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Vats M, Cillero-Pastor B, Cuypers E, Heeren RMA. Mass spectrometry imaging in plants, microbes, and food: a review. Analyst 2024; 149:4553-4582. [PMID: 39196541 DOI: 10.1039/d4an00644e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Plant health, which affects the nutritional quality and safety of derivative food products, is influenced by symbiotic interactions with microorganisms. These interactions influence the local molecular profile at the tissue level. Therefore, studying the distribution of molecules within plants, microbes, and plant-based food is crucial to assess plant health, ensure the safety and quality of the agricultural products that become part of our food supply, and plan agricultural management practices. Within this framework, the molecular distribution within plant-based samples can be visualized with mass spectrometry imaging (MSI). This review describes key MSI methodologies, highlighting the role they play in unraveling the localization of metabolites, lipids, proteins, pigments, and elemental components across plants, microbes, and food products. Furthermore, investigations that involve multimodal molecular imaging approaches combining MSI with other imaging techniques are described. The advantages and limitations of the different MSI techniques that influence their applicability in diverse agro-food studies are described to enable informed choices for tailored analyses. For example, some MSI technologies involve meticulous sample preparation while others compromise spatial resolution to gain throughput. Key parameters such as sensitivity, ionization bias and fragmentation, reference database and compound class specificity are described and discussed in this review. With the ongoing refinements in instrumentation, data analysis, and integration of complementary techniques, MSI deepens our insight into the molecular biology of the agricultural ecosystem. This in turn empowers the quest for sustainable and productive agricultural practices.
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Affiliation(s)
- Mudita Vats
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
| | - Berta Cillero-Pastor
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
- MERLN Institute for Technology-inspired Regenerative Medicine, Department of Cell Biology-Inspired Tissue Engineering (cBITE), Maastricht University, Maastricht, the Netherlands
| | - Eva Cuypers
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
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2
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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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3
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Zhuang Y, Wang H, Tan F, Wu B, Liu L, Qin H, Yang Z, He M. Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108619. [PMID: 38604013 DOI: 10.1016/j.plaphy.2024.108619] [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: 12/06/2023] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.
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Affiliation(s)
- Yong Zhuang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
| | - Hao Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Furong Tan
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Linpei Liu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Han Qin
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - ZhiJuan Yang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Mingxiong He
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
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4
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Chen Y, Liu Y, Li X, He Y, Li W, Peng Y, Zheng J. Recent Advances in Mass Spectrometry-Based Spatially Resolved Molecular Imaging of Drug Disposition and Metabolomics. Drug Metab Dispos 2023; 51:1273-1283. [PMID: 37295949 DOI: 10.1124/dmd.122.001069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 05/04/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
Mass spectrometric imaging is a nontargeted, tag-free, high-throughput, and highly responsive analytical approach. The highly accurate molecular visualization detection technology enables qualitative and quantitative analyses of biologic tissues or cells scanned by mass spectrometry in situ, extracting known and unknown multiple compounds, and simultaneously assessing relative contents of targeting molecules by monitoring their molecular ions and pinpointing the spatial locations of those molecules distributed. Five mass spectrometric imaging techniques and their characteristics are introduced in the review, including matrix-assisted laser desorption ionization mass spectrometry, secondary ion mass spectrometry, desorption electrospray ionization mass spectrometry, laser ablation electrospray ionization mass spectrometry, and laser ablation inductively coupled plasma mass spectrometry. The mass spectrometry-based techniques provide the possibility for spatial metabolomics with the capability of high throughput and precision detection. The approaches have been widely employed to spatially image not only metabolome of endogenous amino acids, peptides, proteins, neurotransmitters, and lipids but also the disposition of exogenous chemicals, such as pharmaceutical agents, environmental pollutants, toxicants, natural products, and heavy metals. The techniques also provide us with spatial distribution imaging of analytes in single cells, tissue microregions, organs, and whole animals. SIGNIFICANCE STATEMENT: The review article includes an overview of five commonly used mass spectrometers for spatial imaging and describes the advantages and disadvantages of each. Examples of the technology applications cover drug disposition, diseases, and omics. Technical aspects of relative and absolute quantification by mass spectrometric imaging and challenges for future new applications are discussed as well. The reviewed knowledge may benefit the development of new drugs and provide a better understanding of biochemical processes related to physiology and diseases.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ying Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ximei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Yan He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Weiwei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ying Peng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Jiang Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
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5
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Moore K, Reeksting SB, Nair V, Pannakal ST, Roy N, Eilstein J, Grégoire S, Delgado-Charro MB, Guy RH. Extraction of phytochemicals from the pomegranate ( Punica granatum L., Punicaceae) by reverse iontophoresis. RSC Adv 2023; 13:11261-11268. [PMID: 37057274 PMCID: PMC10087384 DOI: 10.1039/d3ra01242e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023] Open
Abstract
Plant metabolic profiling can provide a wealth of information regarding the biochemical status of the organism, but sample acquisition typically requires an invasive and/or destructive extraction process. Reverse iontophoresis (RI) imposes a small electric field across a biological membrane to substantially enhance the transport of charged and polar compounds and has been employed, in particular, to extract biomarkers of interest across human skin. The objective of this work was to examine the capability of RI to sample phytochemicals in a minimally invasive fashion in fructo (i.e., from the intact fruit). RI was principally used to extract a model, bioactive compound - specifically, ellagic acid - from the fruit peel of Punica granatum L. The RI sampling protocol was refined using isolated peel, and a number of experimental factors were examined and optimised, including preparation of the peel samples, the current intensity applied and the pH of the medium into which samples were collected. The most favourable conditions (3 mA current for a period of 1 hour, into a buffer at pH 7.4) were then applied to the successful RI extraction of ellagic acid from intact pomegranates. Multiple additional phytochemicals were also extracted and identified by liquid chromatography with tandem mass spectrometry (LC-MS/MS). A successful proof-of-concept has been achieved, demonstrating the capability to non-destructively extract phytochemicals of interest from intact fruit.
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Affiliation(s)
- Kieran Moore
- Department of Life Sciences, University of Bath UK
| | | | - Vimal Nair
- Advanced Research, L'Oréal Research and Innovation India Bangalore India
| | - Steve T Pannakal
- Advanced Research, L'Oréal Research and Innovation India Bangalore India
| | - Nita Roy
- Advanced Research, L'Oréal Research and Innovation India Bangalore India
| | - Joan Eilstein
- Advanced Research, L'Oréal Research and Innovation India Bangalore India
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6
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Liu L, Wang Z, Zhang Q, Mei Y, Li L, Liu H, Wang Z, Yang L. Ion Mobility Mass Spectrometry for the Separation and Characterization of Small Molecules. Anal Chem 2023; 95:134-151. [PMID: 36625109 DOI: 10.1021/acs.analchem.2c02866] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Longchan Liu
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Ziying Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Qian Zhang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Yuqi Mei
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Linnan Li
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Zhengtao Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Li Yang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China.,Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
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7
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Pereira I, Ramalho RRF, Maciel LIL, de Aguiar DVA, Trindade Y, da Cruz GF, Vianna AM, Júnior IM, Lima GDS, Vaz BG. Directly Mapping the Spatial Distribution of Organic Compounds on Mineral Rock Surfaces by DESI and LAESI Mass Spectrometry Imaging. Anal Chem 2022; 94:13691-13699. [PMID: 36154021 DOI: 10.1021/acs.analchem.2c01154] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we present a new application of desorption electrospray ionization (DESI) and laser ablation electrospray ionization (LAESI) mass spectrometry imaging to assess the spatial location of organic compounds, both polar and nonpolar, directly from rock surfaces. Three carbonaceous rocks collected from an aquatic environment and a berea sandstone subjected to a small-scale oil recovery experiment were analyzed by DESI and LAESI. No rock pretreatment was required before DESI and LAESI analyses. DESI detected and spatially mapped several fatty acids and a disaccharide on the surfaces of carbonaceous rocks, and various nitrogenated and oxygenated compounds on the surfaces of berea sandstone. In contrast, LAESI using a 3.4 μm infrared laser beam was able to detect and map hydrocarbons on the surfaces of all rock samples. Both techniques can be combined to analyze polar and nonpolar compounds. DESI can be used first to detect polar compounds, as it does not destroy the rock surface, and LAESI can then be used to analyze nonpolar analytes, as it destroys a layer of the sample surface. Both techniques have the potential to be used in several scientific areas involving rocks and minerals, such as in the analysis of industry-derived contaminants in aquatic sediments or in small-scale rock-fluid interaction experiments.
