, Da Violante G, Pineau C. On-tissue chemical derivatization reagents for matrix-assisted laser desorption/ionization mass spectrometry imaging. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4731. [PMID: 34080257 DOI: 10.1002/jms.4731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/26/2021] [Accepted: 04/13/2021] [Indexed: 05/27/2023]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a key tool for the analysis of biological tissues. It provides spatial and quantitative information about different types of analytes within tissue sections. Despite the increasing improvements of this technique, the low detection sensitivity of some compounds remains an important challenge to overcome. Poor sensitivity is related to weak ionization efficiency, low abundance of analytes and matrix ions, or endogenous interferences. On-tissue chemical derivatization (OTCD) has proven to be an important solution to these issues and is increasingly employed in MALDI MSI studies. OTCD reagents, synthesized or commercially available, have been essentially used for the detection of small exogenous or endogenous molecules within tissues. Optimally, an OTCD reaction is performed in mild conditions, in an acceptable range of time, preserves the integrity of the tissues, and prevents the delocalization. In addition to their reactivity with a targeted chemical function, some OTCD reagents can also be used as a matrix, which simplifies the sample preparation procedure. In this review, we present an exhaustive overview of OTCD reagents and methods used in MALDI MSI studies.
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Affiliation(s)
- Mira Merdas
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, F-35042, France
- Protim, Univ Rennes, Rennes, F-35042, France
- DMPK Department, Technologie Servier, Orléans, 45007, France
| | - Mélanie Lagarrigue
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, F-35042, France
- Protim, Univ Rennes, Rennes, F-35042, France
| | | | | | | | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, F-35042, France
- Protim, Univ Rennes, Rennes, F-35042, France
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30
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Chen Y, Alba M, Tieu T, Tong Z, Minhas RS, Rudd D, Voelcker NH, Cifuentes-Rius A, Elnathan R. Engineering Micro–Nanomaterials for Biomedical Translation. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202100002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yaping Chen
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - Maria Alba
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - Terence Tieu
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing Commonwealth Scientific and Industrial Research Organisation (CSIRO) Clayton VIC 3168 Australia
| | - Ziqiu Tong
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
| | - Rajpreet Singh Minhas
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - David Rudd
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - Nicolas H. Voelcker
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
- Department of Materials Science and Engineering Monash University 22 Alliance Lane Clayton VIC 3168 Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing Commonwealth Scientific and Industrial Research Organisation (CSIRO) Clayton VIC 3168 Australia
- INM-Leibniz Institute for New Materials Campus D2 2 Saarbrücken 66123 Germany
| | - Anna Cifuentes-Rius
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
| | - Roey Elnathan
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
- Department of Materials Science and Engineering Monash University 22 Alliance Lane Clayton VIC 3168 Australia
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31
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Gallart-Ayala H, Teav T, Ivanisevic J. Metabolomics meets lipidomics: Assessing the small molecule component of metabolism. Bioessays 2021; 42:e2000052. [PMID: 33230910 DOI: 10.1002/bies.202000052] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 09/11/2020] [Indexed: 12/16/2022]
Abstract
Metabolomics, including lipidomics, is emerging as a quantitative biology approach for the assessment of energy flow through metabolism and information flow through metabolic signaling; thus, providing novel insights into metabolism and its regulation, in health, healthy ageing and disease. In this forward-looking review we provide an overview on the origins of metabolomics, on its role in this postgenomic era of biochemistry and its application to investigate metabolite role and (bio)activity, from model systems to human population studies. We present the challenges inherent to this analytical science, and approaches and modes of analysis that are used to resolve, characterize and measure the infinite chemical diversity contained in the metabolome (including lipidome) of complex biological matrices. In the current outbreak of metabolic diseases such as cardiometabolic disorders, cancer and neurodegenerative diseases, metabolomics appears to be ideally situated for the investigation of disease pathophysiology from a metabolite perspective.
