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Berrell N, Sadeghirad H, Blick T, Bidgood C, Leggatt GR, O'Byrne K, Kulasinghe A. Metabolomics at the tumor microenvironment interface: Decoding cellular conversations. Med Res Rev 2024; 44:1121-1146. [PMID: 38146814 DOI: 10.1002/med.22010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/08/2023] [Accepted: 12/07/2023] [Indexed: 12/27/2023]
Abstract
Cancer heterogeneity remains a significant challenge for effective cancer treatments. Altered energetics is one of the hallmarks of cancer and influences tumor growth and drug resistance. Studies have shown that heterogeneity exists within the metabolic profile of tumors, and personalized-combination therapy with relevant metabolic interventions could improve patient response. Metabolomic studies are identifying novel biomarkers and therapeutic targets that have improved treatment response. The spatial location of elements in the tumor microenvironment are becoming increasingly important for understanding disease progression. The evolution of spatial metabolomics analysis now allows scientists to deeply understand how metabolite distribution contributes to cancer biology. Recently, these techniques have spatially resolved metabolite distribution to a subcellular level. It has been proposed that metabolite mapping could improve patient outcomes by improving precision medicine, enabling earlier diagnosis and intraoperatively identifying tumor margins. This review will discuss how altered metabolic pathways contribute to cancer progression and drug resistance and will explore the current capabilities of spatial metabolomics technologies and how these could be integrated into clinical practice to improve patient outcomes.
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Affiliation(s)
- Naomi Berrell
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Habib Sadeghirad
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Tony Blick
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Charles Bidgood
- APCRC-Q, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Graham R Leggatt
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Ken O'Byrne
- Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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Wittek O, Jahreis B, Römpp A. MALDI MS Imaging of Chickpea Seeds ( Cicer arietinum) and Crab's Eye Vine ( Abrus precatorius) after Tryptic Digestion Allows Spatially Resolved Identification of Plant Proteins. Anal Chem 2023; 95:14972-14980. [PMID: 37749896 PMCID: PMC10568532 DOI: 10.1021/acs.analchem.3c02428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) imaging following in situ enzymatic digestion is a versatile analytical method for the untargeted investigation of protein distributions, which has rarely been used for plants so far. The present study describes a workflow for in situ tryptic digestion of plant seed tissue for MALDI MS imaging. Substantial modifications to the sample preparation procedure for mammalian tissues were necessary to cater to the specific properties of plant materials. For the first time, distributions of tryptic peptides were successfully visualized in plant tissue using MS imaging with accurate mass detection. Sixteen proteins were visualized and identified in chickpea seeds showing different distribution patterns, e.g., in the cotyledons, radicle, or testa. All tryptic peptides were detected with a mass resolution higher than 60,000 as well as a mass accuracy better than 1.5 ppm root-mean-square error and were matched to results from complementary liquid chromatography-MS/MS (LC-MS/MS) data. The developed method was also applied to crab's eye vine seeds for targeted MS imaging of the toxic protein abrin, showing the presence of abrin-a in all compartments. Abrin (59 kDa), as well as the majority of proteins visualized in chickpeas, was larger than 50 kDa and would thus not be readily accessible by top-down MS imaging. Since antibodies for plant proteins are often not readily available, in situ digestion MS imaging provides unique information, as it makes the distribution and identification of larger proteins in plant tissues accessible in an untargeted manner. This opens up new possibilities in the field of plant science as well as to assess the nutritional quality and/or safety of crops.
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Affiliation(s)
| | - Bastian Jahreis
- Bioanalytical Sciences and
Food Analysis, University of Bayreuth, Universitaetsstrasse 30, D-95447 Bayreuth, Germany
| | - Andreas Römpp
- Bioanalytical Sciences and
Food Analysis, University of Bayreuth, Universitaetsstrasse 30, D-95447 Bayreuth, Germany
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3
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Impacts of Binary Oxide Nanoparticles on the Soybean Plant and Its Rhizosphere, Associated Phytohormones, and Enzymes. Molecules 2023; 28:molecules28031326. [PMID: 36770994 PMCID: PMC9919940 DOI: 10.3390/molecules28031326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
The utilization of binary oxide nanoparticles is geometrically increasing due to their numerous applications. Their intentional or accidental release after usage has led to their omnipresence in the environment. The usage of sludge or fertilizer containing binary oxide nanoparticles is likely to increase the chance of the plants being exposed to these binary oxide nanoparticles. The aim of the present review is to assess the detailed positive and negative impacts of these oxide nanoparticles on the soybean plants and its rhizosphere. In this study, methods of synthesizing binary oxide nanoparticles, as well as the merits and demerits of these methods, are discussed. Furthermore, various methods of characterizing the binary oxide nanoparticles in the tissues of soybean are highlighted. These characterization techniques help to track the nanoparticles inside the soybean plant. In addition, the assessment of rhizosphere microbial communities of soybean that have been exposed to these binary oxide nanoparticles is discussed. The impacts of binary oxide nanoparticles on the leaf, stem, root, seeds, and rhizosphere of soybean plant are comprehensively discussed. The impacts of binary oxides on the bioactive compounds such as phytohormones are also highlighted. Overall, it was observed that the impacts of the oxide nanoparticles on the soybean, rhizosphere, and bioactive compounds were dose-dependent. Lastly, the way forward on research involving the interactions of binary oxide nanoparticles and soybean plants is suggested.
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Maia M, McCann A, Malherbe C, Far J, Cunha J, Eiras-Dias J, Cordeiro C, Eppe G, Quinton L, Figueiredo A, De Pauw E, Sousa Silva M. Grapevine leaf MALDI-MS imaging reveals the localisation of a putatively identified sucrose metabolite associated to Plasmopara viticola development. FRONTIERS IN PLANT SCIENCE 2022; 13:1012636. [PMID: 36299787 PMCID: PMC9589281 DOI: 10.3389/fpls.2022.1012636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Despite well-established pathways and metabolites involved in grapevine-Plasmopara viticola interaction, information on the molecules involved in the first moments of pathogen contact with the leaf surface and their specific location is still missing. To understand and localise these molecules, we analysed grapevine leaf discs infected with P. viticola with MSI. Plant material preparation was optimised, and different matrices and solvents were tested. Our data shows that trichomes hamper matrix deposition and the ion signal. Results show that putatively identified sucrose presents a higher accumulation and a non-homogeneous distribution in the infected leaf discs in comparison with the controls. This accumulation was mainly on the veins, leading to the hypothesis that sucrose metabolism is being manipulated by the development structures of P. viticola. Up to our knowledge this is the first time that the localisation of a putatively identified sucrose metabolite was shown to be associated to P. viticola infection sites.
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Affiliation(s)
- Marisa Maia
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
- Grapevine Pathogen Systems Lab (GPS Lab), Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Andréa McCann
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Cédric Malherbe
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Jorge Cunha
- Estação Vitivinícola Nacional, Instituto Nacional de Investigação Agrária e Veterinária (INIAV), Torres-Vedras, Portugal
| | - José Eiras-Dias
- Estação Vitivinícola Nacional, Instituto Nacional de Investigação Agrária e Veterinária (INIAV), Torres-Vedras, Portugal
| | - Carlos Cordeiro
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Gauthier Eppe
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Andreia Figueiredo
- Grapevine Pathogen Systems Lab (GPS Lab), Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Edwin De Pauw
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Marta Sousa Silva
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
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Tiquet M, La Rocca R, Kirnbauer S, Zoratto S, Van Kruining D, Quinton L, Eppe G, Martinez-Martinez P, Marchetti-Deschmann M, De Pauw E, Far J. FT-ICR Mass Spectrometry Imaging at Extreme Mass Resolving Power Using a Dynamically Harmonized ICR Cell with 1ω or 2ω Detection. Anal Chem 2022; 94:9316-9326. [PMID: 35604839 PMCID: PMC9260710 DOI: 10.1021/acs.analchem.2c00754] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
MALDI mass spectrometry
imaging (MALDI MSI) is a powerful analytical
method for achieving 2D localization of compounds from thin sections
of typically but not exclusively biological samples. The dynamically
harmonized ICR cell (ParaCell) was recently introduced to achieve
extreme spectral resolution capable of providing the isotopic fine
structure of ions detected in complex samples. The latest improvement
in the ICR technology also includes 2ω detection, which significantly
reduces the transient time while preserving the nominal mass resolving
power of the ICR cell. High-resolution MS images acquired on FT-ICR
instruments equipped with 7T and 9.4T superconducting magnets and
the dynamically harmonized ICR cell operating at suboptimal parameters
suffered severely from the pixel-to-pixel shifting of m/z peaks due to space-charge effects. The resulting
profile average mass spectra have depreciated mass measurement accuracy
and mass resolving power under the instrument specifications that
affect the confidence level of the identified ions. Here, we propose
an analytical workflow based on the monitoring of the total ion current
to restrain the pixel-to-pixel m/z shift. Adjustment of the laser parameters is proposed to maintain
high spectral resolution and mass accuracy measurement within the
instrument specifications during MSI analyses. The optimized method
has been successfully employed in replicates to perform high-quality
MALDI MS images at resolving power (FWHM) above 1,000,000 in the lipid
mass range across the whole image for superconducting magnets of 7T
and 9.4T using 1 and 2ω detection. Our data also compare favorably
with MALDI MSI experiments performed on higher-magnetic-field superconducting
magnets, including the 21T MALDI FT-ICR prototype instrument of the
NHMFL group at Tallahassee, Florida.