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Affiliation(s)
- Igor Pereira
- Chemistry Institute, Federal University of Goiás, Goiânia, Goiás 74690-900, Brazil.,Department of Chemistry, Vancouver Island University, Nanaimo, British Columbia V9R 5S5, Canada
| | - Ruver R F Ramalho
- Chemistry Institute, Federal University of Goiás, Goiânia, Goiás 74690-900, Brazil
| | - Lanaia I L Maciel
- Chemistry Institute, Federal University of Goiás, Goiânia, Goiás 74690-900, Brazil
| | | | - Yan Trindade
- Science and Technology Center, North Fluminense State University "Darcy Ribeiro", Macaé, Rio de Janeiro 27910-970, Brazil
| | - Georgiana F da Cruz
- Science and Technology Center, North Fluminense State University "Darcy Ribeiro", Macaé, Rio de Janeiro 27910-970, Brazil
| | | | - Iris M Júnior
- CENPES, PETROBRAS, Rio de Janeiro, Rio de Janeiro 21941-915, Brazil
| | - Gesiane da S Lima
- Chemistry Institute, Federal University of Goiás, Goiânia, Goiás 74690-900, Brazil
| | - Boniek G Vaz
- Chemistry Institute, Federal University of Goiás, Goiânia, Goiás 74690-900, Brazil
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Walton CL, Khalid M, Bible AN, Kertesz V, Retterer ST, Morrell-Falvey J, Cahill JF. In Situ Detection of Amino Acids from Bacterial Biofilms and Plant Root Exudates by Liquid Microjunction Surface-Sampling Probe Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1615-1625. [PMID: 35904879 DOI: 10.1021/jasms.2c00081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The plant rhizosphere is a complex and dynamic chemical environment where the exchange of molecular signals between plants, microbes, and fungi drives the development of the entire biological system. Exogenous compounds in the rhizosphere are known to affect plant-microbe organization, interactions between organisms, and ultimately, growth and survivability. The function of exogenous compounds in the rhizosphere is still under much investigation, specifically with respect to their roles in plant growth and development, the assembly of the associated microbial community, and the spatiotemporal distribution of molecular components. A major challenge for spatiotemporal measurements is developing a nondisruptive and nondestructive technique capable of analyzing the exogenous compounds contained within the environment. A methodology using liquid microjunction-surface sampling probe-mass spectrometry (LMJ-SSP-MS) and microfluidic devices with attached microporous membranes was developed for in situ, spatiotemporal measurement of amino acids (AAs) from bacterial biofilms and plant roots. Exuded arginine was measured from a living Pantoea YR343 biofilm, which resulted in a chemical image indicative of biofilm growth within the device. Spot sampling along the roots of Populus trichocarpa with the LMJ-SSP-MS resulted in the detection of 15 AAs. Variation in AA concentrations across the root system was observed, indicating that exudation is not homogeneous and may be linked to local rhizosphere architecture and different biological processes along the root.
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Affiliation(s)
- Courtney L Walton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Muneeba Khalid
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Amber N Bible
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Vilmos Kertesz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Scott T Retterer
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Jennifer Morrell-Falvey
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - John F Cahill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
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9
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Meng Y, Song X, Zare RN. Laser Ablation Electrospray Ionization Achieves 5 μm Resolution Using a Microlensed Fiber. Anal Chem 2022; 94:10278-10282. [PMID: 35797218 DOI: 10.1021/acs.analchem.2c01942] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A pulsed (10 Hz) infrared (IR) (1064 nm) laser is focused on a sample surface by means of a microlensed fiber. Analytes desorbed from the surface are captured by charged microdroplets before entering a mass spectrometer. By translating the sample surface, a chemical map is generated with a resolution of 5 μm, defined as the change from 20 to 80% of the analyte signal intensity. As a demonstration of the power of this new imaging technique, analytes from a parsnip root section are imaged and compared with that obtained from conventional laser ablation electrospray ionization mass spectrometry. The improvement in spatial resolution is about a factor of 20.
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Affiliation(s)
- Yifan Meng
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Xiaowei Song
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Richard N Zare
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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10
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te Brinke E, Arrizabalaga-Larrañaga A, Blokland MH. Insights of ion mobility spectrometry and its application on food safety and authenticity: A review. Anal Chim Acta 2022; 1222:340039. [DOI: 10.1016/j.aca.2022.340039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/01/2022]
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11
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Krejčí P, Cechová MZ, Nádvorníková J, Barták P, Kobrlová L, Balarynová J, Smýkal P, Bednář P. Combination of electronically driven micromanipulation with laser desorption ionization mass spectrometry – The unique tool for analysis of seed coat layers and revealing the mystery of seed dormancy. Talanta 2022; 242:123303. [DOI: 10.1016/j.talanta.2022.123303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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12
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Khoshravesh R, Hoffmann N, Hanson DT. Leaf microscopy applications in photosynthesis research: identifying the gaps. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1868-1893. [PMID: 34986250 DOI: 10.1093/jxb/erab548] [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: 08/23/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure-function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.
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Affiliation(s)
| | - Natalie Hoffmann
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - David T Hanson
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
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13
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Bartels B, Svatoš A. Influence of Ion Source Geometry on the Repeatability of Topographically Guided LAESI-MSI. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:265-272. [PMID: 35020389 PMCID: PMC8815068 DOI: 10.1021/jasms.1c00262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/07/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Spatially resolving the relative distribution of analyte molecules in biological matter holds great promise in the life sciences. Mass spectrometry imaging (MSI) is a technique that can provide such spatial resolution but remains underused in fields such as chemical ecology, as traditional MSI sample preparation is often chemically or morphologically invasive. Laser ablation electrospray ionization (LAESI)-MSI is a variation of MSI particularly well-suited for situations where chemical sample preparation is too invasive but provides new challenges related to the repeatability of measurement outcomes. We assess the repeatability of LAESI-MSI by sampling a droplet of [ring-13C6]l-phenylalanine with known concentration and expressing the resulting variability as a coefficient of variation, cv. In doing so, we entirely eliminate variability caused by surface morphology or underlying true sample gradients. We determine the limit of detection (LOD) for13C6-Phe by sampling from droplets with successively decreasing but known concentration. We assess the influence of source geometry on the LOD and repeatability by performing these experiments using four distinct variations of sources: one commercial and three custom-built ones. Finally, we extend our study to leaf and stem samples Arabidopsis thaliana and Gossypium hirsutum. We overcome the challenges of LAESI associated with three-dimensional surface morphology by relying on work previously published. Our measurements on both controlled standard and realistic samples give strong evidence that LAESI-MSI's repeatability in current implementations is insufficient for MSI in chemical ecology.
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14
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Moreno-Pedraza A, Garcia-Rojas NS, Winkler R. Analyzing the Distribution of Specialized Metabolites from Plant Native Tissues with Laser Desorption Low-Temperature Plasma Mass Spectrometry Imaging. Methods Mol Biol 2022; 2469:145-154. [PMID: 35508836 DOI: 10.1007/978-1-0716-2185-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The localization of metabolites in plant tissues is often related to their biological function and biosynthesis. Mass spectrometry imaging (MSI) provides comprehensive information about the distribution of known and unknown compounds in tissues. In this protocol, we describe the use of laser desorption low-temperature plasma (LD-LTP) ionization MSI. This technology enables the direct analysis of native tissues under ambient conditions.