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Affiliation(s)
- Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Tony Teav
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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32
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Tinte MM, Chele KH, van der Hooft JJJ, Tugizimana F. Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview. Metabolites 2021; 11:445. [PMID: 34357339 PMCID: PMC8305945 DOI: 10.3390/metabo11070445] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 12/27/2022] Open
Abstract
Plants are constantly challenged by changing environmental conditions that include abiotic stresses. These are limiting their development and productivity and are subsequently threatening our food security, especially when considering the pressure of the increasing global population. Thus, there is an urgent need for the next generation of crops with high productivity and resilience to climate change. The dawn of a new era characterized by the emergence of fourth industrial revolution (4IR) technologies has redefined the ideological boundaries of research and applications in plant sciences. Recent technological advances and machine learning (ML)-based computational tools and omics data analysis approaches are allowing scientists to derive comprehensive metabolic descriptions and models for the target plant species under specific conditions. Such accurate metabolic descriptions are imperatively essential for devising a roadmap for the next generation of crops that are resilient to environmental deterioration. By synthesizing the recent literature and collating data on metabolomics studies on plant responses to abiotic stresses, in the context of the 4IR era, we point out the opportunities and challenges offered by omics science, analytical intelligence, computational tools and big data analytics. Specifically, we highlight technological advancements in (plant) metabolomics workflows and the use of machine learning and computational tools to decipher the dynamics in the chemical space that define plant responses to abiotic stress conditions.
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Affiliation(s)
- Morena M. Tinte
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.T.); (K.H.C.)
| | - Kekeletso H. Chele
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.T.); (K.H.C.)
| | | | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.T.); (K.H.C.)
- International Research and Development Division, Omnia Group, Ltd., Johannesburg 2021, South Africa
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33
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Taylor M, Lukowski JK, Anderton CR. Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:872-894. [PMID: 33656885 PMCID: PMC8033567 DOI: 10.1021/jasms.0c00439] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 05/02/2023]
Abstract
Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.
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Affiliation(s)
- Michael
J. Taylor
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jessica K. Lukowski
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher R. Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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34
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Forsman TT, Dueñas ME, Lee YJ. On-tissue boronic acid derivatization for the analysis of vicinal diol metabolites in maize with MALDI-MS imaging. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4709. [PMID: 33629378 DOI: 10.1002/jms.4709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 05/22/2023]
Abstract
Derivatization reactions are commonly used in mass spectrometry to improve analyte signals, specifically by enhancing the ionization efficiency of those compounds. Vicinal diols are one group of biologically important compounds that have been commonly derivatized using boronic acid. In this study, a boronic acid with a tertiary amine was adapted for the derivatization of vicinal diol metabolites in B73 maize tissue cross-sections for mass spectrometry imaging analysis. Using this method, dozens of vicinal diol metabolites were derivatized, effectively improving the signal of those metabolites. Many of these metabolites were tentatively assigned using high-resolution accurate mass measurements. In addition, reaction interference and cross-reactivity with various other functional groups were systematically studied to verify data interpretation.
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Affiliation(s)
- Trevor T Forsman
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011, USA
| | | | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011, USA
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35
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Dueñas ME, Lee YJ. Single-Cell Metabolomics by Mass Spectrometry Imaging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1280:69-82. [PMID: 33791975 DOI: 10.1007/978-3-030-51652-9_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Multicellular organisms achieve their complex living activities through the highly organized metabolic interplay of individual cells and tissues. This complexity has driven the need to spatially resolve metabolomics down to the cellular and subcellular level. Recent technological advances have enabled mass spectrometry imaging (MSI), especially matrix-assisted laser desorption/ionization (MALDI), to become a powerful tool for the visualization of molecular species down to subcellular spatial resolution. In the present chapter, we summarize recent advances in the field of MALDI-MSI, with respect to single-cell level resolution metabolomics directly on tissue. In more detail, we focus on advancements in instrumentation for MSI at single-cell resolution, and the applications towards metabolomic scale imaging. Finally, we discuss new computational tools to aid in metabolite identification, future perspective, and the overall direction that the field of single-cell metabolomics directly on tissue may take in the years to come.