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Affiliation(s)
- Mathieu Tiquet
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Allée de la Chimie 6-Quartier Agora, 4000 Liège, Belgium
| | - Raphaël La Rocca
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Allée de la Chimie 6-Quartier Agora, 4000 Liège, Belgium
| | - Stefan Kirnbauer
- Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), Getreidemarkt 9/164, 1060 Vienna, Austria.,Austrian Cluster for Tissue Regeneration, TU Wien (Vienna University of Technology), Getreidemarkt 9/164, 1060 Vienna, Austria
| | - Samuele Zoratto
- Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), Getreidemarkt 9/164, 1060 Vienna, Austria.,Austrian Cluster for Tissue Regeneration, TU Wien (Vienna University of Technology), Getreidemarkt 9/164, 1060 Vienna, Austria.,Christian Doppler Laboratory for Skin Multimodal Imaging of Aging and Senescence, TU Wien (Vienna University of Technology), Getreidemarkt 9/164, 1060 Vienna, Austria
| | - Daan Van Kruining
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229ER Maastricht, the Netherlands
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Allée de la Chimie 6-Quartier Agora, 4000 Liège, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Allée de la Chimie 6-Quartier Agora, 4000 Liège, Belgium
| | - Pilar Martinez-Martinez
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229ER Maastricht, the Netherlands
| | - Martina Marchetti-Deschmann
- Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), Getreidemarkt 9/164, 1060 Vienna, Austria.,Austrian Cluster for Tissue Regeneration, TU Wien (Vienna University of Technology), Getreidemarkt 9/164, 1060 Vienna, Austria.,Christian Doppler Laboratory for Skin Multimodal Imaging of Aging and Senescence, TU Wien (Vienna University of Technology), Getreidemarkt 9/164, 1060 Vienna, Austria
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Allée de la Chimie 6-Quartier Agora, 4000 Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Allée de la Chimie 6-Quartier Agora, 4000 Liège, Belgium
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Jiang H, Zhang Y, Liu Z, Wang X, He J, Jin H. Advanced applications of mass spectrometry imaging technology in quality control and safety assessments of traditional Chinese medicines. JOURNAL OF ETHNOPHARMACOLOGY 2022; 284:114760. [PMID: 34678417 PMCID: PMC9715987 DOI: 10.1016/j.jep.2021.114760] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 05/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Traditional Chinese medicines (TCMs) have made great contributions to the prevention and treatment of human diseases in China, and especially in cases of COVID-19. However, due to quality problems, the lack of standards, and the diversity of dosage forms, adverse reactions to TCMs often occur. Moreover, the composition of TCMs makes them extremely challenging to extract and isolate, complicating studies of toxicity mechanisms. AIM OF THE REVIEW The aim of this paper is therefore to summarize the advanced applications of mass spectrometry imaging (MSI) technology in the quality control, safety evaluations, and determination of toxicity mechanisms of TCMs. MATERIALS AND METHODS Relevant studies from the literature have been collected from scientific databases, such as "PubMed", "Scifinder", "Elsevier", "Google Scholar" using the keywords "MSI", "traditional Chinese medicines", "quality control", "metabolomics", and "mechanism". RESULTS MSI is a new analytical imaging technology that can detect and image the metabolic changes of multiple components of TCMs in plants and animals in a high throughput manner. Compared to other chemical analysis methods, such as liquid chromatography-mass spectrometry (LC-MS), this method does not require the complex extraction and separation of TCMs, and is fast, has high sensitivity, is label-free, and can be performed in high-throughput. Combined with chemometrics methods, MSI can be quickly and easily used for quality screening of TCMs. In addition, this technology can be used to further focus on potential biomarkers and explore the therapeutic/toxic mechanisms of TCMs. CONCLUSIONS As a new type of analysis method, MSI has unique advantages to metabolic analysis, quality control, and mechanisms of action explorations of TCMs, and contributes to the establishment of quality standards to explore the safety and toxicology of TCMs.
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Affiliation(s)
- Haiyan Jiang
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yaxin Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhigang Liu
- School of Biological Science and Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiangyi Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing 100050, China.
| | - Hongtao Jin
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; Beijing Union-Genius Pharmaceutical Technology Development Co., Ltd., Beijing 100176, China; NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing 100050, China.
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7
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Maia M, Figueiredo A, Cordeiro C, Sousa Silva M. FT-ICR-MS-based metabolomics: A deep dive into plant metabolism. MASS SPECTROMETRY REVIEWS 2021. [PMID: 34545595 DOI: 10.1002/mas.21731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Metabolomics involves the identification and quantification of metabolites to unravel the chemical footprints behind cellular regulatory processes and to decipher metabolic networks, opening new insights to understand the correlation between genes and metabolites. In plants, it is estimated the existence of hundreds of thousands of metabolites and the majority is still unknown. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a powerful analytical technique to tackle such challenges. The resolving power and sensitivity of this ultrahigh mass accuracy mass analyzer is such that a complex mixture, such as plant extracts, can be analyzed and thousands of metabolite signals can be detected simultaneously and distinguished based on the naturally abundant elemental isotopes. In this review, FT-ICR-MS-based plant metabolomics studies are described, emphasizing FT-ICR-MS increasing applications in plant science through targeted and untargeted approaches, allowing for a better understanding of plant development, responses to biotic and abiotic stresses, and the discovery of new natural nutraceutical compounds. Improved metabolite extraction protocols compatible with FT-ICR-MS, metabolite analysis methods and metabolite identification platforms are also explored as well as new in silico approaches. Most recent advances in MS imaging are also discussed.
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Affiliation(s)
- Marisa Maia
- Departamento de Química e Bioquímica, Laboratório de FTICR e Espectrometria de Massa Estrutural, MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Grapevine Pathogen Systems Lab (GPS Lab), Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Lisboa, Portugal
| | - Andreia Figueiredo
- Departamento de Biologia Vegetal, Faculdade de Ciências, Grapevine Pathogen Systems Lab (GPS Lab), Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Lisboa, Portugal
| | - Carlos Cordeiro
- Departamento de Química e Bioquímica, Laboratório de FTICR e Espectrometria de Massa Estrutural, MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Marta Sousa Silva
- Departamento de Química e Bioquímica, Laboratório de FTICR e Espectrometria de Massa Estrutural, MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Dos Santos NA, de Almeida CM, Gonçalves FF, Ortiz RS, Kuster RM, Saquetto D, Romão W. Analysis of Erythroxylum coca Leaves by Imaging Mass Spectrometry (MALDI-FT-ICR IMS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:946-955. [PMID: 33715356 DOI: 10.1021/jasms.0c00449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) can determine the chemical identity and spatial distribution of several molecules in a single analysis, conserving its natural histology. However, there are no specific studies on the spatial distribution of alkaloids in Erythroxylum coca leaves by MALDI IMS, preserving the histology of the monitored compounds. Therefore, in this work, positive-ion mode MALDI Fourier-transform ion cyclotron resonance imaging mass spectrometry (MALDI(+)FT-ICR IMS) was applied to identify and analyze the distribution of alkaloids on the surface of coca leaves, evaluating the ionization efficiency of three matrices (α-cyano-4-hydroxycinnamic acid (CHCA), 2-mercaptobenzothiazole (MBT), and 2,5-dihydroxybenzoic acid (DHB)). The last was chosen as the best matrix in this study, and it was studied in five concentrations (0.5, 1.0, 2.0, 4.0, and 8.0 mg·mL-1), where 2 mg·mL-1 was the most efficient. The washing of coca leaves with the organic solvents (acetonitrile, methanol, toluene, and dichloromethane) tested did not improve the performance of the ionization process. Finally, a tissue section, 50 μm thick, was used to study the inner part of the leaf tissue, where alkaloids and flavonoid molecules were detected.