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Affiliation(s)
- Abigail Moreno-Pedraza
- Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV), Irapuato, Gto, Mexico
| | - Nancy Shyrley Garcia-Rojas
- Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV), Irapuato, Gto, Mexico
| | - Robert Winkler
- Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV), Irapuato, Gto, Mexico.
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15
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Hieta JP, Sipari N, Räikkönen H, Keinänen M, Kostiainen R. Mass Spectrometry Imaging of Arabidopsis thaliana Leaves at the Single-Cell Level by Infrared Laser Ablation Atmospheric Pressure Photoionization (LAAPPI). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2895-2903. [PMID: 34738804 PMCID: PMC8640987 DOI: 10.1021/jasms.1c00295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In this study, we show that infrared laser ablation atmospheric pressure photoionization mass spectrometry (LAAPPI-MS) imaging with 70 μm lateral resolution allows for the analysis of Arabidopsis thaliana (A. thaliana) leaf substructures ranging from single-cell trichomes and the interveinal leaf lamina to primary, secondary, and tertiary veins. The method also showed its potential for depth profiling analysis for the first time by mapping analytes at the different depths of the leaf and spatially resolving the topmost trichomes and cuticular wax layer from the underlying tissues. Negative ion LAAPPI-MS detected many different flavonol glycosides, fatty acids, fatty acid esters, galactolipids, and glycosphingolipids, whose distributions varied significantly between the different substructures of A. thaliana leaves. The results show that LAAPPI-MS provides a highly promising new tool to study the role of metabolites in plants.
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Affiliation(s)
- Juha-Pekka Hieta
- Drug
Research Program and Division of Pharmaceutical Chemistry and Technology,
Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Helsinki 00014, Finland
| | - Nina Sipari
- Viikki
Metabolomics Unit, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, Helsinki 00014, Finland
| | - Heikki Räikkönen
- Drug
Research Program and Division of Pharmaceutical Chemistry and Technology,
Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Helsinki 00014, Finland
| | - Markku Keinänen
- Department
of Environmental and Biological Sciences, Institute of Photonics,
Faculty of Science and Forestry, University
of Eastern Finland, P.O. Box 111, Joensuu 80101, Finland
| | - Risto Kostiainen
- Drug
Research Program and Division of Pharmaceutical Chemistry and Technology,
Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Helsinki 00014, Finland
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16
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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. MASS SPECTROMETRY REVIEWS 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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17
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Schmidt MP, Mamet SD, Ferrieri RA, Peak D, Siciliano SD. From the Outside in: An Overview of Positron Imaging of Plant and Soil Processes. Mol Imaging 2020; 19:1536012120966405. [PMID: 33119419 PMCID: PMC7605056 DOI: 10.1177/1536012120966405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Positron-emitting nuclides have long been used as imaging agents in medical science to spatially trace processes non-invasively, allowing for real-time molecular imaging using low tracer concentrations. This ability to non-destructively visualize processes in real time also makes positron imaging uniquely suitable for probing various processes in plants and porous environmental media, such as soils and sediments. Here, we provide an overview of historical and current applications of positron imaging in environmental research. We highlight plant physiological research, where positron imaging has been used extensively to image dynamics of macronutrients, signalling molecules, trace elements, and contaminant metals under various conditions and perturbations. We describe how positron imaging is used in porous soils and sediments to visualize transport, flow, and microbial metabolic processes. We also address the interface between positron imaging and other imaging approaches, and present accompanying chemical analysis of labelled compounds for reviewed topics, highlighting the bridge between positron imaging and complementary techniques across scales. Finally, we discuss possible future applications of positron imaging and its potential as a nexus of interdisciplinary biogeochemical research.
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Affiliation(s)
- Michael P Schmidt
- Department of Soil Science, College of Agriculture and Bioresources, 7235University of Saskatchewan, Saskatoon, Canada
| | - Steven D Mamet
- Department of Soil Science, College of Agriculture and Bioresources, 7235University of Saskatchewan, Saskatoon, Canada
| | - Richard A Ferrieri
- Interdisciplinary Plant Group, Division of Plant Sciences, Department of Chemistry, Missouri Research Reactor Center, 14716University of Missouri, Columbia, MO, USA
| | - Derek Peak
- Department of Soil Science, College of Agriculture and Bioresources, 7235University of Saskatchewan, Saskatoon, Canada
| | - Steven D Siciliano
- Department of Soil Science, College of Agriculture and Bioresources, 7235University of Saskatchewan, Saskatoon, Canada
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18
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Crandall SG, Gold KM, Jiménez-Gasco MDM, Filgueiras CC, Willett DS. A multi-omics approach to solving problems in plant disease ecology. PLoS One 2020; 15:e0237975. [PMID: 32960892 PMCID: PMC7508392 DOI: 10.1371/journal.pone.0237975] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/04/2020] [Indexed: 12/11/2022] Open
Abstract
The swift rise of omics-approaches allows for investigating microbial diversity and plant-microbe interactions across diverse ecological communities and spatio-temporal scales. The environment, however, is rapidly changing. The introduction of invasive species and the effects of climate change have particular impact on emerging plant diseases and managing current epidemics. It is critical, therefore, to take a holistic approach to understand how and why pathogenesis occurs in order to effectively manage for diseases given the synergies of changing environmental conditions. A multi-omics approach allows for a detailed picture of plant-microbial interactions and can ultimately allow us to build predictive models for how microbes and plants will respond to stress under environmental change. This article is designed as a primer for those interested in integrating -omic approaches into their plant disease research. We review -omics technologies salient to pathology including metabolomics, genomics, metagenomics, volatilomics, and spectranomics, and present cases where multi-omics have been successfully used for plant disease ecology. We then discuss additional limitations and pitfalls to be wary of prior to conducting an integrated research project as well as provide information about promising future directions.
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Affiliation(s)
- Sharifa G. Crandall
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States of America
| | - Kaitlin M. Gold
- Plant Pathology & Plant Microbe Biology Section, Cornell AgriTech, Cornell University, Geneva, NY, United States of America
| | - María del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States of America
| | - Camila C. Filgueiras
- Applied Chemical Ecology Technology, Cornell AgriTech, Cornell University, Geneva, NY, United States of America
| | - Denis S. Willett
- Applied Chemical Ecology Technology, Cornell AgriTech, Cornell University, Geneva, NY, United States of America
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19
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Halouzka R, Zeljković SĆ, Klejdus B, Tarkowski P. Analytical methods in strigolactone research. PLANT METHODS 2020; 16:76. [PMID: 32514284 PMCID: PMC7257151 DOI: 10.1186/s13007-020-00616-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/15/2020] [Indexed: 05/02/2023]
Abstract
Strigolactones (SLs) are important plant hormones that are produced via the carotenoid biosynthetic pathway and occur at extremely low concentrations in various plant species. They regulate root development, play important roles in symbioses between higher plants and mycorrhizal fungi, and stimulate germination of plant-parasitic Orobanche and Striga species. Chemical analysis is central to research on the biochemistry of SLs and their roles in developmental biology and plant physiology. Here we summarize key issues relating to the identification and quantification of SLs isolated from plant tissues and exudates. The advantages and drawbacks of different protocols used for strigolactone analysis are discussed, and guidelines for selecting a procedure that will minimize losses during isolation and purification prior to final analysis are proposed. Hyphenated techniques suitable for SL analysis such as GC-MS and LC-MS/MS are also discussed, and newer ambient techniques such as HR-DART-MS and DESI-MS are highlighted as tools with considerable potential in SL research. A key advantage of these methods is that they require only simply sample preparation.
