1
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Balvers M, Gordijn IF, Voskamp-Visser IA, Schelling MF, Schuurman R, Heikens E, Braakman R, Stingl C, van Leeuwen HC, Luider TM, Dekker LJ, Levin E, Paauw A. Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification. JOURNAL OF CLINICAL VIROLOGY PLUS 2023. [DOI: 10.1016/j.jcvp.2023.100147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
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2
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Simultaneous monitoring of eight human respiratory viruses including SARS-CoV-2 using liquid chromatography-tandem mass spectrometry. Sci Rep 2022; 12:13392. [PMID: 35927299 PMCID: PMC9352774 DOI: 10.1038/s41598-022-16250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection has primarily been achieved using reverse transcriptase polymerase chain reaction (RT-PCR) for acute infection, and serology for prior infection. Assay with RT-PCR provides data on presence or absence of viral RNA, with no information on virus replication competence, infectivity, or virus characterisation. Liquid chromatography-tandem mass spectrometry (LC–MS/MS) is typically not used in clinical virology, despite its potential to provide supplemental data about the presence of viral proteins and thus the potential for replication-competent, transmissible virus. Using the SARS-CoV-2 as a model virus, we developed a fast ‘bottom-up’ proteomics workflow for discovery of target virus peptides using ‘serum-free’ culture conditions, providing high coverage of viral proteins without the need for protein or peptide fractionation techniques. This workflow was then applied to Coronaviruses OC43 and 229E, Influenza A/H1N1 and H3N2, Influenza B, and Respiratory Syncytial Viruses A and B. Finally, we created an LC–MS/MS method for targeted detection of the eight-virus panel in clinical specimens, successfully detecting peptides from the SARS-CoV-2 ORF9B and nucleoprotein in RT-PCR positive samples. The method provides specific detection of respiratory viruses from clinical samples containing moderate viral loads and is an important further step to the use of LC–MS/MS in diagnosis of viral infection.
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3
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Mass Spectrometry Approaches for SARS-CoV-2 Detection: Harnessing for Application in Food and Environmental Samples. Viruses 2022; 14:v14050872. [PMID: 35632614 PMCID: PMC9144875 DOI: 10.3390/v14050872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
The public health crisis caused by the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in 2019 has drastically changed our lifestyle in virtually all contexts around the world. SARS-CoV-2 is mainly airborne, transmitted by the salivary droplets produced when infected people cough or sneeze. In addition, diarrhea symptoms and the detection of SARS-CoV-2 in feces suggest a fecal–oral route of contagion. Currently, the high demand for SARS-CoV-2 diagnosis has surpassed the availability of PCR and immunodetection probes and has prompted the development of other diagnostic alternatives. In this context, mass spectrometry (MS) represents a mature, robust alternative platform for detection of SARS-CoV-2 and other human viruses. This possibility has raised great interest worldwide. Therefore, it is time for the global application of MS as a feasible option for detecting SARS-CoV-2, not only in human fluids, but also in other matrices such as foods and wastewater. This review covers the most relevant established methods for MS-based SARS-CoV-2 detection and discusses the future application of these tools in different matrices. Significance: The Coronavirus Disease 2019 (COVID-19) pandemic highlighted the pros and cons of currently available PCR and immunodetection tools. The great concern over the infective potential of SARS-CoV-2 viral particles that can persist for several hours on different surfaces under various conditions further evidenced the need for reliable alternatives and high-throughput methods to meet the needs for mass detection of SARS-CoV-2. In this context, MS-based proteomics emerging from fundamental studies in life science can offer a robust option for SARS-CoV-2 detection in human fluids and other matrices. In addition, the substantial efforts towards detecting SARS-CoV-2 in clinal samples, position MS to support the detection of this virus in different matrices such as the surfaces of the packing food process, frozen foods, and wastewaters. Proteomics and mass spectrometry are, therefore, well positioned to play a role in the epidemiological control of COVID-19 and other future diseases. We are currently witnessing the opportunity to generate technologies to overcome prolonged pandemics for the first time in human history.