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Affiliation(s)
- Nayara Araujo Dos Santos
- Laboratório de Petroleômica e Forense, Universidade Federal do Espírito Santo (UFES), Avenida Fernando Ferrari, 514, Goiabeiras, Vitória, ES 29075-910, Brazil
- Instituto Nacional de Ciência e Tecnologia Forense (INCT Forense), Av. Ministro Salgado Filho, Soteco, Vila Velha, Espírito Santo 29106-010, Brazil
| | - Camila Medeiros de Almeida
- Laboratório de Petroleômica e Forense, Universidade Federal do Espírito Santo (UFES), Avenida Fernando Ferrari, 514, Goiabeiras, Vitória, ES 29075-910, Brazil
- Instituto Nacional de Ciência e Tecnologia Forense (INCT Forense), Av. Ministro Salgado Filho, Soteco, Vila Velha, Espírito Santo 29106-010, Brazil
| | - Fernanda Fachim Gonçalves
- Laboratório de Petroleômica e Forense, Universidade Federal do Espírito Santo (UFES), Avenida Fernando Ferrari, 514, Goiabeiras, Vitória, ES 29075-910, Brazil
| | - Rafael Scorsatto Ortiz
- Instituto Nacional de Ciência e Tecnologia Forense (INCT Forense), Av. Ministro Salgado Filho, Soteco, Vila Velha, Espírito Santo 29106-010, Brazil
- Superintendência da Polícia Federal no Rio Grande Sul, Porto Alegre, RS 90040-410, Brazil
| | - Ricardo Machado Kuster
- Laboratório de Petroleômica e Forense, Universidade Federal do Espírito Santo (UFES), Avenida Fernando Ferrari, 514, Goiabeiras, Vitória, ES 29075-910, Brazil
| | - Diemerson Saquetto
- Instituto Federal de Educação, Ciência e Tecnologia do Espírito Santo (IFES), Av. Ministro Salgado Filho, Soteco, Vila Velha, Espírito Santo 29106-010, Brazil
| | - Wanderson Romão
- Laboratório de Petroleômica e Forense, Universidade Federal do Espírito Santo (UFES), Avenida Fernando Ferrari, 514, Goiabeiras, Vitória, ES 29075-910, Brazil
- Instituto Nacional de Ciência e Tecnologia Forense (INCT Forense), Av. Ministro Salgado Filho, Soteco, Vila Velha, Espírito Santo 29106-010, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Espírito Santo (IFES), Av. Ministro Salgado Filho, Soteco, Vila Velha, Espírito Santo 29106-010, Brazil
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9
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Rajpoot R, Srivastava RK, Rani A, Pandey P, Dubey RS. Manganese-induced oxidative stress, ultrastructural changes, and proteomics studies in rice plants. PROTOPLASMA 2021; 258:319-335. [PMID: 33070243 DOI: 10.1007/s00709-020-01575-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
Manganese (Mn) is an essential element for plant growth but it becomes phytotoxic at higher concentrations. The effect of Mn-excess in hydroponics medium was examined on growth, oxidative stress, and ultrastructural changes in chloroplasts and mitochondria as well proteomic alterations in rice (Oryza sativa L.) seedlings. Seedlings grown with 1 mM and 2 mM Mn in nutrient medium for 8 days showed decline in length and fresh biomass, and decline in net photosynthetic rate, transpiration rate, and stomatal conductance. Shoots of the seedlings had higher Mn content than roots. Mn-treated seedlings showed increased production of O2·-, H2O2, and .OH, increased lipid peroxidation, increased carbonylation of proteins, and increased proteolytic activity compared to untreated seedlings. Mn-treated seedlings showed disorganization and swelling of chloroplasts with appearance of plastoglobuli in TEM images and deformity in shape of mitochondria. Using confocal microscopy depolarization of mitochondrial membrane was observed marked by green fluorescence of JC-1 dye monomers in Mn-treated roots. Proteomics studies from leaves of Mn-treated seedlings involving 2DE and PDQuest analysis showed differential expression of 23 proteins, among which MALDI-TOF/TOF mass spectrometry analysis revealed Mn-led downregulation of photosynthesis-related proteins, namely oxygen-evolving complex protein associated with PSII, PAP-3, enzyme involved in protein folding peptidyl-prolyl cis-trans isomerase (PPIase) and carbohydrate metabolizing enzymes hydrolase, fructose-bisphosphate aldolase, transketolase, and isocitrate dehydrogenase, whereas ATP-dependent Clp protease, peroxidase, and nucleic acid-binding proteins were downregulated due to Mn treatment. Results indicate that Mn-excess inhibits growth of rice plants with induction of oxidative stress, causing structural alterations in chloroplasts, mitochondria, inhibiting photosynthesis, and downregulating many photosynthesis and carbohydrate metabolism-related proteins.
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Affiliation(s)
- Ritika Rajpoot
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | | | - Anjana Rani
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Poonam Pandey
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - R S Dubey
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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10
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Jayathirtha M, Dupree EJ, Manzoor Z, Larose B, Sechrist Z, Neagu AN, Petre BA, Darie CC. Mass Spectrometric (MS) Analysis of Proteins and Peptides. Curr Protein Pept Sci 2020; 22:92-120. [PMID: 32713333 DOI: 10.2174/1389203721666200726223336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 01/09/2023]
Abstract
The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zaen Manzoor
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Brianna Larose
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zach Sechrist
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania
| | - Brindusa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, Al. I. Cuza University of Iasi, Iasi, Romania, Center for Fundamental Research and Experimental Development in Translation Medicine - TRANSCEND, Regional Institute of Oncology, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
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Loupit G, Cookson SJ. Identifying Molecular Markers of Successful Graft Union Formation and Compatibility. FRONTIERS IN PLANT SCIENCE 2020; 11:610352. [PMID: 33343610 PMCID: PMC7738326 DOI: 10.3389/fpls.2020.610352] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/09/2020] [Indexed: 05/04/2023]
Abstract
Grafting is a technique used for millennia for vegetative propagation, especially in perennial fruit crops. This method, used on woody and herbaceous plants, can improve several agronomic characteristics, such as yield or vigor, as well as tolerance to biotic and abiotic stresses. However, some scion/rootstock combinations suffer from poor graft compatibility, i.e., they are unable to form and/or sustain a successful graft union. Identifying symptoms of graft incompatibility is difficult because they are not always present in the first years after grafting and in most cases the causes of incompatibility are still poorly understood. Studies of changes in transcript abundance during graft union formation indicate that grafting responses are similar to responses to wounding and include the differential expression of genes related to hormone signaling, oxidative stress, formation of new vascular vessels, cell development, and secondary metabolites, in particular polyphenols. This review summarizes current knowledge of the changes in transcript abundance, redox status and metabolites accumulation during graft union formation and in cases of graft incompatibility. The goal of this review is to discuss the possibility of identifying marker transcripts, enzyme activities and/or metabolites of grafting success and graft compatibility which could be used to score grafting success for genetic research and in breeding programs. We highlight gaps in current knowledge and potential research directions in this field.
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12
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Keller C, Gemperline E, Li L. MALDI Mass Spectrometry Imaging of Peptides in Medicago truncatula Root Nodules. Methods Mol Biol 2020; 2139:341-351. [PMID: 32462598 PMCID: PMC7430052 DOI: 10.1007/978-1-0716-0528-8_25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mass spectrometry imaging is routinely used to visualize the distributions of biomolecules in tissue sections. In plants, mass spectrometry imaging of metabolites is more often conducted, but the imaging of larger molecules is less frequently performed despite the importance of proteins and endogenous peptides to the plant. Here, we describe a matrix-assisted laser desorption/ionization mass spectrometry imaging method for the imaging of peptides in Medicago truncatula root nodules. Sample preparation steps including embedding in gelatin, sectioning, and matrix application are described. The method described is employed to determine the spatial distribution of hundreds of peptide peaks.
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Affiliation(s)
- Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Erin Gemperline
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. .,School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
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13
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Claes BSR, Takeo E, Fukusaki E, Shimma S, Heeren RMA. Imaging Isomers on a Biological Surface: A Review. Mass Spectrom (Tokyo) 2019; 8:A0078. [PMID: 32158629 PMCID: PMC7035452 DOI: 10.5702/massspectrometry.a0078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/31/2019] [Indexed: 12/30/2022] Open
Abstract
Mass spectrometry imaging is an imaging technology that allows the localization and identification of molecules on (biological) sample surfaces. Obtaining the localization of a compound in tissue is of great value in biological research. Yet, the identification of compounds remains a challenge. Mass spectrometry alone, even with high-mass resolution, cannot always distinguish between the subtle structural differences of isomeric compounds. This review discusses recent advances in mass spectrometry imaging of lipids, steroid hormones, amino acids and proteins that allow imaging with isomeric resolution. These improvements in detailed identification can give new insights into the local biological activity of isomers.
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Affiliation(s)
- Britt S. R. Claes
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University
| | - Emi Takeo
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Ron M. A. Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University
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14
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Shimma S, Sagawa T. Microscopy and Mass Spectrometry Imaging Reveals the Distributions of Curcumin Species in Dried Turmeric Root. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9652-9657. [PMID: 31361133 DOI: 10.1021/acs.jafc.9b02768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Plants contain many secondary metabolites, which are sometimes used as spices and herbal medicines. However, the three-dimensional distribution of metabolites is usually unknown. In this study, the spatial distribution of curcumin, one of the main components of dried turmeric root, was examined. Because dried turmeric samples are extremely hard and impossible to section with existing cryomicrotomes, we introduced a new sectioning method and analyzed the two-dimensional distribution of curcumin in turmeric sections cut in different directions. The geometrical analysis of the imaging results suggested that curcumin forms tubular components inside turmeric. The wide-target analysis showed that the spatial distribution of curcumin analogues was similar to that of curcumin. Thus, mass spectrometry imaging was successfully implemented for clarifying the distribution of secondary metabolites in dry plant samples. Understanding the distribution of metabolites inside the plant body might contribute to improving their production processes, including the methods for extraction of active ingredients.