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Affiliation(s)
- Rostislav Halouzka
- Centre of Region Haná for Biotechnological and Agricultural Research, Department of Phytochemistry, Faculty of Science, Palacky University, Šlechtitelů 27, 78371 Olomouc, Czechia
| | - Sanja Ćavar Zeljković
- Centre of Region Haná for Biotechnological and Agricultural Research, Department of Phytochemistry, Faculty of Science, Palacky University, Šlechtitelů 27, 78371 Olomouc, Czechia
- Centre of Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Šlechtitelů 29, 78371 Olomouc, Czechia
| | - Bořivoj Klejdus
- Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czechia
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czechia
| | - Petr Tarkowski
- Centre of Region Haná for Biotechnological and Agricultural Research, Department of Phytochemistry, Faculty of Science, Palacky University, Šlechtitelů 27, 78371 Olomouc, Czechia
- Centre of Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Šlechtitelů 29, 78371 Olomouc, Czechia
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20
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Ram H, Gandass N, Sharma A, Singh A, Sonah H, Deshmukh R, Pandey AK, Sharma TR. Spatio-temporal distribution of micronutrients in rice grains and its regulation. Crit Rev Biotechnol 2020; 40:490-507. [DOI: 10.1080/07388551.2020.1742647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hasthi Ram
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Nishu Gandass
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Ankita Sharma
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Anmol Singh
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Humira Sonah
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Rupesh Deshmukh
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Ajay Kumar Pandey
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Tilak Raj Sharma
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
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21
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Open-Source Software Tools, Databases, and Resources for Single-Cell and Single-Cell-Type Metabolomics. Methods Mol Biol 2020; 2064:191-217. [PMID: 31565776 DOI: 10.1007/978-1-4939-9831-9_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this age of -omics data-guided big data revolution, metabolomics has received significant attention as compared to genomics, transcriptomics, and proteomics for its proximity to the phenotype, the promises it makes and the challenges it throws. Although metabolomes of entire organisms, organs, biofluids, and tissues are of immense interest, a cell-specific resolution is deemed critical for biomedical applications where a granular understanding of cellular metabolism at cell-type and subcellular resolution is desirable. Mass spectrometry (MS) is a versatile technique that is used to analyze a broad range of compounds from different species and cell-types, with high accuracy, resolution, sensitivity, selectivity, and fast data acquisition speeds. With recent advances in MS and spectroscopy-based platforms, the research community is able to generate high-throughput data sets from single cells. However, it is challenging to handle, store, process, analyze, and interpret data in a routine manner. In this treatise, I present a workflow of metabolomics data generation from single cells and single-cell types to their analysis, visualization, and interpretation for obtaining biological insights.
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22
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Pegiou E, Mumm R, Acharya P, de Vos RCH, Hall RD. Green and White Asparagus (Asparagus officinalis): A Source of Developmental, Chemical and Urinary Intrigue. Metabolites 2019; 10:E17. [PMID: 31881716 PMCID: PMC7022954 DOI: 10.3390/metabo10010017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/23/2022] Open
Abstract
Asparagus (Asparagus officinalis) is one of the world's top 20 vegetable crops. Both green and white shoots (spears) are produced; the latter being harvested before becoming exposed to light. The crop is grown in nearly all areas of the world, with the largest production regions being China, Western Europe, North America and Peru. Successful production demands high farmer input and specific environmental conditions and cultivation practices. Asparagus materials have also been used for centuries as herbal medicine. Despite this widespread cultivation and consumption, we still know relatively little about the biochemistry of this crop and how this relates to the nutritional, flavour, and neutra-pharmaceutical properties of the materials used. To date, no-one has directly compared the contrasting compositions of the green and white crops. In this short review, we have summarised most of the literature to illustrate the chemical richness of the crop and how this might relate to key quality parameters. Asparagus has excellent nutritional properties and its flavour/fragrance is attributed to a set of volatile components including pyrazines and sulphur-containing compounds. More detailed research, however, is needed and we propose that (untargeted) metabolomics should have a more prominent role to play in these investigations.
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Affiliation(s)
- Eirini Pegiou
- Laboratory of Plant Physiology, Wageningen University & Research, P.O. Box 16, 6700AA Wageningen, The Netherlands;
| | - Roland Mumm
- Business Unit Bioscience, Wageningen University & Research, P.O. Box 16, 6700AA Wageningen, The Netherlands; (R.M.); (R.C.H.d.V.)
| | - Parag Acharya
- Unilever Foods Innovation Centre, Bronland 14, 6708WH Wageningen, The Netherlands;
| | - Ric C. H. de Vos
- Business Unit Bioscience, Wageningen University & Research, P.O. Box 16, 6700AA Wageningen, The Netherlands; (R.M.); (R.C.H.d.V.)
| | - Robert D. Hall
- Laboratory of Plant Physiology, Wageningen University & Research, P.O. Box 16, 6700AA Wageningen, The Netherlands;
- Business Unit Bioscience, Wageningen University & Research, P.O. Box 16, 6700AA Wageningen, The Netherlands; (R.M.); (R.C.H.d.V.)
- Netherlands Metabolomics Centre, Einsteinweg 55, 2333CC Leiden, The Netherlands
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23
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Wang T, Cheng X, Xu H, Meng Y, Yin Z, Li X, Hang W. Perspective on Advances in Laser-Based High-Resolution Mass Spectrometry Imaging. Anal Chem 2019; 92:543-553. [DOI: 10.1021/acs.analchem.9b04067] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tongtong Wang
- Department of Chemistry, MOE Key Lab of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaoling Cheng
- Department of Chemistry, MOE Key Lab of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hexin Xu
- Department of Chemistry, MOE Key Lab of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yifan Meng
- Department of Chemistry, MOE Key Lab of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhibin Yin
- Department of Chemistry, MOE Key Lab of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaoping Li
- Department of Chemistry, MOE Key Lab of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wei Hang
- Department of Chemistry, MOE Key Lab of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
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24
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Applications of MicroArrays for Mass Spectrometry (MAMS) in Single-Cell Metabolomics. Methods Mol Biol 2019. [PMID: 31565767 DOI: 10.1007/978-1-4939-9831-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The metabolic network is the endpoint in the flow of information that begins with the "gene" and ends with "phenotype" (observable function) of the cell. Previously, due to the variety of metabolites analyzed inside cells, the metabolomic measurements were performed with samples including multiple cells. Unfortunately, this sampling process may mask important metabolic phenomena, such as cell-to-cell heterogeneity. For these studies, we must use analytical techniques that can robustly deliver reproducible results with single-cell sensitivity. In this chapter, we summarize laser-based methods for single-cell analysis and a novel approach of MicroArrays for Mass Spectrometry (or MAMS) is described in full detail. This particular type of microarrays was tailored for the study of cells grown in liquid medium using multiple-analytical read-outs, such as optical and laser desorption/ionization (LDI) or MALDI mass spectrometry.
