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Drouin N, Elfrink HL, Boers SA, van Hugten S, Wessels E, de Vries JJC, Groeneveld GH, Miggiels P, Van Puyvelde B, Dhaenens M, Budding AE, Ran L, Masius R, Takats Z, Boogaerds A, Bulters M, Muurlink W, Oostvogel P, Harms AC, van der Lubben M, Hankemeier T. A Targeted LC-MRM 3 Proteomic Approach for the Diagnosis of SARS-CoV-2 Infection in Nasopharyngeal Swabs. Mol Cell Proteomics 2024; 23:100805. [PMID: 38897290 PMCID: PMC11284538 DOI: 10.1016/j.mcpro.2024.100805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 05/30/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024] Open
Abstract
Since its first appearance, severe acute respiratory syndrome coronavirus 2 quickly spread around the world and the lack of adequate PCR testing capacities, especially during the early pandemic, led the scientific community to explore new approaches such as mass spectrometry (MS). We developed a proteomics workflow to target several tryptic peptides of the nucleocapsid protein. A highly selective multiple reaction monitoring-cubed (MRM3) strategy provided a sensitivity increase in comparison to conventional MRM acquisition. Our MRM3 approach was first tested on an Amsterdam public health cohort (alpha-variant, 760 participants) detecting viral nucleocapsid protein peptides from nasopharyngeal swabs samples presenting a cycle threshold value down to 35 with sensitivity and specificity of 94.2% and 100.0%, without immunopurification. A second iteration of the MS-diagnostic test, able to analyze more than 400 samples per day, was clinically validated on a Leiden-Rijswijk public health cohort (delta-variant, 2536 participants) achieving 99.9% specificity and 93.1% sensitivity for patients with cycle threshold values up to 35. In this manuscript, we also developed and brought the first proof of the concept of viral variant monitoring in a complex matrix using targeted MS.
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Affiliation(s)
- Nicolas Drouin
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
| | - Hyung L Elfrink
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Stefan A Boers
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, The Netherlands
| | - Sam van Hugten
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, The Netherlands
| | - Els Wessels
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, The Netherlands
| | - Jutte J C de Vries
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, The Netherlands
| | - Geert H Groeneveld
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, The Netherlands; Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Paul Miggiels
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | | | | | - Zoltan Takats
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | | | | | | | - Paul Oostvogel
- Regional Laboratory, Municipal Health Service (GGD) Amsterdam, Amsterdam, The Netherlands
| | - Amy C Harms
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Mariken van der Lubben
- Regional Laboratory, Municipal Health Service (GGD) Amsterdam, Amsterdam, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
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2
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Van Puyvelde B, Hunter CL, Zhgamadze M, Savant S, Wang YO, Hoedt E, Raedschelders K, Pope M, Huynh CA, Ramanujan VK, Tourtellotte W, Razavi M, Anderson NL, Martens G, Deforce D, Fu Q, Dhaenens M, Van Eyk JE. Acoustic ejection mass spectrometry empowers ultra-fast protein biomarker quantification. Nat Commun 2024; 15:5114. [PMID: 38879593 PMCID: PMC11180209 DOI: 10.1038/s41467-024-48563-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/07/2024] [Indexed: 06/19/2024] Open
Abstract
The global scientific response to COVID 19 highlighted the urgent need for increased throughput and capacity in bioanalytical laboratories, especially for the precise quantification of proteins that pertain to health and disease. Acoustic ejection mass spectrometry (AEMS) represents a much-needed paradigm shift for ultra-fast biomarker screening. Here, a quantitative AEMS assays is presented, employing peptide immunocapture to enrich (i) 10 acute phase response (APR) protein markers from plasma, and (ii) SARS-CoV-2 NCAP peptides from nasopharyngeal swabs. The APR proteins were quantified in 267 plasma samples, in triplicate in 4.8 h, with %CV from 4.2% to 10.5%. SARS-CoV-2 peptides were quantified in triplicate from 145 viral swabs in 10 min. This assay represents a 15-fold speed improvement over LC-MS, with instrument stability demonstrated across 10,000 peptide measurements. The combination of speed from AEMS and selectivity from peptide immunocapture enables ultra-high throughput, reproducible quantitative biomarker screening in very large cohorts.
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Affiliation(s)
- Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Ghent, Belgium
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | | | - Maxim Zhgamadze
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | | | - Y Oliver Wang
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Esthelle Hoedt
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Koen Raedschelders
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Matt Pope
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC, 20009, USA
| | - Carissa A Huynh
- Cedars Sinai Biobank & Research Pathology Resource, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - V Krishnan Ramanujan
- Cedars Sinai Biobank & Research Pathology Resource, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Warren Tourtellotte
- Cedars Sinai Biobank & Research Pathology Resource, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Morteza Razavi
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC, 20009, USA
| | - N Leigh Anderson
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC, 20009, USA
| | - Geert Martens
- AZ Delta Medical Laboratories, AZ Delta General Hospital, 8800, Roeselare, Belgium
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Qin Fu
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Ghent, Belgium.