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Affiliation(s)
- Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering , Osaka University , Suita 565-0871 , Japan
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Neagu AN. Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:55-98. [PMID: 31347042 DOI: 10.1007/978-3-030-15950-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In order to overcome the limitations of classic imaging in Histology during the actually era of multiomics, the multi-color "molecular microscope" by its emerging "molecular pictures" offers quantitative and spatial information about thousands of molecular profiles without labeling of potential targets. Healthy and diseased human tissues, as well as those of diverse invertebrate and vertebrate animal models, including genetically engineered species and cultured cells, can be easily analyzed by histology-directed MALDI imaging mass spectrometry. The aims of this review are to discuss a range of proteomic information emerging from MALDI mass spectrometry imaging comparative to classic histology, histochemistry and immunohistochemistry, with applications in biology and medicine, concerning the detection and distribution of structural proteins and biological active molecules, such as antimicrobial peptides and proteins, allergens, neurotransmitters and hormones, enzymes, growth factors, toxins and others. The molecular imaging is very well suited for discovery and validation of candidate protein biomarkers in neuroproteomics, oncoproteomics, aging and age-related diseases, parasitoproteomics, forensic, and ecotoxicology. Additionally, in situ proteome imaging may help to elucidate the physiological and pathological mechanisms involved in developmental biology, reproductive research, amyloidogenesis, tumorigenesis, wound healing, neural network regeneration, matrix mineralization, apoptosis and oxidative stress, pain tolerance, cell cycle and transformation under oncogenic stress, tumor heterogeneity, behavior and aggressiveness, drugs bioaccumulation and biotransformation, organism's reaction against environmental penetrating xenobiotics, immune signaling, assessment of integrity and functionality of tissue barriers, behavioral biology, and molecular origins of diseases. MALDI MSI is certainly a valuable tool for personalized medicine and "Eco-Evo-Devo" integrative biology in the current context of global environmental challenges.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania.
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Sugahara K, Kitao K, Watanabe T, Yamagaki T. Imaging Mass Spectrometry Analysis of Flavonoids in Blue Viola Petals and Their Enclosure Effects on Violanin during Color Expression. Anal Chem 2018; 91:896-902. [DOI: 10.1021/acs.analchem.8b03815] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kohtaro Sugahara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Kazunori Kitao
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Takehiro Watanabe
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Tohru Yamagaki
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
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Barbosa EA, Bonfim MF, Bloch C, Engler G, Rocha T, de Almeida Engler J. Imaging Mass Spectrometry of Endogenous Polypeptides and Secondary Metabolites from Galls Induced by Root-Knot Nematodes in Tomato Roots. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1048-1059. [PMID: 29663868 DOI: 10.1094/mpmi-02-18-0049-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nematodes are devastating pests that infect most cultivated plant species and cause considerable agricultural losses worldwide. The understanding of metabolic adjustments induced during plant-nematode interaction is crucial to generate resistant plants or to select more efficient molecules to fight against this pest. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has been used herein for in situ detection and mapping endogenous polypeptides and secondary metabolites from nematode-induced gall tissue. One of the major critical features of this technique is sample preparation; mainly, the generation of intact sections of plant cells with their rigid cell walls and vacuolated cytoplasm. Our experimental settings allowed us to obtain sections without contamination of exogenous ions or diffusion of molecules and to map the differential presence of low and high molecular weight ions in uninfected roots compared with nematode-induced galls. We predict the presence of lipids in both uninfected roots and galls, which was validated by MALDI time-of-flight tandem mass spectrometry and high-resolution mass spectrometry analysis of lipid extracts. Based on the isotopic ion distribution profile, both esters and glycerophospholipids were predicted compounds and may be playing an important role in gall development. Our results indicate that the MALDI-MSI technology is a promising tool to identify secondary metabolites as well as peptides and proteins in complex plant tissues like galls to decipher molecular processes responsible for infection and maintenance of these feeding sites during nematode parasitism.
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Affiliation(s)
- Eder Alves Barbosa
- 1 Laboratório de espectrometria de massa, Embrapa Recursos Genéticos e Biotecnologia, PqEB, 70770-900, Brasília-DF, Brazil
- 2 Laboratório de Síntese e Análise de Biomoléculas, Instituto de Química, Universidade de Brasília, 70910-900, Brasília-DF, Brazil
| | - Mauro Ferreira Bonfim
- 2 Laboratório de Síntese e Análise de Biomoléculas, Instituto de Química, Universidade de Brasília, 70910-900, Brasília-DF, Brazil
- 3 Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB; and
| | - Carlos Bloch
- 1 Laboratório de espectrometria de massa, Embrapa Recursos Genéticos e Biotecnologia, PqEB, 70770-900, Brasília-DF, Brazil
| | - Gilbert Engler
- 4 INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Thales Rocha
- 3 Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB; and
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Qin L, Zhang Y, Liu Y, He H, Han M, Li Y, Zeng M, Wang X. Recent advances in matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for in situ analysis of endogenous molecules in plants. PHYTOCHEMICAL ANALYSIS : PCA 2018; 29:351-364. [PMID: 29667236 DOI: 10.1002/pca.2759] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/01/2018] [Accepted: 02/04/2018] [Indexed: 05/27/2023]
Abstract
INTRODUCTION Mass spectrometry imaging (MSI) as a label-free and powerful imaging technique enables in situ evaluation of a tissue metabolome and/or proteome, becoming increasingly popular in the detection of plant endogenous molecules. OBJECTIVE The characterisation of structure and spatial information of endogenous molecules in plants are both very important aspects to better understand the physiological mechanism of plant organism. METHODS Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a commonly-used tissue imaging technique, which requires matrix to assist in situ detection of a variety of molecules on the surface of a tissue section. In previous studies, MALDI-MSI was mostly used for the detection of molecules from animal tissue sections, compared to plant samples due to cell structural limitations, such as plant cuticles, epicuticular waxes, and cell walls. Despite the enormous progress that has been made in tissue imaging, there is still a challenge for MALDI-MSI suitable for the imaging of endogenous compounds in plants. RESULTS This review summarises the recent advances in MALDI-MSI, focusing on the application of in situ detection of endogenous molecules in different plant organs, i.e. root, stem, leaf, flower, fruit, and seed. CONCLUSION Further improvements on instrumentation sensitivity, matrix selection, image processing and sample preparation will expand the application of MALDI-MSI in plant research.
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Affiliation(s)
- Liang Qin
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
| | - Yawen Zhang
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
| | - Yaqin Liu
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
| | - Huixin He
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
| | - Manman Han
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
| | - Yanyan Li
- The Hospital of Minzu University of China, Minzu University of China, Beijing, P. R. China
| | - Maomao Zeng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- Collaborative Innovation Centre of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, P. R. China
| | - Xiaodong Wang
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
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Arendowski A, Ruman T. Laser Desorption/Ionisation Mass Spectrometry Imaging of European Yew (Taxus baccata) on Gold Nanoparticle-enhanced Target. PHYTOCHEMICAL ANALYSIS : PCA 2017; 28:448-453. [PMID: 28523824 DOI: 10.1002/pca.2693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/22/2017] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
INTRODUCTION European yew (Taxus baccata) is a plant known to man for centuries as it produces many interesting and important metabolites. These chemical compounds were repeatedly analysed by various analytical techniques, but none of the methods used so far allowed the localisation of the chemical compounds within the tissue and also correlation between plant morphology and its biochemistry. OBJECTIVE Visualisation of the spatial distribution of yew metabolites with nanoparticle-based mass spectrometry imaging. METHODOLOGY Compounds occurring on cross-section of a one-year yew sprig has been transferred to gold nanoparticle-enhanced target (AuNPET) by imprinting. The imprint was then subjected to mass spectrometry imaging analysis. RESULTS Nanoparticle-enhanced mass spectrometry imaging made it possible to study the distribution of selected compounds in the European yew tissue, including taxanes - terpene alkaloids characteristic for the Taxus genus. Results prove that aspartate, taxinine M, baccatin IV and taxine B are located mainly in the cortex. Taxuspine W was located in the vascular tissue. Maleate was found to be located mainly in the phloem tissue. In contrast, the proton adduct of chlorophyll b was found in the external layer of twigs. CONCLUSION The results presented a high correlation between the location of compounds and the morphology of the plant, thus giving the opportunity to see the selected details of chemical structure of the analysed tissue for the first time. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Adrian Arendowski
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959, Rzeszów, Poland
| | - Tomasz Ruman
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959, Rzeszów, Poland
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Brentan Silva D, Aschenbrenner AK, Lopes NP, Spring O. Direct Analyses of Secondary Metabolites by Mass Spectrometry Imaging (MSI) from Sunflower (Helianthus annuus L.) Trichomes. Molecules 2017; 22:molecules22050774. [PMID: 28489027 PMCID: PMC6154581 DOI: 10.3390/molecules22050774] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/07/2017] [Accepted: 05/08/2017] [Indexed: 01/11/2023] Open
Abstract
Helianthus annuus (sunflower) displays non-glandular trichomes (NGT), capitate glandular trichomes (CGT), and linear glandular trichomes (LGT), which reveal different chemical compositions and locations in different plant tissues. With matrix-assisted laser desorption/ionization (MALDI) and laser desorption/ionization (LDI) mass spectrometry imaging (MSI) techniques, efficient methods were developed to analyze the tissue distribution of secondary metabolites (flavonoids and sesquiterpenes) and proteins inside of trichomes. Herein, we analyzed sesquiterpene lactones, present in CGT, from leaf transversal sections using the matrix 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA) (mixture 1:1) with sodium ions added to increase the ionization in positive ion mode. The results observed for sesquiterpenes and polymethoxylated flavones from LGT were similar. However, upon desiccation, LGT changed their shape in the ionization source, complicating analyses by MSI mainly after matrix application. An alternative method could be applied to LGT regions by employing LDI (without matrix) in negative ion mode. The polymethoxylated flavones were easily ionized by LDI, producing images with higher resolution, but the sesquiterpenes were not observed in spectra. Thus, the application and viability of MALDI imaging for the analyses of protein and secondary metabolites inside trichomes were confirmed, highlighting the importance of optimization parameters.
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Affiliation(s)
- Denise Brentan Silva
- Laboratório de Produtos Naturais e Espectrometria de Massas (LaPNEM), Universidade Federal de Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil.