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4
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Consolidating the potency of Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) in viral diagnosis: extrapolating its applicability for COVID diagnosis? Trends Analyt Chem 2022; 150:116569. [PMID: 35221399 PMCID: PMC8861128 DOI: 10.1016/j.trac.2022.116569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
MALDI-TOF-MS has essentially delivered more than expected with respect to clinical pathogens. Viruses are the most versatile entities of clinical pathogens that have challenged well-established microbiological methodologies. This review evaluates the existing scenario with respect to MALDI TOF-MS analytical technique in the successful analysis of viral pathogens. The milestones achieved with respect to detection and identification of COVID-19 has been presented. The fact that only a handful of scattered applications for COVID-19 exist has been pointed out in the review. Further, the lapses in the utilization of the available state-of-the art MALDI-TOF-MS variants/benchmark sophistications for COVID-19 analysis, are highlighted. When the world is seeking for rapid solutions for early, sensitive, rapid COVID-19 diagnosis, maybe MALDI-TOF-MS, may be the actual ‘gold standard’. Reverting to the title, this review emphasizes that there is a need for extrapolating MALDI-TOF-MS for COVID-19 analysis and this calls for urgent scientific attention.
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5
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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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6
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Rais Y, Fu Z, Drabovich AP. Mass spectrometry-based proteomics in basic and translational research of SARS-CoV-2 coronavirus and its emerging mutants. Clin Proteomics 2021; 18:19. [PMID: 34384361 PMCID: PMC8358260 DOI: 10.1186/s12014-021-09325-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/07/2021] [Indexed: 01/08/2023] Open
Abstract
Molecular diagnostics of the coronavirus disease of 2019 (COVID-19) now mainly relies on the measurements of viral RNA by RT-PCR, or detection of anti-viral antibodies by immunoassays. In this review, we discussed the perspectives of mass spectrometry-based proteomics as an analytical technique to identify and quantify proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to enable basic research and clinical studies on COVID-19. While RT-PCR and RNA sequencing are indisputably powerful techniques for the detection of SARS-CoV-2 and identification of the emerging mutations, proteomics may provide confirmatory diagnostic information and complimentary biological knowledge on protein abundance, post-translational modifications, protein-protein interactions, and the functional impact of the emerging mutations. Pending advances in sensitivity and throughput of mass spectrometry and liquid chromatography, shotgun and targeted proteomic assays may find their niche for the differential quantification of viral proteins in clinical and environmental samples. Targeted proteomic assays in combination with immunoaffinity enrichments also provide orthogonal tools to evaluate cross-reactivity of serology tests and facilitate development of tests with the nearly perfect diagnostic specificity, this enabling reliable testing of broader populations for the acquired immunity. The coronavirus pandemic of 2019-2021 is another reminder that the future global pandemics may be inevitable, but their impact could be mitigated with the novel tools and assays, such as mass spectrometry-based proteomics, to enable continuous monitoring of emerging viruses, and to facilitate rapid response to novel infectious diseases.
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Affiliation(s)
- Yasmine Rais
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Zhiqiang Fu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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7
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Hasan MR, Suleiman M, Pérez-López A. Metabolomics in the Diagnosis and Prognosis of COVID-19. Front Genet 2021; 12:721556. [PMID: 34367265 PMCID: PMC8343128 DOI: 10.3389/fgene.2021.721556] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/05/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic triggered an unprecedented global effort in developing rapid and inexpensive diagnostic and prognostic tools. Since the genome of SARS-CoV-2 was uncovered, detection of viral RNA by RT-qPCR has played the most significant role in preventing the spread of the virus through early detection and tracing of suspected COVID-19 cases and through screening of at-risk population. However, a large number of alternative test methods based on SARS-CoV-2 RNA or proteins or host factors associated with SARS-CoV-2 infection have been developed and evaluated. The application of metabolomics in infectious disease diagnostics is an evolving area of science that was boosted by the urgency of COVID-19 pandemic. Metabolomics approaches that rely on the analysis of volatile organic compounds exhaled by COVID-19 patients hold promise for applications in a large-scale screening of population in point-of-care (POC) setting. On the other hand, successful application of mass-spectrometry to detect specific spectral signatures associated with COVID-19 in nasopharyngeal swab specimens may significantly save the cost and turnaround time of COVID-19 testing in the diagnostic microbiology and virology laboratories. Active research is also ongoing on the discovery of potential metabolomics-based prognostic markers for the disease that can be applied to serum or plasma specimens. Several metabolic pathways related to amino acid, lipid and energy metabolism were found to be affected by severe disease with COVID-19. In particular, tryptophan metabolism via the kynurenine pathway were persistently dysregulated in several independent studies, suggesting the roles of several metabolites of this pathway such as tryptophan, kynurenine and 3-hydroxykynurenine as potential prognostic markers of the disease. However, standardization of the test methods and large-scale clinical validation are necessary before these tests can be applied in a clinical setting. With rapidly expanding data on the metabolic profiles of COVID-19 patients with varying degrees of severity, it is likely that metabolomics will play an important role in near future in predicting the outcome of the disease with a greater degree of certainty.