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
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3
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Wang R, Lu S, Deng F, Wu L, Yang G, Chong S, Liu Y. Enhancing the understanding of SARS-CoV-2 protein with structure and detection methods: An integrative review. Int J Biol Macromol 2024; 270:132237. [PMID: 38734351 DOI: 10.1016/j.ijbiomac.2024.132237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
As the rapid and accurate screening of infectious diseases can provide meaningful information for outbreak prevention and control, as well as owing to the existing limitations of the polymerase chain reaction (PCR), it is imperative to have new and validated detection techniques for SARS-CoV-2. Therefore, the rationale for outlining the techniques used to detect SARS-CoV-2 proteins and performing a comprehensive comparison to serve as a practical benchmark for future identification of similar viral proteins is clear. This review highlights the urgent need to strengthen pandemic preparedness by emphasizing the importance of integrated measures. These include improved tools for pathogen characterization, optimized societal precautions, the establishment of early warning systems, and the deployment of highly sensitive diagnostics for effective surveillance, triage, and resource management. Additionally, with an improved understanding of the virus' protein structure, considerable advances in targeted detection, treatment, and prevention strategies are expected to greatly improve our ability to respond to future outbreaks.
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Affiliation(s)
- Ruiqi Wang
- Shenyang University of Chemical Technology, Shenyang 110142, China; National Institute of Metrology, Beijing 100029, China
| | - Song Lu
- National Institute of Metrology, Beijing 100029, China
| | - Fanyu Deng
- National Institute of Metrology, Beijing 100029, China; North University of China, Taiyuan 030051, China
| | - Liqing Wu
- National Institute of Metrology, Beijing 100029, China
| | - Guowu Yang
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen 518055, China
| | - Siying Chong
- Shenyang University of Chemical Technology, Shenyang 110142, China
| | - Yahui Liu
- National Institute of Metrology, Beijing 100029, China.
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4
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Lane D, Allsopp R, Holmes CW, Slingsby OC, Jukes-Jones R, Bird P, Anderson NL, Razavi M, Yip R, Pearson TW, Pope M, Khunti K, Doykov I, Hällqvist J, Mills K, Skipp P, Carling R, Ng L, Shaw J, Gupta P, Jones DJL. A high throughput immuno-affinity mass spectrometry method for detection and quantitation of SARS-CoV-2 nucleoprotein in human saliva and its comparison with RT-PCR, RT-LAMP, and lateral flow rapid antigen test. Clin Chem Lab Med 2024; 62:1206-1216. [PMID: 38253336 DOI: 10.1515/cclm-2023-0243] [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: 03/06/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
OBJECTIVES Many reverse transcription polymerase chain reaction (RT-PCR) methods exist that can detect SARS-CoV-2 RNA in different matrices. RT-PCR is highly sensitive, although viral RNA may be detected long after active infection has taken place. SARS-CoV-2 proteins have shorter detection windows hence their detection might be more meaningful. Given salivary droplets represent a main source of transmission, we explored the detection of viral RNA and protein using four different detection platforms including SISCAPA peptide immunoaffinity liquid chromatography-mass spectrometry (SISCAPA-LC-MS) using polyclonal capture antibodies. METHODS The SISCAPA-LC MS method was compared to RT-PCR, RT-loop-mediated isothermal amplification (RT-LAMP), and a lateral flow rapid antigen test (RAT) for the detection of virus material in the drool saliva of 102 patients hospitalised after infection with SARS-CoV-2. Cycle thresholds (Ct) of RT-PCR (E gene) were compared to RT-LAMP time-to-positive (TTP) (NE and Orf1a genes), RAT optical densitometry measurements (test line/control line ratio) and to SISCAPA-LC-MS for measurements of viral protein. RESULTS SISCAPA-LC-MS showed low sensitivity (37.7 %) but high specificity (89.8 %). RAT showed lower sensitivity (24.5 %) and high specificity (100 %). RT-LAMP had high sensitivity (83.0 %) and specificity (100.0 %). At high initial viral RNA loads (<20 Ct), results obtained using SISCAPA-LC-MS correlated with RT-PCR (R2 0.57, p-value 0.002). CONCLUSIONS Detection of SARS-CoV-2 nucleoprotein in saliva was less frequent than the detection of viral RNA. The SISCAPA-LC-MS method allowed processing of multiple samples in <150 min and was scalable, enabling high throughput.