- Núcleo de Pesquisas em Produtos Naturais e Sintéticos (NPPNS), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-020, SP, Brazil.
| | | | - Norberto Peporine Lopes
- Núcleo de Pesquisas em Produtos Naturais e Sintéticos (NPPNS), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-020, SP, Brazil.
| | - Otmar Spring
- Institute of Botany, University of Hohenheim, Garbenstraße 30, Stuttgart 70593, Germany.
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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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Yoshimura Y, Goto-Inoue N, Moriyama T, Zaima N. Significant advancement of mass spectrometry imaging for food chemistry. Food Chem 2016; 210:200-11. [DOI: 10.1016/j.foodchem.2016.04.096] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 02/17/2016] [Accepted: 04/20/2016] [Indexed: 11/30/2022]
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Gemperline E, Keller C, Jayaraman D, Maeda J, Sussman MR, Ané JM, Li L. Examination of Endogenous Peptides in Medicago truncatula Using Mass Spectrometry Imaging. J Proteome Res 2016; 15:4403-4411. [PMID: 27726374 DOI: 10.1021/acs.jproteome.6b00471] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plant science is an important, rapidly developing area of study. Within plant science, one area of study that has grown tremendously with recent technological advances, such as mass spectrometry, is the field of plant-omics; however, plant peptidomics is relatively underdeveloped in comparison with proteomics and metabolomics. Endogenous plant peptides can act as signaling molecules and have been shown to affect cell division, development, nodulation, reproduction, symbiotic associations, and defense reactions. There is a growing need to uncover the role of endogenous peptides on a molecular level. Mass spectrometric imaging (MSI) is a valuable tool for biological analyses as it allows for the detection of thousands of analytes in a single experiment and also displays spatial information for the detected analytes. Despite the prediction of a large number of plant peptides, their detection and imaging with spatial localization and chemical specificity is currently lacking. Here we analyzed the endogenous peptides and proteins in Medicago truncatula using matrix-assisted laser desorption/ionization (MALDI)-MSI. Hundreds of endogenous peptides and protein fragments were imaged, with interesting peptide spatial distribution changes observed between plants in different developmental stages.
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Affiliation(s)
- Erin Gemperline
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Dhileepkumar Jayaraman
- Department of Agronomy, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Junko Maeda
- Department of Agronomy, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Michael R Sussman
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
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Canela N, Rodríguez MÁ, Baiges I, Nadal P, Arola L. Foodomics imaging by mass spectrometry and magnetic resonance. Electrophoresis 2016; 37:1748-67. [DOI: 10.1002/elps.201500494] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/22/2015] [Accepted: 01/05/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Núria Canela
- Group of Research on Omic Methodologies (GROM); Universitat Rovira i Virgili; Reus Spain
- Centre for Omic Sciences (COS); Universitat Rovira i Virgili; Reus Spain
| | - Miguel Ángel Rodríguez
- Group of Research on Omic Methodologies (GROM); Universitat Rovira i Virgili; Reus Spain
- Centre for Omic Sciences (COS); Universitat Rovira i Virgili; Reus Spain
| | - Isabel Baiges
- Group of Research on Omic Methodologies (GROM); Universitat Rovira i Virgili; Reus Spain
- Centre for Omic Sciences (COS); Universitat Rovira i Virgili; Reus Spain
| | - Pedro Nadal
- Group of Research on Omic Methodologies (GROM); Universitat Rovira i Virgili; Reus Spain
- Centre for Omic Sciences (COS); Universitat Rovira i Virgili; Reus Spain
- Centre Tecnològic de Nutriciò i Salut (CTNS); Reus Spain
| | - Lluís Arola
- Centre for Omic Sciences (COS); Universitat Rovira i Virgili; Reus Spain
- Centre Tecnològic de Nutriciò i Salut (CTNS); Reus Spain
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25
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Abstract
Plant-omics is rapidly becoming an important field of study in the scientific community due to the urgent need to address many of the most important questions facing humanity today with regard to agriculture, medicine, biofuels, environmental decontamination, ecological sustainability, etc. High-performance mass spectrometry is a dominant tool for interrogating the metabolomes, peptidomes, and proteomes of a diversity of plant species under various conditions, revealing key insights into the functions and mechanisms of plant biochemistry.
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Affiliation(s)
- Erin Gemperline
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
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26
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Dong Y, Li B, Malitsky S, Rogachev I, Aharoni A, Kaftan F, Svatoš A, Franceschi P. Sample Preparation for Mass Spectrometry Imaging of Plant Tissues: A Review. FRONTIERS IN PLANT SCIENCE 2016; 7:60. [PMID: 26904042 PMCID: PMC4748743 DOI: 10.3389/fpls.2016.00060] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/14/2016] [Indexed: 05/18/2023]
Abstract
Mass spectrometry imaging (MSI) is a mass spectrometry based molecular ion imaging technique. It provides the means for ascertaining the spatial distribution of a large variety of analytes directly on tissue sample surfaces without any labeling or staining agents. These advantages make it an attractive molecular histology tool in medical, pharmaceutical, and biological research. Likewise, MSI has started gaining popularity in plant sciences; yet, information regarding sample preparation methods for plant tissues is still limited. Sample preparation is a crucial step that is directly associated with the quality and authenticity of the imaging results, it therefore demands in-depth studies based on the characteristics of plant samples. In this review, a sample preparation pipeline is discussed in detail and illustrated through selected practical examples. In particular, special concerns regarding sample preparation for plant imaging are critically evaluated. Finally, the applications of MSI techniques in plants are reviewed according to different classes of plant metabolites.
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Affiliation(s)
- Yonghui Dong
- Biostatistics and Data Management, Research and Innovation Centre - Fondazione Edmund MachS. Michele all'Adige, Italy
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovot, Israel
| | - Bin Li
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-ChampaignUrbana, IL, USA
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovot, Israel
| | - Ilana Rogachev
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovot, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovot, Israel
| | - Filip Kaftan
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical EcologyJena, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical EcologyJena, Germany
| | - Pietro Franceschi
- Biostatistics and Data Management, Research and Innovation Centre - Fondazione Edmund MachS. Michele all'Adige, Italy
- *Correspondence: Pietro Franceschi
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27
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Li B, Dunham SJ, Dong Y, Yoon S, Zeng M, Sweedler JV. Analytical capabilities of mass spectrometry imaging and its potential applications in food science. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2015.10.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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28
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OZAWA T, OSAKA I, HAMADA S, MURAKAMI T, MIYAZATO A, KAWASAKI H, ARAKAWA R. Direct Imaging Mass Spectrometry of Plant Leaves Using Surface-assisted Laser Desorption/Ionization with Sputter-deposited Platinum Film. ANAL SCI 2016; 32:587-91. [DOI: 10.2116/analsci.32.587] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Tomoyuki OZAWA
- Department of Chemistry and Materials Engineering, Faculty of Chemistry, Materials, and Bioengineering, Kansai University
| | - Issey OSAKA
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology
| | - Satoshi HAMADA
- Analysis Research Department, Chemical Research Laboratories, Nissan Chemical Industries, Ltd
| | - Tatsuya MURAKAMI
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology
| | - Akio MIYAZATO
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology
| | - Hideya KAWASAKI
- Department of Chemistry and Materials Engineering, Faculty of Chemistry, Materials, and Bioengineering, Kansai University
| | - Ryuichi ARAKAWA
- Department of Chemistry and Materials Engineering, Faculty of Chemistry, Materials, and Bioengineering, Kansai University
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29
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Handberg E, Chingin K, Wang N, Dai X, Chen H. Mass spectrometry imaging for visualizing organic analytes in food. MASS SPECTROMETRY REVIEWS 2015; 34:641-58. [PMID: 24687728 DOI: 10.1002/mas.21424] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/18/2014] [Accepted: 02/18/2014] [Indexed: 05/27/2023]
Abstract
The demand for rapid chemical imaging of food products steadily increases. Mass spectrometry (MS) is featured by excellent molecular specificity of analysis and is, therefore, a very attractive method for chemical profiling. MS for food imaging has increased significantly over the past decade, aided by the emergence of various ambient ionization techniques that allow direct and rapid analysis in ambient environment. In this article, the current status of food imaging with MSI is reviewed. The described approaches include matrix-assisted laser desorption/ionization (MALDI), but emphasize desorption atmospheric pressure photoionization (DAPPI), electrospray-assisted laser desorption/ionization (ELDI), probe electrospray ionization (PESI), surface desorption atmospheric pressure chemical ionization (SDAPCI), and laser ablation flowing atmospheric pressure afterglow (LA-FAPA). The methods are compared with regard to spatial resolution; analysis speed and time; limit of detection; and technical aspects. The performance of each method is illustrated with the description of a related application. Specific requirements in food imaging are discussed.