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Affiliation(s)
- Mohammad Rubayet Hasan
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
| | | | - Andrés Pérez-López
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
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8
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MALDI-TOF Mass Spectroscopy Applications in Clinical Microbiology. Adv Pharmacol Pharm Sci 2021; 2021:9928238. [PMID: 34041492 PMCID: PMC8121603 DOI: 10.1155/2021/9928238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
There is a range of proteomics methods to spot and analyze bacterial protein contents such as liquid chromatography-mass spectrometry (LC-MS), two-dimensional gel electrophoresis, and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS), which give comprehensive information about the microorganisms that may be helpful within the diagnosis and coverings of infections. Microorganism identification by mass spectrometry is predicted on identifying a characteristic spectrum of every species so matched with an outsized database within the instrument. MALDI-TOF MS is one of the diagnostic methods, which is a straightforward, quick, and precise technique, and is employed in microbial diagnostic laboratories these days and may replace other diagnostic methods. This method identifies various microorganisms such as bacteria, fungi, parasites, and viruses, which supply comprehensive information. One of the MALDI-TOF MS's crucial applications is bacteriology, which helps identify bacterial species, identify toxins, and study bacterial antibiotic resistance. By knowing these cases, we will act more effectively against bacterial infections.
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9
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Deulofeu M, García-Cuesta E, Peña-Méndez EM, Conde JE, Jiménez-Romero O, Verdú E, Serrando MT, Salvadó V, Boadas-Vaello P. Detection of SARS-CoV-2 Infection in Human Nasopharyngeal Samples by Combining MALDI-TOF MS and Artificial Intelligence. Front Med (Lausanne) 2021; 8:661358. [PMID: 33869258 PMCID: PMC8047105 DOI: 10.3389/fmed.2021.661358] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/11/2021] [Indexed: 12/20/2022] Open
Abstract
The high infectivity of SARS-CoV-2 makes it essential to develop a rapid and accurate diagnostic test so that carriers can be isolated at an early stage. Viral RNA in nasopharyngeal samples by RT-PCR is currently considered the reference method although it is not recognized as a strong gold standard due to certain drawbacks. Here we develop a methodology combining the analysis of from human nasopharyngeal (NP) samples by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with the use of machine learning (ML). A total of 236 NP samples collected in two different viral transport media were analyzed with minimal sample preparation and the subsequent mass spectra data was used to build different ML models with two different techniques. The best model showed high performance in terms of accuracy, sensitivity and specificity, in all cases reaching values higher than 90%. Our results suggest that the analysis of NP samples by MALDI-TOF MS and ML is a simple, safe, fast and economic diagnostic test for COVID-19.
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Affiliation(s)
- Meritxell Deulofeu
- Research Group of Clinical Anatomy, Embryology and Neuroscience (NEOMA), Department of Medical Sciences, University of Girona, Girona, Spain.,ICS-IAS Girona Clinical Laboratory, Santa Caterina Hospital, Parc Sanitari Martí i Julià, Salt, Spain
| | - Esteban García-Cuesta
- Science, Computation, and Technology Department, School of Architecture, Design, and Engineering, European University of Madrid, Madrid, Spain.,Instant Biosensing Technologies, Carson, NV, United States
| | - Eladia María Peña-Méndez
- Analytical Chemistry Division, Department of Chemistry, Faculty of Science, University of La Laguna, La Laguna, Spain
| | - José Elías Conde
- Analytical Chemistry Division, Department of Chemistry, Faculty of Science, University of La Laguna, La Laguna, Spain
| | - Orlando Jiménez-Romero
- Research Group of Clinical Anatomy, Embryology and Neuroscience (NEOMA), Department of Medical Sciences, University of Girona, Girona, Spain.,ICS-IAS Girona Clinical Laboratory, Santa Caterina Hospital, Parc Sanitari Martí i Julià, Salt, Spain
| | - Enrique Verdú
- Research Group of Clinical Anatomy, Embryology and Neuroscience (NEOMA), Department of Medical Sciences, University of Girona, Girona, Spain
| | - María Teresa Serrando