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25
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Perez CJ, Bagga AK, Prova SS, Yousefi Taemeh M, Ifa DR. Review and perspectives on the applications of mass spectrometry imaging under ambient conditions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 3:27-53. [PMID: 29698560 DOI: 10.1002/rcm.8145] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/06/2018] [Accepted: 04/12/2018] [Indexed: 05/18/2023]
Abstract
Ambient mass spectrometry (AMS)-based techniques are performed under ambient conditions in which the ionization and desorption occur in the open environment allowing the direct analysis of molecules with minimal or no sample preparation. A selected group of AMS techniques demonstrate imaging capabilities that can provide information about the localization of molecules on complex sample surfaces such as biological tissues. 2D, 3D, and multimodal imaging have unlocked an array of applications to systematically address complex problems in many areas of research such as drug monitoring, natural products, forensics, and cancer diagnostics. In the present review, we summarize recent advances in the field with respect to the implementation of new ambient ionization techniques and current applications in the last 5 years. In more detail, we mainly focus on imaging applications in topics related to animal whole bodies and tissues, single cells, cancer diagnostics and biomarkers, microbial cultures and co-cultures, plant and natural product metabolomics, and forensic applications. 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)
- Consuelo J Perez
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Aafreen K Bagga
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Shamina S Prova
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Maryam Yousefi Taemeh
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Demian R Ifa
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
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26
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Pereira I, Banstola B, Wang K, Donnarumma F, Vaz BG, Murray KK. Matrix-Assisted Laser Desorption Ionization Imaging and Laser Ablation Sampling for Analysis of Fungicide Distribution in Apples. Anal Chem 2019; 91:6051-6056. [DOI: 10.1021/acs.analchem.9b00566] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Igor Pereira
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Chemistry Institute, Federal University of Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Bijay Banstola
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kelin Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Boniek G. Vaz
- Chemistry Institute, Federal University of Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Kermit K. Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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27
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Galiová MV, Száková J, Prokeš L, Čadková Z, Coufalík P, Kanický V, Otruba V, Tlustoš P. Variability of trace element distribution in Noccaea spp., Arabidopsis spp., and Thlaspi arvense leaves: the role of plant species and element accumulation ability. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:181. [PMID: 30798372 DOI: 10.1007/s10661-019-7331-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/15/2019] [Indexed: 06/09/2023]
Abstract
Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was applied for the determination of Cd and Zn distributions within the leaves of Cd- and Zn-hyperaccumulating plants, Noccaea caerulescens, N. praecox, and Arabidopsis halleri, in contrast to nonaccumulator species, Thlaspi arvense and A. thaliana. The elemental mapping of the selected leaf area was accomplished via line scans with a 110-μm-diameter laser beam at a 37-μm s-1 scan speed and repetition rate of 10 Hz. The lines were spaced 180 μm apart and ablated at an energy density of 2 J cm-2. The elemental imaging clearly confirmed that Cd was predominantly distributed within the parenchyma of the T. arvense, whereas in the Noccaea spp. and A. halleri, the highest intensity Cd signal was observed in the veins of the leaves. For Zn, higher intensities were observed in the veins for all the plant species except for A. thaliana. Close relationships between Zn and Ca were identified for the Noccaea spp. leaves. These relationships were not confirmed for A. halleri. Significant correlations were also proved between the Cd and Zn distribution in A. halleri, but not for the Noccaea spp. For both T. arvense and A. thaliana, no relevant significant relationship for the interpretation of the results was observed. Thus, the LA-ICP-MS imaging is proved as a relevant technique for the description and understanding of the elements in hyperaccumulating or highly accumulating plant species, although its sensitivity for the natural element contents in nonaccumulator plant species is still insufficient.
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Affiliation(s)
- Michaela Vašinová Galiová
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jiřina Száková
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Kamýcká 129, 165 21, Prague-Suchdol, Czech Republic.
| | - Lubomír Prokeš
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Zuzana Čadková
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Kamýcká 129, 165 21, Prague-Suchdol, Czech Republic
| | - Pavel Coufalík
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
- Institute of Analytical Chemistry, The Czech Academy of Sciences, v.v.i., Veveří 97, 602 00, Brno, Czech Republic
| | - Viktor Kanický
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Vítězslav Otruba
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Pavel Tlustoš
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Kamýcká 129, 165 21, Prague-Suchdol, Czech Republic
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Moreno-Pedraza A, Rosas-Román I, Garcia-Rojas NS, Guillén-Alonso H, Ovando-Vázquez C, Díaz-Ramírez D, Cuevas-Contreras J, Vergara F, Marsch-Martínez N, Molina-Torres J, Winkler R. Elucidating the Distribution of Plant Metabolites from Native Tissues with Laser Desorption Low-Temperature Plasma Mass Spectrometry Imaging. Anal Chem 2019; 91:2734-2743. [PMID: 30636413 DOI: 10.1021/acs.analchem.8b04406] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Secondary metabolites of plants have important biological functions, which often depend on their localization in tissues. Ideally, a fresh untreated material should be directly analyzed to obtain a realistic view of the true sample chemistry. Therefore, there is a large interest for ambient mass-spectrometry-based imaging (MSI) methods. Our aim was to simplify this technology and to find an optimal combination of desorption/ionization principles for a fast ambient MSI of macroscopic plant samples. We coupled a 405 nm continuous wave (CW) ultraviolet (UV) diode laser to a three-dimensionally (3D) printed low-temperature plasma (LTP) probe. By moving the sample with a RepRap-based sampling stage, we could perform imaging of samples up to 16 × 16 cm2. We demonstrate the system performance by mapping mescaline in a San Pedro cactus ( Echinopsis pachanoi) cross section, tropane alkaloids in jimsonweed ( Datura stramonium) fruits and seeds, and nicotine in tobacco ( Nicotiana tabacum) seedlings. In all cases, the anatomical regions of enriched compound concentrations were correctly depicted. The modular design of the laser desorption (LD)-LTP MSI platform, which is mainly assembled from commercial and 3D-printed components, facilitates its adoption by other research groups. The use of the CW-UV laser for desorption enables fast imaging measurements. A complete tobacco seedling with an image size of 9.2 × 15.0 mm2 was analyzed at a pixel size of 100 × 100 μm2 (14 043 mass scans), in less than 2 h. Natural products can be measured directly from native tissues, which inspires a broad use of LD-LTP MSI in plant chemistry studies.
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Affiliation(s)
- Abigail Moreno-Pedraza
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Ignacio Rosas-Román
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Nancy Shyrley Garcia-Rojas
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Héctor Guillén-Alonso
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Cesaré Ovando-Vázquez
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
- CONACYT Potosino Institute of Scientific and Technological Research, National Supercomputing Center , Camino a la Presa San José 2055 , Colonia Lomas 4ta Sección, 78216 San Luis Potosí , Mexico
| | - David Díaz-Ramírez
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Jessica Cuevas-Contreras
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Fredd Vergara
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig , Deutscher Platz 5e , 04103 Leipzig , Germany
| | - Nayelli Marsch-Martínez
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Jorge Molina-Torres
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Robert Winkler
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
- Mass Spectrometry Group , Max Planck Institute for Chemical Ecology , Beutenberg Campus, Hans-Knoell-Strasse 8 , 07745 Jena , Germany
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McVey PA, Alexander LE, Fu X, Xie B, Galayda KJ, Nikolau BJ, Houk RS. Light-Dependent Changes in the Spatial Localization of Metabolites in Solenostemon scutellarioides (Coleus Henna) Visualized by Matrix-Free Atmospheric Pressure Electrospray Laser Desorption Ionization Mass Spectrometry Imaging. FRONTIERS IN PLANT SCIENCE 2018; 9:1348. [PMID: 30283472 PMCID: PMC6156358 DOI: 10.3389/fpls.2018.01348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/27/2018] [Indexed: 05/05/2023]
Abstract
The visualization of foliage color in plants provides immediate insight into some of the compounds that exist in the leaf. However, many non-colored compounds are also present; their cellular distributions are not readily identifiable optically. In this study we evaluate the applicability of mass spectrometry imaging (MSI) via electrospray laser desorption ionization (ELDI) to reveal the spatial distribution of metabolites. ELDI-MSI is a matrix free, atmospheric pressure ionization method that utilizes a UV laser coupled with supplemental ionization by electrospray. We specifically applied ELDI-MSI to determine the spatial distribution of metabolites in Coleus Henna half leaves that were grown with half-sections either fully illuminated or shaded. We monitored dynamic changes in the spatial distribution of metabolites in response to the change of illumination every 7 days for a 28 day period. A novel source-sink relationship was observed between the 2 halves of the experimental leaf. Furthermore, Coleus Henna leaves present visually recognizable sectors associated with the differential accumulation of flavonoids. Thus, we correlated the effect of differential illumination and presence or absence of flavonoids with metabolic changes revealed by the accumulation of carbohydrates, amino acids, and organic acids. The results show the potential of ELDI-MSI to provide spatial information for a variety of plant metabolites with little sample preparation.