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Affiliation(s)
- Maria Emilia Dueñas
- Department of Chemistry, Iowa State University, Ames, IA, USA.
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, IA, USA
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36
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McLaughlin N, Bielinski TM, Tressler CM, Barton E, Glunde K, Stumpo KA. Pneumatically Sprayed Gold Nanoparticles for Mass Spectrometry Imaging of Neurotransmitters. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2452-2461. [PMID: 32841002 DOI: 10.1021/jasms.0c00156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Using citrate-capped gold nanoparticles (AuNPs) for laser desorption ionization mass spectrometry (LDI-MS) is an approach that has demonstrated broad applicability to ionization of different classes of molecules. Here, we show a simple AuNP-based approach for the ionization of neurotransmitters. Specifically, the detection of acetylcholine, dopamine, epinephrine, glutamine, 4-aminobutyric acid, norepinephrine, octopamine, and serotonin was achieved at physiologically relevant concentrations in serum and homogenized tissue. Additionally, pneumatic spraying of AuNPs onto tissue sections facilitated mass spectrometry imaging (MSI) of rabbit brain tissue sections, zebrafish embryos, and neuroblastoma cells for several neurotransmitters simultaneously using this quick and simple sample preparation. AuNP LDI-MS achieved mapping of neurotransmitters in fine structures of zebrafish embryos and neuroblastoma cells at a lateral spatial resolution of 5 μm. The use of AuNPs to ionize small aminergic neurotransmitters in situ provides a fast, high-spatial resolution method for simultaneous detection of a class of molecules that typically evade comprehensive detection with traditional matrixes.
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Affiliation(s)
- Nolan McLaughlin
- Department of Chemistry, University of Scranton, Scranton, Pennsylvania 18510, United States
| | - Tyler M Bielinski
- Department of Chemistry, University of Scranton, Scranton, Pennsylvania 18510, United States
| | - Caitlin M Tressler
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Eric Barton
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Kristine Glunde
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Katherine A Stumpo
- Department of Chemistry, University of Scranton, Scranton, Pennsylvania 18510, United States
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37
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de Souza LP, Borghi M, Fernie A. Plant Single-Cell Metabolomics-Challenges and Perspectives. Int J Mol Sci 2020; 21:E8987. [PMID: 33256100 PMCID: PMC7730874 DOI: 10.3390/ijms21238987] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Omics approaches for investigating biological systems were introduced in the mid-1990s and quickly consolidated to become a fundamental pillar of modern biology. The idea of measuring the whole complement of genes, transcripts, proteins, and metabolites has since become widespread and routinely adopted in the pursuit of an infinity of scientific questions. Incremental improvements over technical aspects such as sampling, sensitivity, cost, and throughput pushed even further the boundaries of what these techniques can achieve. In this context, single-cell genomics and transcriptomics quickly became a well-established tool to answer fundamental questions challenging to assess at a whole tissue level. Following a similar trend as the original development of these techniques, proteomics alternatives for single-cell exploration have become more accessible and reliable, whilst metabolomics lag behind the rest. This review summarizes state-of-the-art technologies for spatially resolved metabolomics analysis, as well as the challenges hindering the achievement of sensu stricto metabolome coverage at the single-cell level. Furthermore, we discuss several essential contributions to understanding plant single-cell metabolism, finishing with our opinion on near-future developments and relevant scientific questions that will hopefully be tackled by incorporating these new exciting technologies.