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Affiliation(s)
- Eric Handberg
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, Department of Applied Chemistry, East China Institute of Technology, Nanchang, 330013, P.R. China
| | - Konstantin Chingin
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, Department of Applied Chemistry, East China Institute of Technology, Nanchang, 330013, P.R. China
| | - Nannan Wang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, Department of Applied Chemistry, East China Institute of Technology, Nanchang, 330013, P.R. China
| | - Ximo Dai
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, Department of Applied Chemistry, East China Institute of Technology, Nanchang, 330013, P.R. China
| | - Huanwen Chen
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, Department of Applied Chemistry, East China Institute of Technology, Nanchang, 330013, P.R. China
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30
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Hölscher D, Fuchser J, Knop K, Menezes RC, Buerkert A, Svatoš A, Schubert US, Schneider B. High resolution mass spectrometry imaging reveals the occurrence of phenylphenalenone-type compounds in red paracytic stomata and red epidermis tissue of Musa acuminata ssp. zebrina cv. 'Rowe Red'. PHYTOCHEMISTRY 2015; 116:239-245. [PMID: 26004822 DOI: 10.1016/j.phytochem.2015.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 06/04/2023]
Abstract
The banana epidermis and in particular their stomata are conducive sites for the penetration of pathogenic fungi which can severely limit global banana production. The red pseudostem of the ornamental banana Musa acuminata ssp. zebrina cv. 'Rowe Red' was used to study the chemical constituents of the epidermal cell layer using matrix-free laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometric imaging (LDI-FT-ICR-MSI). The high resolution of this technique allowed phenylphenalenone-type compounds to be located in single plant cells. Some of these secondary metabolites were identified as constitutive compounds and found in specialized epidermal cells in banana pseudostem tissue. Especially the red paracytic stomata revealed higher signal intensities of certain phenylphenalenones than normal epidermis cells. The ease of detection of polycyclic aromatic compounds on the cellular level is discussed with regard to future investigations of plant-pathogen interactions.
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Affiliation(s)
- Dirk Hölscher
- Research Group Biosynthesis/NMR, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, D-07745 Jena, Germany; Organic Plant Production and Agroecosystems Research in the Tropics and Subtropics (OPATS), University of Kassel, Steinstr. 19, D-37213 Witzenhausen, Germany.
| | - Jens Fuchser
- Application Development Pharma, Bruker Daltonik GmbH, Fahrenheitstrasse 4, D-28359 Bremen, Germany
| | - Katrin Knop
- Laboratory of Organic and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstrasse 10, D-07743 Jena, Germany; Jena Center of Soft Matter, Friedrich Schiller University Jena, Humboldtstrasse 10, D-07743 Jena, Germany
| | - Riya C Menezes
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, D-07745 Jena, Germany
| | - Andreas Buerkert
- Organic Plant Production and Agroecosystems Research in the Tropics and Subtropics (OPATS), University of Kassel, Steinstr. 19, D-37213 Witzenhausen, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, D-07745 Jena, Germany
| | - Ulrich S Schubert
- Laboratory of Organic and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstrasse 10, D-07743 Jena, Germany; Jena Center of Soft Matter, Friedrich Schiller University Jena, Humboldtstrasse 10, D-07743 Jena, Germany
| | - Bernd Schneider
- Research Group Biosynthesis/NMR, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, D-07745 Jena, Germany.
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31
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Takahashi K, Kozuka T, Anegawa A, Nagatani A, Mimura T. Development and Application of a High-Resolution Imaging Mass Spectrometer for the Study of Plant Tissues. PLANT & CELL PHYSIOLOGY 2015; 56:1329-38. [PMID: 26063395 DOI: 10.1093/pcp/pcv083] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/30/2015] [Indexed: 05/27/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) or imaging mass spectrometry (imaging MS) has been a powerful tool to map the spatial distribution of molecules on the surface of biological materials. This technique has frequently been applied to animal tissue slices for the purpose of mapping proteins, peptides, lipids, sugars or small metabolites to find disease-specific biomarkers or to study drug metabolism. Recently, it has also been applied to intact plant tissues or thin slices thereof using commercial mass spectrometers. The present work is concerned with the refinement of MALDI/laser desorption/ionization (LDI)-Fourier transform ion cyclotron resonance (FTICR)-MS incorporating certain specific features namely, ultra-high mass resolution (>100,000), ultra-high molecular mass accuracy (<1 p.p.m.) and high spatial resolution (<10 µm) for imaging MS of plant tissues. Employing an in-house built mass spectrometer, the imaging MS analysis of intact Arabidopsis thaliana tissues, namely etiolated seedlings and roots of seedlings, glued to a small transparent ITO (indium tin oxide)-coated conductive glass was performed. A matrix substance was applied to the vacuum-dried intact tissues by sublimation prior to the imaging MS analysis. The images of various small metabolites representing their two-dimensional distribution on the dried intact tissues were obtained with or without different matrix substances. The effects of MALDI matrices on the ionization of small metabolites during imaging MS acquisition are discussed.
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Affiliation(s)
- Katsutoshi Takahashi
- National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568 Japan
| | - Toshiaki Kozuka
- Kyoto University, Kyoto, 606-8502 Japan Hiroshima University, Hiroshima, 739-8526 Japan These authors contributed equally to this work
| | - Aya Anegawa
- Kobe University, Kobe, 657-8501 Japan These authors contributed equally to this work
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32
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Affiliation(s)
- Bernhard Spengler
- Justus Liebig University Giessen, Institute of Inorganic and Analytical
Chemistry, Schubertstrasse
60, Building 16, 35392 Giessen, Germany
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33
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Bhandari DR, Schott M, Römpp A, Vilcinskas A, Spengler B. Metabolite localization by atmospheric pressure high-resolution scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging in whole-body sections and individual organs of the rove beetle Paederus riparius. Anal Bioanal Chem 2014; 407:2189-201. [PMID: 25424178 PMCID: PMC4357651 DOI: 10.1007/s00216-014-8327-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/04/2014] [Accepted: 11/06/2014] [Indexed: 11/25/2022]
Abstract
Mass spectrometry imaging provides for non-targeted, label-free chemical imaging. In this study, atmospheric pressure high-resolution scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging (AP-SMALDI MSI) was used for the first time to describe the chemical distribution of the defensive compounds pederin, pseudopederin, and pederon in tissue sections (16 μm thick) of the rove beetle Paederus riparius. The whole-insect tissue section was scanned with a 20-μm step size. Mass resolution of the orbital trapping mass spectrometer was set to 100,000 at m/z 200. Additionally, organ-specific compounds were identified for brain, nerve cord, eggs, gut, ovaries, and malpighian tubules. To confirm the distribution of the specific compounds, individual organs from the insect were dissected, and MSI experiments were performed on the dissected organs. Three ganglia of the nerve cord, with a dimension of 250–500 μm, were measured with 10-μm spatial resolution. High-quality m/z images, based on high spatial resolution and high mass accuracy were generated. These features helped to assign mass spectral peaks with high confidence. Mass accuracy of the imaging experiments was <3 ppm root mean square error, and mapping of different compound classes from a single experiment was possible. This approach improved the understanding of the biochemistry of P. riparius. Concentration differences and distributions of pederin and its analogues could be visualized in the whole-insect section. Without any labeling, we assigned key lipids for specific organs to describe their location in the body and to identify morphological structures with a specificity higher than with staining or immunohistology methods.
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Affiliation(s)
- Dhaka Ram Bhandari
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Schubertstraße 60, Building 16, 35392 Giessen, Germany
| | - Matthias Schott
- Institute of Phytopathology and Applied Zoology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Andreas Römpp
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Schubertstraße 60, Building 16, 35392 Giessen, Germany
| | - Andreas Vilcinskas
- Institute of Phytopathology and Applied Zoology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Schubertstraße 60, Building 16, 35392 Giessen, Germany
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34
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Seaman C, Flinders B, Eijkel G, Heeren RMA, Bricklebank N, Clench MR. "Afterlife experiment": use of MALDI-MS and SIMS imaging for the study of the nitrogen cycle within plants. Anal Chem 2014; 86:10071-7. [PMID: 25230319 DOI: 10.1021/ac501191w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As part of a project to demonstrate the science of decay, a series of mass spectrometry imaging experiments were performed. The aim was to demonstrate that decay and decomposition are only part of the story and to show pictorially that atoms and molecules from dead plants and animals are incorporated into new life. Radish plants (Raphanus sativus) were grown hydroponically using a nutrient system containing (15)N KNO3 (98% labeled) as the only source of nitrogen. Plants were cropped and left to ferment in water for 2 weeks to create a radish "tea", which was used as a source of nitrogen for radish grown in a second hydroponics experiment. After 5 weeks of growth, the radish plants were harvested and cryosectioned, and sections were imaged by positive-ion MALDI and SIMS mass spectrometry imaging. The presence of labeled species in the plants grown using (15)N KNO3 as nutrient and those grown from the radish "tea" was readily discernible. The uptake of (15)N into a number of identifiable metabolites has been studied by MALDI-MS and SIMS imaging.
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Affiliation(s)
- Callie Seaman
- Biomedical Research Centre, City Campus, Sheffield Hallam University , Howard Street, Sheffield S1 1WB, United Kingdom
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35
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Becker L, Carré V, Poutaraud A, Merdinoglu D, Chaimbault P. MALDI mass spectrometry imaging for the simultaneous location of resveratrol, pterostilbene and viniferins on grapevine leaves. Molecules 2014; 19:10587-600. [PMID: 25050857 PMCID: PMC6271053 DOI: 10.3390/molecules190710587] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/01/2014] [Accepted: 07/16/2014] [Indexed: 02/06/2023] Open
Abstract
To investigate the in-situ response to a stress, grapevine leaves have been subjected to mass spectrometry imaging (MSI) experiments. The Matrix Assisted Laser Desorption/Ionisation (MALDI) approach using different matrices has been evaluated. Among all the tested matrices, the 2,5-dihydroxybenzoic acid (DHB) was found to be the most efficient matrix allowing a broader range of detected stilbene phytoalexins. Resveratrol, but also more toxic compounds against fungi such as pterostilbene and viniferins, were identified and mapped. Their spatial distributions on grapevine leaves irradiated by UV show their specific colocation around the veins. Moreover, MALDI MSI reveals that resveratrol (and piceids) and viniferins are not specifically located on the same area when leaves are infected by Plasmopara viticola. Results obtained by MALDI mass spectrometry imaging demonstrate that this technique would be essential to improve the level of knowledge concerning the role of the stilbene phytoalexins involved in a stress event.