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Affiliation(s)
- Patrick A. McVey
- Department of Chemistry, Iowa State University, Ames, IA, United States
- Ames Laboratory-US DOE, Ames, IA, United States
| | - Liza E. Alexander
- Ames Laboratory-US DOE, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Xinyu Fu
- Ames Laboratory-US DOE, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Bo Xie
- Ames Laboratory-US DOE, Ames, IA, United States
| | - Katherine-Jo Galayda
- Department of Chemistry, Iowa State University, Ames, IA, United States
- Ames Laboratory-US DOE, Ames, IA, United States
| | - Basil J. Nikolau
- Ames Laboratory-US DOE, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Robert S. Houk
- Department of Chemistry, Iowa State University, Ames, IA, United States
- Ames Laboratory-US DOE, Ames, IA, United States
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30
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Parrot D, Papazian S, Foil D, Tasdemir D. Imaging the Unimaginable: Desorption Electrospray Ionization - Imaging Mass Spectrometry (DESI-IMS) in Natural Product Research. PLANTA MEDICA 2018; 84:584-593. [PMID: 29388184 PMCID: PMC6053038 DOI: 10.1055/s-0044-100188] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/15/2017] [Accepted: 12/27/2017] [Indexed: 05/06/2023]
Abstract
Imaging mass spectrometry (IMS) has recently established itself in the field of "spatial metabolomics." Merging the sensitivity and fast screening of high-throughput mass spectrometry with spatial and temporal chemical information, IMS visualizes the production, location, and distribution of metabolites in intact biological models. Since metabolite profiling and morphological features are combined in single images, IMS offers an unmatched chemical detail on complex biological and microbiological systems. Thus, IMS-type "spatial metabolomics" emerges as a powerful and complementary approach to genomics, transcriptomics, and classical metabolomics studies. In this review, we summarize the current state-of-the-art IMS methods with a strong focus on desorption electrospray ionization (DESI)-IMS. DESI-IMS utilizes the original principle of electrospray ionization, but in this case solvent droplets are rastered and desorbed directly on the sample surface. The rapid and minimally destructive DESI-IMS chemical screening is achieved at ambient conditions and enables the accurate view of molecules in tissues at the µm-scale resolution. DESI-IMS analysis does not require complex sample preparation and allows repeated measurements on samples from different biological sources, including microorganisms, plants, and animals. Thanks to its easy workflow and versatility, DESI-IMS has successfully been applied to many different research fields, such as clinical analysis, cancer research, environmental sciences, microbiology, chemical ecology, and drug discovery. Herein we discuss the present applications of DESI-IMS in natural product research.
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Affiliation(s)
- Delphine Parrot
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Stefano Papazian
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Daniel Foil
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
- Kiel University, Kiel, Germany
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31
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Spatially resolved chemical analysis of cicada wings using laser-ablation electrospray ionization (LAESI) imaging mass spectrometry (IMS). Anal Bioanal Chem 2018; 410:1911-1921. [DOI: 10.1007/s00216-018-0855-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/21/2017] [Accepted: 01/04/2018] [Indexed: 01/27/2023]
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32
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Laser Ablation Electrospray Ionization-Mass Spectrometry Imaging (LAESI-MS) for Spatially Resolved Plant Metabolomics. Methods Mol Biol 2018; 1778:253-267. [PMID: 29761444 DOI: 10.1007/978-1-4939-7819-9_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is increasing demand to bring the level of metabolomics analyses down to the tissue or cell level. Significant progress has been made involving the use of in situ metabolomics imaging techniques where no tissue collection or extraction is needed prior to analysis. In this chapter we describe a relatively new method which is simple and easy to use. No ectopic matrix or vacuum is required, and analyses are performed with living plant materials directly from (or even still attached to) the plant. Although relatively straightforward, there are still a few caveats as regards this method which are described at the end of the chapter.
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33
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Montes A, Bisson MA, Gardella JA, Aga DS. Uptake and transformations of engineered nanomaterials: Critical responses observed in terrestrial plants and the model plant Arabidopsis thaliana. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:1497-1516. [PMID: 28793406 DOI: 10.1016/j.scitotenv.2017.06.190] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 05/12/2023]
Abstract
With the applications of engineered nanomaterials (ENMs) continually expanding and production quickly growing, residues of ENMs will end up in the environment at levels that may be harmful to non-target organisms. Many of the tunable properties that have made them desirable, such as type, size, charge, or coating, also contribute to the current difficulties in understanding the fate of ENMs in the environment. This review article focuses on studies that investigate plant-ENM interactions, including techniques used to study these interactions and documented plant responses due to the phytotoxic effects of ENMs. The many variables which can be altered for an experiment, such as type, size, and concentration of ENMs, make it difficult to formulate generalizations about the uptake mechanism involved, or to make an inference on the subcellular localization and distribution of the internalized ENMs in plant tissue. In order to avoid these challenges, studies can utilize a model organism such as Arabidopsis thaliana, and a combination of analytical techniques that can reveal complementary information in order to assess how the different experimental conditions influence the uptake and phytotoxicity of ENMs. This review presents recent studies regarding plant-ENM interactions employing Arabidopsis to demonstrate how the use of this model plant can advance our understanding of plant-ENM interactions and guide additional studies using other plant species. Overarching results suggest that more sensitive tests and consistency in experimental designs are needed to fully assess and understand the phytotoxic effects of ENMs in the environment.
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Affiliation(s)
- Angelina Montes
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY, United States
| | - Mary A Bisson
- Department of Biological Sciences, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY, United States
| | - Joseph A Gardella
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY, United States
| | - Diana S Aga
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY, United States.
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34
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Abstract
Since the introduction of desorption electrospray ionization (DESI) mass spectrometry (MS), ambient MS methods have seen increased use in a variety of fields from health to food science. Increasing its popularity in metabolomics, ambient MS offers limited sample preparation, rapid and direct analysis of liquids, solids, and gases, in situ and in vivo analysis, and imaging. The metabolome consists of a constantly changing collection of small (<1.5 kDa) molecules. These include endogenous molecules that are part of primary metabolism pathways, secondary metabolites with specific functions such as signaling, chemicals incorporated in the diet or resulting from environmental exposures, and metabolites associated with the microbiome. Characterization of the responsive changes of this molecule cohort is the principal goal of any metabolomics study. With adjustments to experimental parameters, metabolites with a range of chemical and physical properties can be selectively desorbed and ionized and subsequently analyzed with increased speed and sensitivity. This review covers the broad applications of a variety of ambient MS techniques in four primary fields in which metabolomics is commonly employed.
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Affiliation(s)
- Chaevien S. Clendinen
- School of Chemistry and Biochemistry & Petit Institute for Bioengineering & Bioscience (IBB), Georgia Institute of Technology, 901 Atlantic Drive NW. Atlanta, GA
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad de Buenos Aires, Argentina
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry & Petit Institute for Bioengineering & Bioscience (IBB), Georgia Institute of Technology, 901 Atlantic Drive NW. Atlanta, GA
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35
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Marciniak CD, Ball HB, Hung ATH, Biercuk MJ. Towards fully commercial, UV-compatible fiber patch cords. OPTICS EXPRESS 2017; 25:15643-15661. [PMID: 28789079 DOI: 10.1364/oe.25.015643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
We present and analyze two pathways to produce commercial optical-fiber patch cords with stable long-term transmission in the ultraviolet (UV) at powers up to ~ 200 mW, and typical bulk transmission between 66-75 %. Commercial fiber patch cords in the UV are of great interest across a wide variety of scientific applications ranging from biology to metrology, and the lack of availability has yet to be suitably addressed. We provide a guide to producing such solarization-resistant, hydrogen-passivated, polarization-maintaining, connectorized and jacketed optical fibers compatible with demanding scientific and industrial applications. Our presentation describes the fabrication and hydrogen loading procedure in detail and presents a high-pressure vessel design, calculations of required H2 loading times, and information on patch cord handling and the mitigation of bending sensitivities. Transmission at 313 nm is measured over many months for cumulative energy on the fiber output of > 10 kJ with no demonstrable degradation due to UV solarization, in contrast to standard uncured fibers. Polarization sensitivity and stability are characterized yielding polarization extinction ratios between 15 dB and 25 dB at 313 nm, where we find patch cords become linearly polarizing. We observe that particle deposition at the fiber facet induced by high-intensity UV exposure can (reversibly) deteriorate patch cord performance and describe a technique for nitrogen purging of fiber collimators which mitigates this phenomenon.