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Affiliation(s)
- Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg 1, Golm, 14476 Potsdam, Germany
| | - Monica Borghi
- Department of Biology, Utah State University, 1435 Old Main Hill, Logan, UT 84322, USA;
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg 1, Golm, 14476 Potsdam, Germany
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38
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Zhou Q, Fülöp A, Hopf C. Recent developments of novel matrices and on-tissue chemical derivatization reagents for MALDI-MSI. Anal Bioanal Chem 2020; 413:2599-2617. [PMID: 33215311 PMCID: PMC8007514 DOI: 10.1007/s00216-020-03023-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a fast-growing technique for visualization of the spatial distribution of the small molecular and macromolecular biomolecules in tissue sections. Challenges in MALDI-MSI, such as poor sensitivity for some classes of molecules or limited specificity, for instance resulting from the presence of isobaric molecules or limited resolving power of the instrument, have encouraged the MSI scientific community to improve MALDI-MSI sample preparation workflows with innovations in chemistry. Recent developments of novel small organic MALDI matrices play a part in the improvement of image quality and the expansion of the application areas of MALDI-MSI. This includes rationally designed/synthesized as well as commercially available small organic molecules whose superior matrix properties in comparison with common matrices have only recently been discovered. Furthermore, on-tissue chemical derivatization (OTCD) processes get more focused attention, because of their advantages for localization of poorly ionizable metabolites and their‚ in several cases‚ more specific imaging of metabolites in tissue sections. This review will provide an overview about the latest developments of novel small organic matrices and on-tissue chemical derivatization reagents for MALDI-MSI. Graphical abstract ![]()
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Affiliation(s)
- Qiuqin Zhou
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163, Mannheim, Germany
| | - Annabelle Fülöp
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163, Mannheim, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163, Mannheim, Germany.
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39
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Zhang H, Shi X, Vu NQ, Li G, Li Z, Shi Y, Li M, Wang B, Welham NV, Patankar MS, Weisman P, Li L. On-Tissue Derivatization with Girard's Reagent P Enhances N-Glycan Signals for Formalin-Fixed Paraffin-Embedded Tissue Sections in MALDI Mass Spectrometry Imaging. Anal Chem 2020; 92:13361-13368. [PMID: 32865977 PMCID: PMC7544651 DOI: 10.1021/acs.analchem.0c02704] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023]
Abstract
Glycosylation is a major protein post-translational modification whose dysregulation has been associated with many diseases. Herein, an on-tissue chemical derivatization strategy based on positively charged hydrazine reagent (Girard's reagent P) coupled with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) was developed for analysis of N-glycans from FFPE treated tissue sections. The performance of the proposed approach was evaluated by analysis of monosaccharides, oligosaccharides, N-glycans released from glycoproteins, as well as MS imaging of N-glycans from human cancer tissue sections. The results demonstrated that the signal-to-noise ratios for target saccharides were notably improved after chemical derivatization, in which signals were enhanced by 230-fold for glucose and over 28-fold for maltooctaose. Improved glycome coverage was obtained for N-glycans derived from glycoproteins and tissue samples after chemical derivatization. Furthermore, on-tissue derivatization was applied for MALDI-MSI of N-glycans from human laryngeal cancer and ovarian cancer tissues. Differentially expressed N-glycans among the tumor region, adjacent normal tissue region, and tumor proximal collagen stroma region were imaged, revealing that high-mannose type N-glycans were predominantly expressed in the tumor region. Overall, our results indicate that the on-tissue labeling strategy coupled with MALDI-MSI shows great potential to spatially characterize N-glycan expression within heterogeneous tissue samples with enhanced sensitivity. This study provides a promising approach to better understand the pathogenesis of cancer related aberrant glycosylation, which is beneficial to the design of improved clinical diagnosis and therapeutic strategies.
