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Do T, Guran R, Adam V, Zitka O. Use of MALDI-TOF mass spectrometry for virus identification: a review. Analyst 2022; 147:3131-3154. [DOI: 10.1039/d2an00431c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibilities of virus identification, including SARS-CoV-2, by MALDI-TOF mass spectrometry are discussed in this review.
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Affiliation(s)
- Tomas Do
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Roman Guran
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
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Iles RK, Zmuidinaite R, Iles JK, Carnell G, Sampson A, Heeney JL. Development of a Clinical MALDI-ToF Mass Spectrometry Assay for SARS-CoV-2: Rational Design and Multi-Disciplinary Team Work. Diagnostics (Basel) 2020; 10:E746. [PMID: 32987950 PMCID: PMC7600155 DOI: 10.3390/diagnostics10100746] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 coronavirus has stretched national testing capacities to breaking points in almost all countries of the world. The need to rapidly screen vast numbers of a country's population in order to control the spread of the infection is paramount. However, the logistical requirement for reagent supply (and associated cost) of RT-PCR based testing (the current front-line test) have been hugely problematic. Mass spectrometry-based methods using swab and gargle samples have been reported with promise, but have not approached the task from a systematic analysis of the entire diagnostic process. Here, the pipeline from sample processing, the biological characteristics of the pathogen in human biofluid, the downstream bio- and physical-chemistry and the all-important data processing with clinical interpretation and reporting, are carefully compiled into a single high-throughput and reproducible rapid process. Utilizing MALDI-ToF mass spectrometric detection to viral envelope glycoproteins in a systems biology-multidisciplinary team approach, we have achieved a multifaceted clinical MALDI ToF MS screening test, primarily (but not limited to) SARS-CoV-2, with direct application to other future epidemics/pandemics that may arise. The clinical information generated not only includes SARS-CoV-2 coronavirus detection-(Spike protein fragments S1, S2b, S2a peaks), but other respiratory viral infections detected as well as an assessment of generalised oral upper respiratory immune response (elevated total Ig light chain peak) and a measure of the viral immune response (elevated intensity of IgA heavy chain peak). The advantages of the method include; (1) ease of sampling, (2) speed of analysis, and much reduced cost of testing. These features reveal the diagnostic utility of MALDI-ToF mass spectrometry as a powerful and economically attractive global solution.
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Affiliation(s)
- Ray K. Iles
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
- NISAD, Medicon Village, SE-223 81 Lund, Sweden
| | - Raminta Zmuidinaite
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Jason K. Iles
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - George Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Alex Sampson
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
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Dreier RF, Ahrné E, Broz P, Schmidt A. Global Ion Suppression Limits the Potential of Mass Spectrometry Based Phosphoproteomics. J Proteome Res 2018; 18:493-507. [DOI: 10.1021/acs.jproteome.8b00812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roland Felix Dreier
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Erik Ahrné
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Petr Broz
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Alexander Schmidt
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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Systematic assessment of surfactants for matrix-assisted laser desorption/ionization mass spectrometry imaging. Anal Chim Acta 2017; 963:76-82. [DOI: 10.1016/j.aca.2017.01.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 01/02/2017] [Accepted: 01/13/2017] [Indexed: 11/18/2022]
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Kakimoto Y, Tsuruyama T, Yamamoto T, Furuta M, Kotani H, Ozeki M, Yoshizawa A, Haga H, Tamaki K. Novel in situ pretreatment method for significantly enhancing the signal in MALDI-TOF MS of formalin-fixed paraffin-embedded tissue sections. PLoS One 2012; 7:e41607. [PMID: 22899997 PMCID: PMC3416821 DOI: 10.1371/journal.pone.0041607] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/22/2012] [Indexed: 01/03/2023] Open
Abstract
The application of matrix-assisted laser desorption/ionization (MALDI)-based mass spectrometry (MS) to the proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue presents significant technical challenges. In situ enzymatic digestion is frequently used to unlock formalin-fixed tissues for analysis, but the results are often unsatisfactory. Here, we report a new, simplified in situ pretreatment method for preparing tissue sections for MS that involves heating with vapor containing acetonitrile in a small airtight pressurized space. The utility of the novel method is shown using FFPE tissue of human colon carcinoma. The number and intensity of MALDI peaks obtained from analysis of pretreated tissue was significantly higher than control tissue not subjected to pretreatment. A prominent peak (m/z 850) apparently specific to cancerous tissue was identified as a fragment of histone H2A in FFPE tissue pretreated using our method. This highly sensitive treatment may enable MALDI-MS analysis of archived pathological FFPE samples, thus leading to the identification of new biomarkers.
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Affiliation(s)
- Yu Kakimoto
- Department of Forensic Medicine and Molecular Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tatsuaki Tsuruyama
- Department of Forensic Medicine and Molecular Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- * E-mail:
| | - Takushi Yamamoto
- Analytical and Measuring Instruments Division, Kyoto Applications Development Center, Shimadzu Corporation, Kyoto, Japan
| | - Masaru Furuta
- Analytical and Measuring Instruments Division, Kyoto Applications Development Center, Shimadzu Corporation, Kyoto, Japan
| | - Hirokazu Kotani
- Department of Forensic Medicine and Molecular Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Munetaka Ozeki
- Department of Forensic Medicine and Molecular Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akihiko Yoshizawa
- Department of Diagnostic Pathology, Graduate School of Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Graduate School of Medicine, Kyoto University Hospital, Kyoto, Japan
| | - Keiji Tamaki
- Department of Forensic Medicine and Molecular Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Kakimoto Y, Tsuruyama T, Yamamoto T, Furuta M, Kotani H, Ozeki M, Yoshizawa A, Haga H, Tamaki K. Novel in situ pretreatment method for significantly enhancing the signal in MALDI-TOF MS of formalin-fixed paraffin-embedded tissue sections. PLoS One 2012. [PMID: 22899997 DOI: 10.1371/journal.pone.0041607pone-d-12-07910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The application of matrix-assisted laser desorption/ionization (MALDI)-based mass spectrometry (MS) to the proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue presents significant technical challenges. In situ enzymatic digestion is frequently used to unlock formalin-fixed tissues for analysis, but the results are often unsatisfactory. Here, we report a new, simplified in situ pretreatment method for preparing tissue sections for MS that involves heating with vapor containing acetonitrile in a small airtight pressurized space. The utility of the novel method is shown using FFPE tissue of human colon carcinoma. The number and intensity of MALDI peaks obtained from analysis of pretreated tissue was significantly higher than control tissue not subjected to pretreatment. A prominent peak (m/z 850) apparently specific to cancerous tissue was identified as a fragment of histone H2A in FFPE tissue pretreated using our method. This highly sensitive treatment may enable MALDI-MS analysis of archived pathological FFPE samples, thus leading to the identification of new biomarkers.
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Affiliation(s)
- Yu Kakimoto
- Department of Forensic Medicine and Molecular Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Mandal SM, Migliolo L, Das S, Mandal M, Franco OL, Hazra TK. Identification and characterization of a bactericidal and proapoptotic peptide from cycas revoluta seeds with DNA binding properties. J Cell Biochem 2011; 113:184-93. [DOI: 10.1002/jcb.23343] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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