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36
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Zhang H, Jiang J, Li N, Li M, Wang Y, He J, You H. Surface Desorption Dielectric-Barrier Discharge Ionization Mass Spectrometry. Anal Chem 2017. [DOI: 10.1021/acs.analchem.7b00323] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hong Zhang
- State
Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, People’s Republic of China
- School
of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150090, People’s Republic of China
| | - Jie Jiang
- School
of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, People’s Republic of China
| | - Na Li
- School
of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, People’s Republic of China
| | - Ming Li
- Division
of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, People’s Republic of China
| | - Yingying Wang
- School
of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, People’s Republic of China
| | - Jing He
- School
of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, People’s Republic of China
| | - Hong You
- School
of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, People’s Republic of China
- State
Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, People’s Republic of China
- School
of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150090, People’s Republic of China
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Crecelius AC, Michalzik B, Potthast K, Meyer S, Schubert US. Tracing the fate and transport of secondary plant metabolites in a laboratory mesocosm experiment by employing mass spectrometric imaging. Anal Bioanal Chem 2017; 409:3807-3820. [PMID: 28357483 PMCID: PMC5427159 DOI: 10.1007/s00216-017-0325-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/28/2017] [Accepted: 03/16/2017] [Indexed: 01/06/2023]
Abstract
Mass spectrometric imaging (MSI) has received considerable attention in recent years, since it allows the molecular mapping of various compound classes, such as proteins, peptides, glycans, secondary metabolites, lipids, and drugs in animal, human, or plant tissue sections. In the present study, the application of laser-based MSI analysis of secondary plant metabolites to monitor their transport from the grass leaves of Dactylis glomerata, over the crop of the grasshopper Chorthippus dorsatus to its excrements, and finally in the soil solution is described. This plant-herbivore-soil pathway was investigated under controlled conditions by using laboratory mesocosms. From six targeted secondary plant metabolites (dehydroquinic acid, quinic acid, apigenin, luteolin, tricin, and rosmarinic acid), only quinic acid, and dehydroquinic acid, an in-source-decay (ISD) product of quinic acid, could be traced in nearly all compartments. The tentative identification of secondary plant metabolites was performed by MS/MS analysis of methanol extracts prepared from the investigated compartments, in both the positive and negative ion mode, and subsequently compared with the results generated from the reference standards. Except for tricin, all secondary metabolites could be tentatively identified by this approach. Additional liquid-chromatography mass spectrometry (LC-MS) experiments were carried out to verify the MSI results and revealed the presence of quinic acid only in grass and chewed grass, whereas apigenin-hexoside-pentoside and luteolin-hexoisde-pentoside could be traced in the grasshopper body and excrement extracts. In summary, the MSI technique shows a trade-off between sensitivity and spatial resolution. Graphical abstract Monitoring quinic acid in a mesocosm experiment by mass spectrometric imaging (MSI).
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Affiliation(s)
- Anna C Crecelius
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743, Jena, Germany.
- Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743, Jena, Germany.
| | - Beate Michalzik
- Institute of Geography, Friedrich Schiller University Jena, Löbdergraben 32, 07743, Jena, Germany
| | - Karin Potthast
- Institute of Geography, Friedrich Schiller University Jena, Löbdergraben 32, 07743, Jena, Germany
| | - Stefanie Meyer
- Institute of Geography, Friedrich Schiller University Jena, Löbdergraben 32, 07743, Jena, Germany
| | - Ulrich S Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstrasse 10, 07743, Jena, Germany
- Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743, Jena, Germany
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Sánchez MIG, McCullagh J, Guy RH, Compton RG. Reverse Iontophoretic Extraction of Metabolites from Living Plants and their Identification by Ion-chromatography Coupled to High Resolution Mass Spectrometry. PHYTOCHEMICAL ANALYSIS : PCA 2017; 28:195-201. [PMID: 28029194 DOI: 10.1002/pca.2660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/14/2016] [Accepted: 10/09/2016] [Indexed: 06/06/2023]
Abstract
INTRODUCTION The identification and characterisation of cellular metabolites has now become an important strategy to obtain insight into functional plant biology. However, the extraction of metabolites for identification and analysis is challenging and, at the present time, usually requires destruction of the plant. OBJECTIVE To detect different plant metabolites in living plants with no pre-treatment using the combination of iontophoresis and ion-chromatography with mass spectrometry detection. METHODOLOGY In this work, the simple and non-destructive method of reverse iontophoresis has been used to extract in situ multiple plant metabolites from intact Ocimum basilicum leaves. Subsequently, the analysis of these metabolites has been performed with ion chromatography coupled directly to high resolution mass spectrometric detection (IC-MS). RESULTS The application of reverse iontophoresis to living plant samples has avoided the need for complex pre-treatments. With this approach, no less than 24 compounds, including organic acids and sugars as well as adenosine triphosphate (ATP) were successfully detected. CONCLUSION The research demonstrates that it is feasible to monitor, therefore, a number of important plant metabolites using a simple, relatively fast and non-destructive approach. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Maria Isabel González Sánchez
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, UK
- Department of Physical Chemistry, Castilla-La Mancha University, 02071, Albacete, Spain
| | - James McCullagh
- Mass Spectrometry Research Facility CRL, Department of Chemistry, Oxford University, Mansfield Road, Oxford, UK
| | - Richard H Guy
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, UK
- Department of Pharmacy and Pharmacology, University of Bath, Bath, BA2 7AY, UK
| | - Richard G Compton
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, UK
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39
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Meher AK, Chen YC. Electrospray Modifications for Advancing Mass Spectrometric Analysis. ACTA ACUST UNITED AC 2017; 6:S0057. [PMID: 28573082 DOI: 10.5702/massspectrometry.s0057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/30/2016] [Indexed: 11/23/2022]
Abstract
Generation of analyte ions in gas phase is a primary requirement for mass spectrometric analysis. One of the ionization techniques that can be used to generate gas phase ions is electrospray ionization (ESI). ESI is a soft ionization method that can be used to analyze analytes ranging from small organics to large biomolecules. Numerous ionization techniques derived from ESI have been reported in the past two decades. These ion sources are aimed to achieve simplicity and ease of operation. Many of these ionization methods allow the flexibility for elimination or minimization of sample preparation steps prior to mass spectrometric analysis. Such ion sources have opened up new possibilities for taking scientific challenges, which might be limited by the conventional ESI technique. Thus, the number of ESI variants continues to increase. This review provides an overview of ionization techniques based on the use of electrospray reported in recent years. Also, a brief discussion on the instrumentation, underlying processes, and selected applications is also presented.
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Affiliation(s)
| | - Yu-Chie Chen
- Department of Applied Chemistry, National Chiao Tung University
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40
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Bartels B, Kulkarni P, Danz N, Böcker S, Saluz HP, Svatoš A. Mapping metabolites from rough terrain: laser ablation electrospray ionization on non-flat samples. RSC Adv 2017. [DOI: 10.1039/c6ra26854d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A laser ablation electrospray ionization (LAESI) source was custom-built to accommodate the topography of non-flat sample surfaces. Reproducible ablation mark diameters of 69 ± 7 μm in average have been achieved.