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Affiliation(s)
- Loïc Becker
- Laboratoire de Chimie et Physique-Approche Multi échelle des Milieux Complexes (LCP-A2MC), Institut Jean Barriol (FR 2843), Université de Lorraine, ICPM 1 Boulevard Arago, F-57078 Metz, France.
| | - Vincent Carré
- Laboratoire de Chimie et Physique-Approche Multi échelle des Milieux Complexes (LCP-A2MC), Institut Jean Barriol (FR 2843), Université de Lorraine, ICPM 1 Boulevard Arago, F-57078 Metz, France.
| | - Anne Poutaraud
- Institut National de Recherche en Agronomie (INRA) - Santé de la Vigne et Qualité du Vin (UMR 1131), 28 rue de Herrlisheim, F-68021 Colmar, France.
| | - Didier Merdinoglu
- Institut National de Recherche en Agronomie (INRA) - Santé de la Vigne et Qualité du Vin (UMR 1131), 28 rue de Herrlisheim, F-68021 Colmar, France.
| | - Patrick Chaimbault
- Laboratoire de Chimie et Physique-Approche Multi échelle des Milieux Complexes (LCP-A2MC), Institut Jean Barriol (FR 2843), Université de Lorraine, ICPM 1 Boulevard Arago, F-57078 Metz, France.
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36
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Nelson CJ, Li L, Millar AH. Quantitative analysis of protein turnover in plants. Proteomics 2014; 14:579-92. [DOI: 10.1002/pmic.201300240] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/02/2013] [Accepted: 10/14/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Clark J. Nelson
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; WA Australia
- Centre for Comparative Analysis of Biomolecular Networks; University of Western Australia; WA Australia
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37
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Mandy DE, Goldford JE, Yang H, Allen DK, Libourel IGL. Metabolic flux analysis using ¹³C peptide label measurements. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:476-86. [PMID: 24279886 DOI: 10.1111/tpj.12390] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/08/2013] [Accepted: 11/15/2013] [Indexed: 05/09/2023]
Abstract
¹³C metabolic flux analysis (MFA) has become the experimental method of choice to investigate the cellular metabolism of microbes, cell cultures and plant seeds. Conventional steady-state MFA utilizes isotopic labeling measurements of amino acids obtained from protein hydrolysates. To retain spatial information in conventional steady-state MFA, tissues or subcellular fractions must be dissected or biochemically purified. In contrast, peptides retain their identity in complex protein extracts, and may therefore be associated with a specific time of expression, tissue type and subcellular compartment. To enable 'single-sample' spatially and temporally resolved steady-state flux analysis, we investigated the suitability of peptide mass distributions (PMDs) as an alternative to amino acid label measurements. PMDs are the discrete convolution of the mass distributions of the constituent amino acids of a peptide. We investigated the requirements for the unique deconvolution of PMDs into amino acid mass distributions (AAMDs), the influence of peptide sequence length on parameter sensitivity, and how AAMD and flux estimates that are determined through deconvolution compare to estimates from a conventional GC-MS measurement-based approach. Deconvolution of PMDs of the storage protein β-conglycinin of soybean (Glycine max) resulted in good AAMD and flux estimates if fluxes were directly fitted to PMDs. Unconstrained deconvolution resulted in inferior AAMD and flux estimates. PMD measurements do not include amino acid backbone fragments, which increase the information content in GC-MS-derived analyses. Nonetheless, the resulting flux maps were of comparable quality due to the precision of Orbitrap quantification and the larger number of peptide measurements.
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Affiliation(s)
- Dominic E Mandy
- Department of Plant Biology, University of Minnesota, 1500 Gortner Avenue, St Paul, MN, 55108, USA
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38
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Bjarnholt N, Li B, D'Alvise J, Janfelt C. Mass spectrometry imaging of plant metabolites--principles and possibilities. Nat Prod Rep 2014; 31:818-37. [PMID: 24452137 DOI: 10.1039/c3np70100j] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to the end of 2013 New mass spectrometry imaging (MSI) techniques are gaining importance in the analysis of plant metabolite distributions, and significant technological improvements have been introduced in the past decade. This review provides an introduction to the different MSI techniques and their applications in plant science. The most common methods for sample preparation are described, and the review also features a comprehensive table of published studies in MSI of plant material. A number of significant works are highlighted for their contributions to advance the understanding of plant biology through applications of plant metabolite imaging. Particular attention is given to the possibility for imaging of surface metabolites since this is highly dependent on the methods and techniques which are applied in imaging studies.
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Affiliation(s)
- Nanna Bjarnholt
- Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 17, 1870 Frederiksberg C, Copenhagen, Denmark
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39
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Shelden MC, Roessner U. Advances in functional genomics for investigating salinity stress tolerance mechanisms in cereals. FRONTIERS IN PLANT SCIENCE 2013; 4:123. [PMID: 23717314 PMCID: PMC3650683 DOI: 10.3389/fpls.2013.00123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 04/16/2013] [Indexed: 05/19/2023]
Abstract
Abiotic stresses such as low water availability and high salinity are major causes of cereal crop yield losses and significantly impact on sustainability. Wheat and barley are two of the most important cereal crops (after maize and rice) and are grown in increasingly hostile environments with soil salinity and drought both expected to increase this century, reducing the availability of arable land. Barley and wheat are classified as glycophytes (salt-sensitive), yet they are more salt-tolerant than other cereal crops such as rice and so are good models for studying salt tolerance in cereals. The exploitation of genetic variation of phenotypic traits through plant breeding could significantly improve growth of cereals in salinity-affected regions, thus leading to improved crop yields. Genetic variation in phenotypic traits for abiotic stress tolerance have been identified in land races and wild germplasm but the molecular basis of these differences is often difficult to determine due to the complex genetic nature of these species. High-throughput functional genomics technologies, such as transcriptomics, metabolomics, proteomics, and ionomics are powerful tools for investigating the molecular responses of plants to abiotic stress. The advancement of these technologies has allowed for the identification and quantification of transcript/metabolites in specific cell types and/or tissues. Using these new technologies on plants will provide a powerful tool to uncovering genetic traits in more complex species such as wheat and barley and provide novel insights into the molecular mechanisms of salinity stress tolerance.
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Affiliation(s)
| | - Ute Roessner
- Australian Centre for Plant Functional Genomics, School of Botany, University of MelbourneParkville VIC, Australia
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40
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Prior N, Little SA, Pirone C, Gill JE, Smith D, Han J, Hardie D, O’Leary SJB, Wagner RE, Cross T, Coulter A, Borchers C, Olafson RW, von Aderkas P. Application of proteomics to the study of pollination drops. APPLICATIONS IN PLANT SCIENCES 2013; 1:apps1300008. [PMID: 25202539 PMCID: PMC4105296 DOI: 10.3732/apps.1300008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 03/16/2013] [Indexed: 05/06/2023]
Abstract
PREMISE OF THE STUDY Pollination drops are a formative component in gymnosperm pollen-ovule interactions. Proteomics offers a direct method for the discovery of proteins associated with this early stage of sexual reproduction. • METHODS Pollination drops were sampled from eight gymnosperm species: Chamaecyparis lawsoniana (Port Orford cedar), Ephedra monosperma, Ginkgo biloba, Juniperus oxycedrus (prickly juniper), Larix ×marschlinsii, Pseudotsuga menziesii (Douglas-fir), Taxus ×media, and Welwitschia mirabilis. Drops were collected by micropipette using techniques focused on preventing sample contamination. Drop proteins were separated using both gel and gel-free methods. Tandem mass spectrometric methods were used including a triple quadrupole and an Orbitrap. • RESULTS Proteins are present in all pollination drops. Consistency in the protein complement over time was shown in L. ×marschlinsii. Representative mass spectra from W. mirabilis chitinase peptide and E. monosperma serine carboxypeptidase peptide demonstrated high quality results. We provide a summary of gymnosperm pollination drop proteins that have been discovered to date via proteomics. • DISCUSSION Using proteomic methods, a dozen classes of proteins have been identified to date. Proteomics presents a way forward in deepening our understanding of the biological function of pollination drops.