- Research Group of Clinical Anatomy, Embryology and Neuroscience (NEOMA), Department of Medical Sciences, University of Girona, Girona, Spain.,ICS-IAS Girona Clinical Laboratory, Santa Caterina Hospital, Parc Sanitari Martí i Julià, Salt, Spain
| | - Victoria Salvadó
- Department of Chemistry, Faculty of Science, University of Girona, Girona, Spain
| | - Pere Boadas-Vaello
- Research Group of Clinical Anatomy, Embryology and Neuroscience (NEOMA), Department of Medical Sciences, University of Girona, Girona, Spain.,ICS-IAS Girona Clinical Laboratory, Santa Caterina Hospital, Parc Sanitari Martí i Julià, Salt, Spain
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10
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Saadi J, Oueslati S, Bellanger L, Gallais F, Dortet L, Roque-Afonso AM, Junot C, Naas T, Fenaille F, Becher F. Quantitative Assessment of SARS-CoV-2 Virus in Nasopharyngeal Swabs Stored in Transport Medium by a Straightforward LC-MS/MS Assay Targeting Nucleocapsid, Membrane, and Spike Proteins. J Proteome Res 2021; 20:1434-1443. [PMID: 33497234 DOI: 10.1021/acs.jproteome.0c00887] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Alternative methods to RT-PCR for SARS-CoV-2 detection are investigated to provide complementary data on viral proteins, increase the number of tests performed, or identify false positive/negative results. Here, we have developed a simple mass spectrometry assay for SARS-CoV-2 in nasopharyngeal swab samples using common laboratory reagents. The method employs high sensitivity and selectivity targeted mass spectrometry detection, monitoring nine constitutive peptides representative of the three main viral proteins and a straightforward pellet digestion protocol for convenient routine applications. Absolute quantification of N, M, and S proteins was achieved by addition of isotope-labeled versions of best peptides. Limit of detection, recovery, precision, and linearity were thoroughly evaluated in four representative viral transport media (VTM) containing distinct total protein content. The protocol was sensitive in all swab media with limit of detection determined at 2 × 103 pfu/mL, corresponding to as low as 30 pfu injected into the LC-MS/MS system. When tested on VTM-stored nasopharyngeal swab samples from positive and control patients, sensitivity was similar to or better than rapid immunoassay dipsticks, revealing a corresponding RT-PCR detection threshold at Ct ∼ 24. The study represents the first thorough evaluation of sensitivity and robustness of targeted mass spectrometry in nasal swabs, constituting a promising SARS-CoV-2 antigen assay for the first-line diagnosis of COVID-19 and compatible with the constraints of clinical settings. The raw files generated in this study can be found on PASSEL (Peptide Atlas) under data set identifier PASS01646.
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Affiliation(s)
- Justyna Saadi
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
| | - Saoussen Oueslati
- Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France
| | - Laurent Bellanger
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Fabrice Gallais
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Laurent Dortet
- Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France
| | - Anne-Marie Roque-Afonso
- Service de Virologie, Hôpital Paul-Brousse, APHP Paris Saclay, and UMR 1193 Physiopathogénèse et Traitement des Maladies du Foie, 94800 Villejuif, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
| | - Thierry Naas
- Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
| | - François Becher
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
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11
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Cardozo KHM, Lebkuchen A, Okai GG, Schuch RA, Viana LG, Olive AN, Lazari CDS, Fraga AM, Granato CFH, Pintão MCT, Carvalho VM. Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts. Nat Commun 2020; 11:6201. [PMID: 33273458 PMCID: PMC7713649 DOI: 10.1038/s41467-020-19925-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 96 samples within 4 hours. A TFC-MS system allows multiplexed analysis of 4 samples within 10 min, enabling the processing of more than 500 samples per day. We validate this method qualitatively (Tier 3) and quantitatively (Tier 1) using 985 specimens previously analyzed by real-time RT-PCR, and detect up to 84% of the positive cases with up to 97% specificity. The presented strategy has high sample stability and should be considered as an option for SARS-CoV-2 testing in large populations.