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Affiliation(s)
- Benjamin Bartels
- Research Group Mass Spectrometry/Proteomics
- Max Planck Institute for Chemical Ecology
- Jena
- Germany
| | - Purva Kulkarni
- Research Group Mass Spectrometry/Proteomics
- Max Planck Institute for Chemical Ecology
- Jena
- Germany
- Chair for Bioinformatics
| | - Norbert Danz
- Fraunhofer Institute for Applied Optics and Precision Engineering IOF
- D-07745 Jena
- Germany
| | - Sebastian Böcker
- Chair for Bioinformatics
- Friedrich Schiller University Jena
- Jena
- Germany
| | - Hans Peter Saluz
- Department Cell and Molecular Biology
- Leibniz Institute for Natural Product Research and Infection Biology
- Jena
- Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics
- Max Planck Institute for Chemical Ecology
- Jena
- Germany
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41
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Peukert M, Lim WL, Seiffert U, Matros A. Mass Spectrometry Imaging of Metabolites in Barley Grain Tissues. ACTA ACUST UNITED AC 2016; 1:574-591. [DOI: 10.1002/cppb.20037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Manuela Peukert
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Cologne Germany
| | - Wai Li Lim
- Australian Research Council Centre of Excellence in Plant Cell Walls (ARC CoE), University of Adelaide; Urrbrae Australia
| | - Udo Seiffert
- Biosystems Engineering, Fraunhofer Institute for Factory Operation and Automation IFF; Magdeburg Germany
| | - Andrea Matros
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Applied Biochemistry Group; Gatersleben Germany
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42
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Dong Y, Li B, Aharoni A. More than Pictures: When MS Imaging Meets Histology. TRENDS IN PLANT SCIENCE 2016; 21:686-698. [PMID: 27155743 DOI: 10.1016/j.tplants.2016.04.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/29/2016] [Accepted: 04/07/2016] [Indexed: 05/28/2023]
Abstract
Attaining high-resolution spatial information is a recurrent challenge in biological research, particularly in the case of small-molecule distribution. Mass spectrometry imaging (MSI) is an innovative molecular histology technique that could provide such information. It allows in situ and label-free measurement of both the abundance and distribution of a variety of molecules at the tissue or single cell level. The application of MSI in plant research has received considerable attention; thus, in this review, we describe the current state of MSI in plants. In particular, we present an overview of MSI approaches, highlight the recent technical and methodological developments, and discuss a range of applications contributing to the field of plant science.
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Affiliation(s)
- Yonghui Dong
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Bin Li
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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43
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Hong J, Yang L, Zhang D, Shi J. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science. Int J Mol Sci 2016; 17:ijms17060767. [PMID: 27258266 PMCID: PMC4926328 DOI: 10.3390/ijms17060767] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022] Open
Abstract
As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.
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Affiliation(s)
- Jun Hong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Litao Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- Plant Genomics Center, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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44
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Pittenauer E, Rados E, Koulakiotis NS, Tsarbopoulos A, Allmaier G. Processed stigmas of Crocus sativus
L. imaged by MALDI-based MS. Proteomics 2016; 16:1726-30. [DOI: 10.1002/pmic.201500534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/11/2016] [Accepted: 03/15/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Ernst Pittenauer
- Institute of Chemical Technologies and Analytics; Vienna University of Technologies; Vienna Austria
| | - Edita Rados
- Institute of Chemical Technologies and Analytics; Vienna University of Technologies; Vienna Austria
| | | | - Anthony Tsarbopoulos
- Department of Pharmacology, Medical School; National and Kapodistrian University of Athens; Athens Greece
| | - Günter Allmaier
- Institute of Chemical Technologies and Analytics; Vienna University of Technologies; Vienna Austria
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45
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Timms JF, Hale OJ, Cramer R. Advances in mass spectrometry-based cancer research and analysis: from cancer proteomics to clinical diagnostics. Expert Rev Proteomics 2016; 13:593-607. [DOI: 10.1080/14789450.2016.1182431] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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46
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Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4182071. [PMID: 27088086 PMCID: PMC4818802 DOI: 10.1155/2016/4182071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/18/2016] [Accepted: 02/28/2016] [Indexed: 11/17/2022]
Abstract
The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. In this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses.
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van Dam NM, Bouwmeester HJ. Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication. TRENDS IN PLANT SCIENCE 2016; 21:256-265. [PMID: 26832948 DOI: 10.1016/j.tplants.2016.01.008] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/18/2015] [Accepted: 01/06/2016] [Indexed: 05/19/2023]
Abstract
The rhizosphere is densely populated with a variety of organisms. Interactions between roots and rhizosphere community members are mostly achieved via chemical communication. Root exudates contain an array of primary and secondary plant metabolites that can attract, deter, or kill belowground insect herbivores, nematodes, and microbes, and inhibit competing plants. Metabolomics of root exudates can potentially help us to better understand this chemical dialogue. The main limitations are the proper sampling of the exudate, the sensitivity of the metabolomics platforms, and the multivariate data analysis to identify causal relations. Novel technologies may help to generate a spatially explicit metabolome of the root and its exudates at a scale that is relevant for the rhizosphere community.
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Affiliation(s)
- Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany; Institute of Ecology, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany; Molecular Interaction Ecology, Institute of Water and Wetland Research (IWWR), Radboud University, PO Box 9010, Nijmegen, GL 6500, The Netherlands.
| | - Harro J Bouwmeester
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, PB 6708, The Netherlands.
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48
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Sanchez-Lucas R, Mehta A, Valledor L, Cabello-Hurtado F, Romero-Rodrıguez MC, Simova-Stoilova L, Demir S, Rodriguez-de-Francisco LE, Maldonado-Alconada AM, Jorrin-Prieto AL, Jorrín-Novo JV. A year (2014-2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists. Proteomics 2016; 16:866-76. [PMID: 26621614 DOI: 10.1002/pmic.201500351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 12/23/2022]
Abstract
The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.
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Affiliation(s)
- Rosa Sanchez-Lucas
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brasília, DF, Brazil
| | - Luis Valledor
- Department of Biology of Organisms and Systems (BOS), University of Oviedo, Oviedo, Spain
| | | | - M Cristina Romero-Rodrıguez
- Centro Multidisciplinario de Investigaciones Tecnológicas, and Departamento de Fitoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Sekvan Demir
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Luis E Rodriguez-de-Francisco
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain.,INTEC-Sto. Domingo, Santo Domingo, República Dominicana
| | - Ana M Maldonado-Alconada
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Ana L Jorrin-Prieto
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
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49
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de Raad M, Fischer CR, Northen TR. High-throughput platforms for metabolomics. Curr Opin Chem Biol 2015; 30:7-13. [PMID: 26544850 DOI: 10.1016/j.cbpa.2015.10.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 10/11/2015] [Indexed: 01/06/2023]
Abstract
Mass spectrometry has become a choice method for broad-spectrum metabolite analysis in both fundamental and applied research. This can range from comprehensive analysis achieved through time-consuming chromatography to the rapid analysis of a few target metabolites without chromatography. In this review article, we highlight current high-throughput MS-based platforms and their potential application in metabolomics. Although current MS platforms can reach throughputs up to 0.5 seconds per sample, the metabolite coverage of these platforms are low compared to low-throughput, separation-based MS methods. High-throughput comes at a cost, as it's a trade-off between sample throughput and metabolite coverage. As we will discuss, promising emerging technologies, including microfluidics and miniaturization of separation techniques, have the potential to achieve both rapid and more comprehensive metabolite analysis.
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Affiliation(s)
- Markus de Raad
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States
| | - Curt R Fischer
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States
| | - Trent R Northen
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States.
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