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Affiliation(s)
- Natalie Prior
- Centre for Forest Biology, Department of Biology, University of Victoria, P.O. Box 3020 Station CSC, Victoria, British Columbia V8W 3N5, Canada
- Author for correspondence:
| | - Stefan A. Little
- Centre for Forest Biology, Department of Biology, University of Victoria, P.O. Box 3020 Station CSC, Victoria, British Columbia V8W 3N5, Canada
| | - Cary Pirone
- Arnold Arboretum of Harvard University, 125 Arborway, Boston, Massachusetts 02130-3500 USA
| | - Julia E. Gill
- Centre for Forest Biology, Department of Biology, University of Victoria, P.O. Box 3020 Station CSC, Victoria, British Columbia V8W 3N5, Canada
| | - Derek Smith
- University of Victoria—Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Jun Han
- University of Victoria—Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Darryl Hardie
- University of Victoria—Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Stephen J. B. O’Leary
- Centre for Forest Biology, Department of Biology, University of Victoria, P.O. Box 3020 Station CSC, Victoria, British Columbia V8W 3N5, Canada
| | - Rebecca E. Wagner
- Centre for Forest Biology, Department of Biology, University of Victoria, P.O. Box 3020 Station CSC, Victoria, British Columbia V8W 3N5, Canada
| | - Tyra Cross
- University of Victoria—Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Andrea Coulter
- Centre for Forest Biology, Department of Biology, University of Victoria, P.O. Box 3020 Station CSC, Victoria, British Columbia V8W 3N5, Canada
| | - Christoph Borchers
- University of Victoria—Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Robert W. Olafson
- University of Victoria—Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Patrick von Aderkas
- Centre for Forest Biology, Department of Biology, University of Victoria, P.O. Box 3020 Station CSC, Victoria, British Columbia V8W 3N5, Canada
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Quanico J, Franck J, Dauly C, Strupat K, Dupuy J, Day R, Salzet M, Fournier I, Wisztorski M. Development of liquid microjunction extraction strategy for improving protein identification from tissue sections. J Proteomics 2013; 79:200-18. [DOI: 10.1016/j.jprot.2012.11.025] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/20/2012] [Accepted: 11/30/2012] [Indexed: 12/22/2022]
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Matros A, Mock HP. Mass spectrometry based imaging techniques for spatially resolved analysis of molecules. FRONTIERS IN PLANT SCIENCE 2013; 4:89. [PMID: 23626593 PMCID: PMC3630297 DOI: 10.3389/fpls.2013.00089] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 03/22/2013] [Indexed: 05/18/2023]
Abstract
Higher plants are composed of a multitude of tissues with specific functions, reflected by distinct profiles for transcripts, proteins, and metabolites. Comprehensive analysis of metabolites and proteins has advanced tremendously within recent years, and this progress has been driven by the rapid development of sophisticated mass spectrometric techniques. In most of the current "omics"-studies, analysis is performed on whole organ or whole plant extracts, rendering to the loss of spatial information. Mass spectrometry imaging (MSI) techniques have opened a new avenue to obtain information on the spatial distribution of metabolites and of proteins. Pioneered in the field of medicine, the approaches are now applied to study the spatial profiles of molecules in plant systems. A range of different plant organs and tissues have been successfully analyzed by MSI, and patterns of various classes of metabolites from primary and secondary metabolism could be obtained. It can be envisaged that MSI approaches will substantially contribute to build spatially resolved biochemical networks.
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Affiliation(s)
- Andrea Matros
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
- *Correspondence: Hans-Peter Mock, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany. e-mail:
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Collakova E, Yen JY, Senger RS. Are we ready for genome-scale modeling in plants? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 191-192:53-70. [PMID: 22682565 DOI: 10.1016/j.plantsci.2012.04.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/17/2012] [Accepted: 04/18/2012] [Indexed: 05/02/2023]
Abstract
As it is becoming easier and faster to generate various types of high-throughput data, one would expect that by now we should have a comprehensive systems-level understanding of biology, biochemistry, and physiology at least in major prokaryotic and eukaryotic model systems. Despite the wealth of available data, we only get a glimpse of what is going on at the molecular level from the global perspective. The major reason is the high level of cellular complexity and our limited ability to identify all (or at least important) components and their interactions in virtually infinite number of internal and external conditions. Metabolism can be modeled mathematically by the use of genome-scale models (GEMs). GEMs are in silico metabolic flux models derived from available genome annotation. These models predict the combination of flux values of a defined metabolic network given the influence of internal and external signals. GEMs have been successfully implemented to model bacterial metabolism for over a decade. However, it was not until 2009 when the first GEM for Arabidopsis thaliana cell-suspension cultures was generated. Genome-scale modeling ("GEMing") in plants brings new challenges primarily due to the missing components and complexity of plant cells represented by the existence of: (i) photosynthesis; (ii) compartmentation; (iii) variety of cell and tissue types; and (iv) diverse metabolic responses to environmental and developmental cues as well as pathogens, insects, and competing weeds. This review presents a critical discussion of the advantages of existing plant GEMs, while identifies key targets for future improvements. Plant GEMs tend to be accurate in predicting qualitative changes in selected aspects of central carbon metabolism, while secondary metabolism is largely neglected mainly due to the missing (unknown) genes and metabolites. As such, these models are suitable for exploring metabolism in plants grown in favorable conditions, but not in field-grown plants that have to cope with environmental changes in complex ecosystems. AraGEM is the first GEM describing a photosynthetic and photorespiring plant cell (Arabidopsis thaliana). We demonstrate the use of AraGEM given the current (limited) knowledge of plant metabolism and reveal the unexpected robustness of AraGEM by a series of in silico simulations. The major focus of these simulations is on the assessment of the: (i) network connectivity; (ii) influence of CO₂ and photon uptake rates on cellular growth rates and production of individual biomass components; and (iii) stability of plant central carbon metabolism with internal pH changes.
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Affiliation(s)
- Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, 308 Latham Hall, Virginia Tech, Blacksburg, VA, USA.
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Poth AG, Mylne JS, Grassl J, Lyons RE, Millar AH, Colgrave ML, Craik DJ. Cyclotides associate with leaf vasculature and are the products of a novel precursor in petunia (Solanaceae). J Biol Chem 2012; 287:27033-46. [PMID: 22700981 DOI: 10.1074/jbc.m112.370841] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclotides are a large family of plant peptides that are structurally defined by their cyclic backbone and a trifecta of disulfide bonds, collectively known as the cyclic cystine knot (CCK) motif. Structurally similar cyclotides have been isolated from plants within the Rubiaceae, Violaceae, and Fabaceae families and share the CCK motif with trypsin-inhibitory knottins from a plant in the Cucurbitaceae family. Cyclotides have previously been reported to be encoded by dedicated genes or as a domain within a knottin-encoding PA1-albumin-like gene. Here we report the discovery of cyclotides and related non-cyclic peptides we called "acyclotides" from petunia of the agronomically important Solanaceae plant family. Transcripts for petunia cyclotides and acyclotides encode the shortest known cyclotide precursors. Despite having a different precursor structure, their sequences suggest that petunia cyclotides mature via the same biosynthetic route as other cyclotides. We assessed the spatial distribution of cyclotides within a petunia leaf section by MALDI imaging and observed that the major cyclotide component Phyb A was non-uniformly distributed. Dissected leaf midvein extracts contained significantly higher concentrations of this cyclotide compared with the lamina and outer margins of leaves. This is the third distinct type of cyclotide precursor, and Solanaceae is the fourth phylogenetically disparate plant family to produce these structurally conserved cyclopeptides, suggesting either convergent evolution upon the CCK structure or movement of cyclotide-encoding sequences within the plant kingdom.
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Affiliation(s)
- Aaron G Poth
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
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Imaging mass spectrometry of thin tissue sections: a decade of collective efforts. J Proteomics 2012; 75:4883-4892. [PMID: 22525544 DOI: 10.1016/j.jprot.2012.04.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 04/02/2012] [Accepted: 04/05/2012] [Indexed: 12/21/2022]
Abstract
Imaging mass spectrometry (MS) allows to monitor the spatial distribution and abundance of endogenous and administered compounds present within tissue specimens. Several different but complementary imaging MS technologies have been developed allowing the analysis of a wide variety of compounds including inorganic elementals, metabolites, lipids, peptides, proteins and xenobiotics with spatial resolutions from micrometer to nanometer scales. In the past decade, an enormous collective body of work has been done to develop and improve the imaging MS technology. This article gives a historical perspective, an overview of the principle and status of the technology and lists the main fields of applications. It also enumerates some of the critical challenges we need to collectively address for imaging MS to be considered a mainstream analytical method.
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Kueger S, Steinhauser D, Willmitzer L, Giavalisco P. High-resolution plant metabolomics: from mass spectral features to metabolites and from whole-cell analysis to subcellular metabolite distributions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:39-50. [PMID: 22449042 DOI: 10.1111/j.1365-313x.2012.04902.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The main goal of metabolomics is the comprehensive qualitative and quantitative analysis of the time- and space-resolved distribution of all metabolites present in a given biological system. Because metabolite structures, in contrast to transcript and protein sequences, are not directly deducible from the genomic DNA sequence, the massive increase in genomic information is only indirectly of use to metabolomics, leaving compound annotation as a key problem to be solved by the available analytical techniques. Furthermore, as metabolites vary widely in both concentration and chemical behavior, there is no single analytical procedure allowing the unbiased and comprehensive structural elucidation and determination of all metabolites present in a given biological system. In this review the different approaches for targeted and non-targeted metabolomics analysis will be described with special emphasis on mass spectrometry-based techniques. Particular attention is given to approaches which can be employed for the annotation of unknown compounds. In the second part, the different experimental approaches aimed at tissue-specific or subcellular analysis of metabolites are discussed including a range of non-mass spectrometry based technologies.
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Affiliation(s)
- Stephan Kueger
- Botanical Institute II, University of Cologne, Zülpicherstrasse 47b, Cologne, Germany
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