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Affiliation(s)
| | - Adriana Lebkuchen
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | | | | | - Luciana Godoy Viana
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | - Aline Nogueira Olive
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | | | - Ana Maria Fraga
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
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12
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SoRelle JA, Patel K, Filkins L, Park JY. Mass Spectrometry for COVID-19. Clin Chem 2020; 66:1367-1368. [PMID: 32956447 PMCID: PMC7543316 DOI: 10.1093/clinchem/hvaa222] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 09/09/2020] [Indexed: 11/17/2022]
Abstract
In the United States, response to the COVID-19 coronavirus pandemic has been hampered by inadequate testing resources for the causative virus SARS-CoV-2. In the early part of the pandemic, United States laboratories were initially heavily regulated and slow to provide testing. As the pandemic has progressed, the supply chain for instruments and reagents has been inconsistent and has revealed weaknesses in traditional sophisticated infectious disease testing. Testing capabilities of clinical laboratories could be substantially improved by assays that are more simplified and do not require multiple consumable reagents for extraction, purification, amplification and detection. One such technology with the potential to require minimal reagents is matrix-assisted laser desorption/ionization combined with mass spectrometry (MALDI-MS). Recently, Nachtigall and colleagues reported the development of a MALDI-MS method for the diagnosis of SARS-CoV-2 infection (1).
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Affiliation(s)
- Jeffrey A SoRelle
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Khushbu Patel
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Laura Filkins
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Pathology, Children's Health System of Texas, Dallas, TX
| | - Jason Y Park
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Pathology, Children's Health System of Texas, Dallas, TX.,McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX
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13
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A comprehensive overview of proteomics approach for COVID 19: new perspectives in target therapy strategies. ACTA ACUST UNITED AC 2020; 11:223-232. [PMID: 33162722 PMCID: PMC7605460 DOI: 10.1007/s42485-020-00052-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/09/2020] [Accepted: 10/17/2020] [Indexed: 12/24/2022]
Abstract
World Health Organisation declared COVID-19 a pandemic on March 11, 2020. It was temporarily named as 2019-nCoV then subsequently named as COVID-19 virus. A coronavirus is a group of viruses, known to be zoonotic, causing illness ranging from acute to mild respiratory infections. These are spherical or pleomorphic enveloped particles containing positive sense RNA. The virus enters host cells, its uncoated genetic material transcribes, and translates. Since it has started spreading rapidly, protective measures have been taken all over the world. However, its transmission has been proved to be unstoppable and the absence of an effective drug makes the situation worse. The scientific community has gone all-out to discover and develop a possible vaccine or a competent antiviral drug. Other domains of biological sciences that promise effective results and target somewhat stable entities that are proteins, could be very useful in this time of crisis. Proteomics and metabolomics are the vast fields that are equipped with sufficient technologies to face this challenge. Various protein separation and identification techniques are available which facilitates the analysis of various types of interactions among proteins and their evolutionary lineages. The presented review aims at confronting the question: 'how proteomics can help in tackling SARS-CoV-2?' It deals with the role of upcoming proteome technology in these pandemic situations and discusses the proteomics approach towards the COVID-19 dilemma.
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14
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Milewska A, Ner‐Kluza J, Dabrowska A, Bodzon‐Kulakowska A, Pyrc K, Suder P. MASS SPECTROMETRY IN VIROLOGICAL SCIENCES. MASS SPECTROMETRY REVIEWS 2020; 39:499-522. [PMID: 31876329 PMCID: PMC7228374 DOI: 10.1002/mas.21617] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/15/2019] [Indexed: 05/24/2023]
Abstract
Virology, as a branch of the life sciences, discovered mass spectrometry (MS) to be the pivotal tool around two decades ago. The technique unveiled the complex network of interactions between the living world of pro- and eukaryotes and viruses, which delivered "a piece of bad news wrapped in protein" as defined by Peter Medawar, Nobel Prize Laureate, in 1960. However, MS is constantly evolving, and novel approaches allow for a better understanding of interactions in this micro- and nanoworld. Currently, we can investigate the interplay between the virus and the cell by analyzing proteomes, interactomes, virus-cell interactions, and search for the compounds that build viral structures. In addition, by using MS, it is possible to look at the cell from the broader perspective and determine the role of viral infection on the scale of the organism, for example, monitoring the crosstalk between infected tissues and the immune system. In such a way, MS became one of the major tools for the modern virology, allowing us to see the infection in the context of the whole cell or the organism. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Aleksandra Milewska
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
| | - Joanna Ner‐Kluza
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
| | - Agnieszka Dabrowska
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
- Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityGronostajowa 730‐387KrakowPoland
| | - Anna Bodzon‐Kulakowska
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
| | - Krzysztof Pyrc
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
| | - Piotr Suder
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
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15
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Singh P, Chakraborty R, Marwal R, Radhakrishan VS, Bhaskar AK, Vashisht H, Dhar MS, Pradhan S, Ranjan G, Imran M, Raj A, Sharma U, Singh P, Lall H, Dutta M, Garg P, Ray A, Dash D, Sivasubbu S, Gogia H, Madan P, Kabra S, Singh SK, Agrawal A, Rakshit P, Kumar P, Sengupta S. A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry. ACTA ACUST UNITED AC 2020; 11:159-165. [PMID: 33132628 PMCID: PMC7457902 DOI: 10.1007/s42485-020-00044-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022]
Abstract
In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel coronavirus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation are key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a multiple reaction monitoring we can detect the presence of two peptides specific to SARS-CoV-2 in a 2.3 min gradient run with 100% specificity and 90.5% sensitivity when compared to RT-PCR. Importantly, we further show that these peptides could be detected even in the patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR highlighting the sensitivity of the technique. This method has the translational potential of in terms of the rapid diagnostics of symptomatic and asymptomatic COVID-19 and can augment current methods available for diagnosis of SARS-CoV-2.