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Affiliation(s)
- Hua Zhang
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Xudong Shi
- Division
of Otolaryngology, Department of Surgery, School of Medicine and Public
Health, University of Wisconsin—Madison, Madison, Wisconsin 53792, United States
| | - Nhu Q. Vu
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Gongyu Li
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Zihui Li
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Yatao Shi
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Miyang Li
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Bin Wang
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Nathan V. Welham
- Division
of Otolaryngology, Department of Surgery, School of Medicine and Public
Health, University of Wisconsin—Madison, Madison, Wisconsin 53792, United States
| | - Manish S. Patankar
- Department
of Obstetrics and Gynecology, University
of Wisconsin—Madison, Madison, Wisconsin 54911, United States
| | - Paul Weisman
- Departments
of Pathology and Laboratory Medicine, School of Medicine and Public
Health, University of Wisconsin—Madison, Madison, Wisconsin 53792, United States
| | - Lingjun Li
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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40
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Yukihiro Y, Zaima N. Application of Mass Spectrometry Imaging for Visualizing Food Components. Foods 2020; 9:foods9050575. [PMID: 32375379 PMCID: PMC7278736 DOI: 10.3390/foods9050575] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/15/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023] Open
Abstract
Consuming food is essential for survival, maintaining health, and triggering positive emotions like pleasure. One of the factors that drive us toward such behavior is the presence of various compounds in foods. There are many methods to analyze these molecules in foods; however, it is difficult to analyze the spatial distribution of these compounds using conventional techniques, such as mass spectrometry combined with high-performance liquid chromatography or gas chromatography. Mass spectrometry imaging (MSI) is a two-dimensional ionization technology that enables detection of compounds in tissue sections without extraction, purification, separation, or labeling. There are many methods for ionization of analytes, including secondary ion mass spectrometry, matrix-assisted laser desorption/ionization, and desorption electrospray ionization. Such MSI technologies can provide spatial information on the location of a specific analyte in food. The number of studies utilizing MSI technologies in food science has been increasing in the past decade. This review provides an overview of some of the recent applications of MSI in food science and related fields. In the future, MSI will become one of the most promising technologies for visualizing the distribution of food components and for identifying food-related factors by their molecular weights to improve quality, quality assurance, food safety, nutritional analysis, and to locate administered food factors.
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Affiliation(s)
- Yoshimura Yukihiro
- Department of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe City 651-2180, Japan
| | - Nobuhiro Zaima
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Kindai University, 204-3327 Nakamachi, Nara City 631-8505, Japan
- Agricultural Technology and Innovation Research Institute, Kindai University,204-3327 Nakamachi, Nara City 631-8505, Japan
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Alexandrov T. Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence. Annu Rev Biomed Data Sci 2020; 3:61-87. [PMID: 34056560 DOI: 10.1146/annurev-biodatasci-011420-031537] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Spatial metabolomics is an emerging field of omics research that has enabled localizing metabolites, lipids, and drugs in tissue sections, a feat considered impossible just two decades ago. Spatial metabolomics and its enabling technology-imaging mass spectrometry-generate big hyper-spectral imaging data that have motivated the development of tailored computational methods at the intersection of computational metabolomics and image analysis. Experimental and computational developments have recently opened doors to applications of spatial metabolomics in life sciences and biomedicine. At the same time, these advances have coincided with a rapid evolution in machine learning, deep learning, and artificial intelligence, which are transforming our everyday life and promise to revolutionize biology and healthcare. Here, we introduce spatial metabolomics through the eyes of a computational scientist, review the outstanding challenges, provide a look into the future, and discuss opportunities granted by the ongoing convergence of human and artificial intelligence.