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Affiliation(s)
- Praveen Singh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025 India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Rahul Chakraborty
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025 India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Robin Marwal
- National Center for Disease Control, New Delhi, 110054 India
| | | | - Akash Kumar Bhaskar
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025 India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | | | - Mahesh S Dhar
- National Center for Disease Control, New Delhi, 110054 India
| | - Shalini Pradhan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025 India
| | - Gyan Ranjan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025 India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025 India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Anurag Raj
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025 India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Uma Sharma
- National Center for Disease Control, New Delhi, 110054 India
| | - Priyanka Singh
- National Center for Disease Control, New Delhi, 110054 India
| | - Hemlata Lall
- National Center for Disease Control, New Delhi, 110054 India
| | - Meena Dutta
- National Center for Disease Control, New Delhi, 110054 India
| | - Parth Garg
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, New Delhi, 110020 India
| | - Arjun Ray
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, New Delhi, 110020 India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025 India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025 India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Hema Gogia
- National Center for Disease Control, New Delhi, 110054 India
| | - Preeti Madan
- National Center for Disease Control, New Delhi, 110054 India
| | - Sandhya Kabra
- National Center for Disease Control, New Delhi, 110054 India
| | - Sujeet K Singh
- National Center for Disease Control, New Delhi, 110054 India
| | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025 India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Partha Rakshit
- National Center for Disease Control, New Delhi, 110054 India
| | - Pramod Kumar
- National Center for Disease Control, New Delhi, 110054 India
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025 India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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16
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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17
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Torres I, Giménez E, Vinuesa V, Pascual T, Moya JM, Alberola J, Martínez-Sapiña A, Navarro D. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) proteomic profiling of cerebrospinal fluid in the diagnosis of enteroviral meningitis: a proof-of-principle study. Eur J Clin Microbiol Infect Dis 2018; 37:2331-2339. [PMID: 30264355 DOI: 10.1007/s10096-018-3380-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/11/2018] [Indexed: 12/13/2022]
Abstract
The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for diagnosing viral infections by directly testing clinical specimens has not previously been explored. In this proof-of-principle study, we tested the hypothesis that proteomic profiling of cerebrospinal fluid (CSF) by mass spectrometry may be useful in the diagnosis of enteroviral (EV) meningitis. A total of 114 cryopreserved CSF samples were analyzed, of which 47 were positive for EV and 67 were negative. Total CSF proteins were precipitated and subjected to MALDI-TOF-MS analysis in a low (2-20 kDa) molecular weight range using a MicroFlex LT mass spectrometer. The whole data set was randomly split into a training set (n = 76 specimens) and a validation set (n = 38 samples). Backward/forward stepwise logistic regression analyses identified 30 peaks that were differentially present in EV-positive and EV-negative specimens. These were used to build a model which displayed an overall classification accuracy of 93%. The discriminative ability of the model was confirmed by using a validation sample set (overall accuracy 83%). In fact, the model was able to correctly classify 61 out of 67 EV-negative samples and 42 out of 47 EV-positive specimens. EV meningitis is associated with a distinctive protein profile that may be directly detectable in CSF specimens by MALDI-TOF-MS.
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Affiliation(s)
- Ignacio Torres
- Microbiology Service, Institute for Research INCLIVA, Hospital Clínico Universitario, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Institute for Research INCLIVA, Hospital Clínico Universitario, Valencia, Spain
| | - Víctor Vinuesa
- Microbiology Service, Institute for Research INCLIVA, Hospital Clínico Universitario, Valencia, Spain
| | - Tania Pascual
- Microbiology Service, Institute for Research INCLIVA, Hospital Clínico Universitario, Valencia, Spain
| | - Juan Miguel Moya
- Microbiology Service, Institute for Research INCLIVA, Hospital Clínico Universitario, Valencia, Spain
| | - Juan Alberola
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibáñez 17, 46010, Valencia, Spain
| | | | - David Navarro
- Microbiology Service, Institute for Research INCLIVA, Hospital Clínico Universitario, Valencia, Spain.
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibáñez 17, 46010, Valencia, Spain.
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18
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Camarasa CG, Cobo F. Application of MALDI-TOF Mass Spectrometry in Clinical Virology. THE USE OF MASS SPECTROMETRY TECHNOLOGY (MALDI-TOF) IN CLINICAL MICROBIOLOGY 2018. [PMCID: PMC7150354 DOI: 10.1016/b978-0-12-814451-0.00012-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS) is a diagnostic tool of microbial identification and characterization based on the detection of the mass of molecules. In the majority of clinical laboratories, this technology is currently being used mainly for bacterial diagnosis, but several approaches in the field of virology have been investigated. The introduction of this technology in clinical virology will improve the diagnosis of infections produced by viruses but also the discovery of mutations and variants of these microorganisms as well as the detection of antiviral resistance. This chapter is focused on the main current applications of MALDI-TOF MS techniques in clinical virology showing the state of the art with respect to this exciting new technology.
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19
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Berendsen EM, Levin E, Braakman R, der Riet-van Oeveren DV, Sedee NJA, Paauw A. Identification of microorganisms grown in blood culture flasks using liquid chromatography–tandem mass spectrometry. Future Microbiol 2017; 12:1135-1145. [DOI: 10.2217/fmb-2017-0050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Aim: Bloodstream infections are a common cause of disease and a fast and accurate identification of the causative agent or agents of bloodstream infections would aid the start of adequate treatment. Materials & methods: A liquid chromatography–tandem mass spectrometry (LC–MS/MS) shotgun proteomics method was developed for the identification of bacterial species directly from blood cultures that were simulated by inoculating blood culture bottles with single or multiple clinically relevant microorganisms. Results: Using LC–MS/MS, the single species were correctly identified in 100% of the blood cultures, whereas for polymicrobial infections, 78% of both species were correctly identified in blood cultures. Conclusion: The LC–MS/MS method allows for the identification of the causative agent of positive blood cultures.
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Affiliation(s)
- Erwin M Berendsen
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, Lange Kleiweg 137, 2288 GJ Rijswijk, The Netherlands
| | - Evgeni Levin
- Department of Microbiology & Systems Biology, Netherlands Organization for Applied Scientific Research TNO, Utrechtseweg 48, 3704HE Zeist, The Netherlands
| | - René Braakman
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, Lange Kleiweg 137, 2288 GJ Rijswijk, The Netherlands
| | - Debora van der Riet-van Oeveren
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, Lange Kleiweg 137, 2288 GJ Rijswijk, The Netherlands
| | - Norbert JA Sedee
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, Lange Kleiweg 137, 2288 GJ Rijswijk, The Netherlands
| | - Armand Paauw
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, Lange Kleiweg 137, 2288 GJ Rijswijk, The Netherlands
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20
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21
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Calderaro A, Arcangeletti MC, Rodighiero I, Buttrini M, Montecchini S, Vasile Simone R, Medici MC, Chezzi C, De Conto F. Identification of different respiratory viruses, after a cell culture step, by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Sci Rep 2016; 6:36082. [PMID: 27786297 PMCID: PMC5081539 DOI: 10.1038/srep36082] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023] Open
Abstract
In this study matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), a reliable identification method for the diagnosis of bacterial and fungal infections, is presented as an innovative tool to investigate the protein profile of cell cultures infected by the most common viruses causing respiratory tract infections in humans. MALDI-TOF MS was applied to the identification of influenza A and B viruses, adenovirus C species, parainfluenza virus types 1, 2 and 3, respiratory syncytial virus, echovirus, cytomegalovirus and metapneumovirus. In this study MALDI-TOF MS was proposed as a model to be applied to the identification of cultivable respiratory viruses using cell culture as a viral proteins enrichment method to the proteome profiling of virus infected and uninfected cell cultures. The reference virus strains and 58 viruses identified from respiratory samples of subjects with respiratory diseases positive for one of the above mentioned viral agents by cell culture were used for the in vitro infection of suitable cell cultures. The isolated viral particles, concentrated by ultracentrifugation, were used for subsequent protein extraction and their spectra profiles were generated by MALDI-TOF MS analysis. The newly created library allowed us to discriminate between uninfected and respiratory virus infected cell cultures.