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Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, USA
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Mussap M, Loddo C, Fanni C, Fanos V. Metabolomics in pharmacology - a delve into the novel field of pharmacometabolomics. Expert Rev Clin Pharmacol 2020; 13:115-134. [PMID: 31958027 DOI: 10.1080/17512433.2020.1713750] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Pharmacometabolomics is an emerging science pursuing the application of precision medicine. Combining both genetic and environmental factors, the so-called pharmacometabolomic approach guides patient selection and stratification in clinical trials and optimizes personalized drug dosage, improving efficacy and safety.Areas covered: This review illustrates the progressive introduction of pharmacometabolomics as an innovative solution for enhancing the discovery of novel drugs and improving research and development (R&D) productivity of the pharmaceutical industry. An extended analysis on published pharmacometabolomics studies both in animal models and humans includes results obtained in several areas such as hepatology, gastroenterology, nephrology, neuropsychiatry, oncology, drug addiction, embryonic cells, neonatology, and microbiomics.Expert opinion: a tailored, individualized therapy based on the optimization of pharmacokinetics and pharmacodynamics, the improvement of drug efficacy, and the abolition of drug toxicity and adverse drug reactions is a key issue in precision medicine. Genetics alone has become insufficient for deciphring intra- and inter-individual variations in drug-response, since they originate both from genetic and environmental factors, including human microbiota composition. The association between pharmacogenomics and pharmacometabolomics may be considered the new strategy for an in-deep knowledge on changes and alterations in human and microbial metabolic pathways due to the action of a drug.
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Affiliation(s)
- Michele Mussap
- Laboratory Unit, Department of Surgical Sciences, University of Cagliari, Cagliari, Italy
| | | | - Claudia Fanni
- Division of Pediatrics, Rovigo Hospital, Rovigo, Italy
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Neonatal Pathology and Neonatal Section, Department of Surgical Sciences, University of Cagliari, Cagliari, Italy
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Hinners P, Thomas M, Lee YJ. Determining Fingerprint Age with Mass Spectrometry Imaging via Ozonolysis of Triacylglycerols. Anal Chem 2020; 92:3125-3132. [DOI: 10.1021/acs.analchem.9b04765] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paige Hinners
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Madison Thomas
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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44
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O’Neill KC, Lee YJ. Visualizing Genotypic and Developmental Differences of Free Amino Acids in Maize Roots With Mass Spectrometry Imaging. FRONTIERS IN PLANT SCIENCE 2020; 11:639. [PMID: 32523598 PMCID: PMC7261921 DOI: 10.3389/fpls.2020.00639] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/24/2020] [Indexed: 05/08/2023]
Abstract
Amino acids are essential biological compounds in plants as they store nitrogen, an essential nutrient, and are the building blocks for proteins that drive biological activity. Amino acids have been studied using a wide variety of analytical techniques in different plant systems, however, mass spectrometry imaging (MSI) is a particularly useful technique as it allows for the simultaneous collection of both chemical and spatial information. In this work, matrix-assisted laser desorption/ionization (MALDI)-MSI is used to study the different localization of free amino acids in the roots of maize inbred lines B73 and Mo17 and their reciprocal hybrids. Because amino acids are difficult to detect in mass spectrometry, especially directly on tissues, a chemical derivatization protocol is utilized to increase the ionization efficiency and improve their detection. We report differences in both abundance and localization of amino acids in B73 and Mo17 maize roots and suggest the hybrids show evidence of inheriting characteristics from both parents. Most genotypic differences are found in the cross-sections near the seed (∼2 cm away) at a later stage of development (10-11 cm in length). Here, B73 has lower amino acid abundance localized primarily to the center of the roots for most amino acids, while Mo17 has much higher abundance localized mainly to the root cortex. This difference in localization is minimized when grown in ammonium ion rich conditions. Roots grown in the presence of 15N-ammonium ions provided additional insight about the amino acid synthesis. The localization of some amino acids, particularly leucine/isoleucine and glutamine, is not affected by the addition of nitrogen and is consistent regardless of the nitrogen source, either from the seeds (14N-labeled) or environment (15N-labeled). Nitrogen uptake from the environment is confined to glutamine, asparagine, and alanine, consistent with their roles in amino acid storage and transportation.