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Affiliation(s)
- Adriana Calderaro
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Maria Cristina Arcangeletti
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Isabella Rodighiero
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Mirko Buttrini
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Sara Montecchini
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Rosita Vasile Simone
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Maria Cristina Medici
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Carlo Chezzi
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
| | - Flora De Conto
- Department of Clinical and Experimental Medicine – Unit of Microbiology and Virology - University of Parma – Parma, Italy
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22
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Challenges and opportunities of using liquid chromatography and mass spectrometry methods to develop complex vaccine antigens as pharmaceutical dosage forms. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1032:23-38. [PMID: 27071526 DOI: 10.1016/j.jchromb.2016.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 12/22/2022]
Abstract
Liquid chromatographic methods, combined with mass spectrometry, offer exciting and important opportunities to better characterize complex vaccine antigens including recombinant proteins, virus-like particles, inactivated viruses, polysaccharides, and protein-polysaccharide conjugates. The current abilities and limitations of these physicochemical methods to complement traditional in vitro and in vivo vaccine potency assays are explored in this review through the use of illustrative case studies. Various applications of these state-of-the art techniques are illustrated that include the analysis of influenza vaccines (inactivated whole virus and recombinant hemagglutinin), virus-like particle vaccines (human papillomavirus and hepatitis B), and polysaccharide linked to protein carrier vaccines (pneumococcal). Examples of utilizing these analytical methods to characterize vaccine antigens in the presence of adjuvants, which are often included to boost immune responses as part of the final vaccine dosage form, are also presented. Some of the challenges of using chromatographic and LC-MS as physicochemical assays to routinely test complex vaccine antigens are also discussed.
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23
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Duriez E, Armengaud J, Fenaille F, Ezan E. Mass spectrometry for the detection of bioterrorism agents: from environmental to clinical applications. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:183-199. [PMID: 26956386 DOI: 10.1002/jms.3747] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/14/2015] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
In the current context of international conflicts and localized terrorist actions, there is unfortunately a permanent threat of attacks with unconventional warfare agents. Among these, biological agents such as toxins, microorganisms, and viruses deserve particular attention owing to their ease of production and dissemination. Mass spectrometry (MS)-based techniques for the detection and quantification of biological agents have a decisive role to play for countermeasures in a scenario of biological attacks. The application of MS to every field of both organic and macromolecular species has in recent years been revolutionized by the development of soft ionization techniques (MALDI and ESI), and by the continuous development of MS technologies (high resolution, accurate mass HR/AM instruments, novel analyzers, hybrid configurations). New possibilities have emerged for exquisite specific and sensitive detection of biological warfare agents. MS-based strategies for clinical application can now address a wide range of analytical questions mainly including issues related to the complexity of biological samples and their available volume. Multiplexed toxin detection, discovery of new markers through omics approaches, and identification of untargeted microbiological or of novel molecular targets are examples of applications. In this paper, we will present these technological advances along with the novel perspectives offered by omics approaches to clinical detection and follow-up.
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Affiliation(s)
| | - Jean Armengaud
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunologie, 30207, Bagnols sur-Cèze, France
| | - François Fenaille
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, CEA Saclay, Building 136, 91191, Gif-sur-Yvette cedex, France
| | - Eric Ezan
- CEA, Programme Transversal Technologies pour la Santé, 91191, Gif sur Yvette, France
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24
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van Belkum A, Chatellier S, Girard V, Pincus D, Deol P, Dunne WM. Progress in proteomics for clinical microbiology: MALDI-TOF MS for microbial species identification and more. Expert Rev Proteomics 2015; 12:595-605. [DOI: 10.1586/14789450.2015.1091731] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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25
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Simultaneous Identification of Multiple β-Lactamases in Acinetobacter baumannii in Relation to Carbapenem and Ceftazidime Resistance, Using Liquid Chromatography-Tandem Mass Spectrometry. J Clin Microbiol 2015; 53:1927-30. [PMID: 25788550 DOI: 10.1128/jcm.00620-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 03/14/2015] [Indexed: 01/15/2023] Open
Abstract
Shotgun proteomics using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was applied to detect β-lactamases in clinical Acinetobacter baumannii isolates. The correlation of the detection of β-lactamase proteins (rather than PCR detection of the corresponding genes) with the resistance phenotypes demonstrated an added value for LC-MS/MS in antimicrobial susceptibility testing.
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