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Spraggins JM, Djambazova KV, Rivera ES, Migas LG, Neumann EK, Fuetterer A, Suetering J, Goedecke N, Ly A, Van de Plas R, Caprioli RM. High-Performance Molecular Imaging with MALDI Trapped Ion-Mobility Time-of-Flight (timsTOF) Mass Spectrometry. Anal Chem 2019; 91:14552-14560. [PMID: 31593446 PMCID: PMC7382025 DOI: 10.1021/acs.analchem.9b03612] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Imaging mass spectrometry (IMS) enables the spatially targeted molecular assessment of biological tissues at cellular resolutions. New developments and technologies are essential for uncovering the molecular drivers of native physiological function and disease. Instrumentation must maximize spatial resolution, throughput, sensitivity, and specificity, because tissue imaging experiments consist of thousands to millions of pixels. Here, we report the development and application of a matrix-assisted laser desorption/ionization (MALDI) trapped ion-mobility spectrometry (TIMS) imaging platform. This prototype MALDI timsTOF instrument is capable of 10 μm spatial resolutions and 20 pixels/s throughput molecular imaging. The MALDI source utilizes a Bruker SmartBeam 3-D laser system that can generate a square burn pattern of <10 × 10 μm at the sample surface. General image performance was assessed using murine kidney and brain tissues and demonstrate that high-spatial-resolution imaging data can be generated rapidly with mass measurement errors <5 ppm and ∼40 000 resolving power. Initial TIMS-based imaging experiments were performed on whole-body mouse pup tissue demonstrating the separation of closely isobaric [PC(32:0) + Na]+ and [PC(34:3) + H]+ (3 mDa mass difference) in the gas phase. We have shown that the MALDI timsTOF platform can maintain reasonable data acquisition rates (>2 pixels/s) while providing the specificity necessary to differentiate components in complex mixtures of lipid adducts. The combination of high-spatial-resolution and throughput imaging capabilities with high-performance TIMS separations provides a uniquely tunable platform to address many challenges associated with advanced molecular imaging applications.
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Affiliation(s)
- Jeffrey M Spraggins
- Department of Biochemistry , Vanderbilt University , 607 Light Hall , Nashville , Tennessee 37205 , United States
- Department of Chemistry , Vanderbilt University , 7330 Stevenson Center, Station B 351822 , Nashville , Tennessee 37235 , United States
| | - Katerina V Djambazova
- Department of Chemistry , Vanderbilt University , 7330 Stevenson Center, Station B 351822 , Nashville , Tennessee 37235 , United States
| | - Emilio S Rivera
- Department of Biochemistry , Vanderbilt University , 607 Light Hall , Nashville , Tennessee 37205 , United States
| | - Lukasz G Migas
- Delft Center for Systems and Control (DCSC) , Delft University of Technology , 2628 CD Delft , The Netherlands
| | - Elizabeth K Neumann
- Department of Biochemistry , Vanderbilt University , 607 Light Hall , Nashville , Tennessee 37205 , United States
| | - Arne Fuetterer
- Bruker Daltonik GmbH , Fahrenheitstraße 4 , 28359 Bremen , Germany
| | | | - Niels Goedecke
- Bruker Daltonik GmbH , Fahrenheitstraße 4 , 28359 Bremen , Germany
| | - Alice Ly
- Bruker Daltonik GmbH , Fahrenheitstraße 4 , 28359 Bremen , Germany
| | - Raf Van de Plas
- Department of Biochemistry , Vanderbilt University , 607 Light Hall , Nashville , Tennessee 37205 , United States
- Delft Center for Systems and Control (DCSC) , Delft University of Technology , 2628 CD Delft , The Netherlands
| | - Richard M Caprioli
- Department of Biochemistry , Vanderbilt University , 607 Light Hall , Nashville , Tennessee 37205 , United States
- Department of Chemistry , Vanderbilt University , 7330 Stevenson Center, Station B 351822 , Nashville , Tennessee 37235 , United States
- Department of Pharmacology , Vanderbilt University , 2220 Pierce Avenue , Nashville , Tennessee 37232 , United States
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