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Affiliation(s)
- Dan Lane
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, University Hospitals of Leicester, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Rebecca Allsopp
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Christopher W Holmes
- Clinical Microbiology, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | | | - Rebekah Jukes-Jones
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, University Hospitals of Leicester, Leicester, UK
| | - Paul Bird
- Clinical Microbiology, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | | | | | - Richard Yip
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | | | - Matt Pope
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | - Kamlesh Khunti
- Leicester Diabetes Centre, Leicester General Hospital, University of Leicester, Leicester, UK
| | - Ivan Doykov
- Genetics & Genomic Medicine Department, Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, UK
- Great Ormond Street Biomedical Research Centre, UCL Institute of Child Health, London, UK
| | - Jenny Hällqvist
- Genetics & Genomic Medicine Department, Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, UK
- Great Ormond Street Biomedical Research Centre, UCL Institute of Child Health, London, UK
| | - Kevin Mills
- Genetics & Genomic Medicine Department, Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, UK
- Great Ormond Street Biomedical Research Centre, UCL Institute of Child Health, London, UK
| | - Paul Skipp
- Centre for Proteomic Research, University of Southampton, Southampton, UK
| | - Rachel Carling
- Biochemical Sciences, Synnovis, Guys & St Thomas' NHSFT, London, UK
- GKT School Medical Education, Kings College London, London, UK
| | - Leong Ng
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Jacqui Shaw
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Pankaj Gupta
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, University Hospitals of Leicester, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Donald J L Jones
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
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5
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Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
- Bioinformatics ProgramBoston University School of MedicineBostonMassachusettsUSA
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6
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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7
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Kollhoff L, Kipping M, Rauh M, Ceglarek U, Barka G, Barka F, Sinz A. Development of a rapid and specific MALDI-TOF mass spectrometric assay for SARS-CoV-2 detection. Clin Proteomics 2023; 20:26. [PMID: 37393264 DOI: 10.1186/s12014-023-09415-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/19/2023] [Indexed: 07/03/2023] Open
Abstract
We have developed a rapid and highly specific assay for detecting and monitoring SARS-CoV-2 infections by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). As MALDI-TOF mass spectrometers are available in a clinical setting, our assay has the potential to serve as alternative to the commonly used reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). Sample preparation prior to MALDI-TOF-MS involves the tryptic digestion of SARS-CoV-2 proteins, followed by an enrichment of virus-specific peptides from SARS-CoV-2 nucleoprotein via magnetic antibody beads. Our MALDI-TOF-MS method allows the detection of SARS-CoV-2 nucleoprotein in sample collection medium as low as 8 amol/µl. MALDI-TOF mass spectra are obtained in just a few seconds, which makes our MS-based assay suitable for a high-throughput screening of SARS-CoV-2 in healthcare facilities in addition to PCR. Due to the specific detection of virus peptides, different SARS-CoV-2 variants are readily distinguished from each other. Specifically, we show that our MALDI-TOF-MS assay discriminates SARS-CoV-2 strain B.1.617.2 "delta variant" from all other variants in patients' samples, making our method highly valuable to monitor the emergence of new virus variants.
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Affiliation(s)
- Lydia Kollhoff
- Department of Pharmaceutical Chemistry and Bioanalytics, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120, Halle (Saale), Germany
| | - Marc Kipping
- Department of Pharmaceutical Chemistry and Bioanalytics, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120, Halle (Saale), Germany
| | - Manfred Rauh
- Department of Pediatrics and Adolescent Medicine, Friedrich Alexander University, Erlangen-Nürnberg, Germany
| | - Uta Ceglarek
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Günes Barka
- SunChrom Wissenschaftliche Geräte GmbH, 61381, Friedrichsdorf, Germany
| | - Frederik Barka
- SunChrom Wissenschaftliche Geräte GmbH, 61381, Friedrichsdorf, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120, Halle (Saale), Germany.
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120, Halle (Saale), Germany.
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Zhou W, Sui Z, Liu J, He Y, Yuan H, Sun Y, Liang Z, Yang K, Zhang L, Zhang Y. High-Sensitivity Detection toward SARS-CoV-2 S1 Glycoprotein by Parallel Reaction Monitoring Mass Spectrometry. Anal Chem 2023; 95:8752-8757. [PMID: 37246519 DOI: 10.1021/acs.analchem.2c05770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) has overwhelmed the global economy and human well-being. On account of the sharp increase in test demand, there is a need for an accurate and alternative diagnosis method for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, with the aim to specifically identify the trace SARS-CoV-2 S1 glycoprotein, we developed a high-sensitivity and high-selectivity diagnostic method based on the targeted parallel reaction monitoring (PRM) assay of eight selected peptides. This study emphasizes the outstanding detection sensitivity of 0.01 pg of the SARS-CoV-2 S1 glycoprotein even in the interference of other structural proteins, which to our knowledge is the current minimum limit of detection for the SARS-CoV-2 S1 glycoprotein. This technology could further identify 0.01 pg of the SARS-CoV-2 S1 glycoprotein in a spike pseudovirus, revealing its practical effectiveness. All our preliminary results throw light on the capability of the mass spectrometry-based targeted PRM assay to identify SARS-CoV-2 as a practicable orthogonal diagnostic tool. Furthermore, this technology could be extended to other pathogens (e.g., MERS-CoV S1 protein or SARS-CoV S1 protein) by quickly adjusting the targeted peptides of MS data acquisition. In summary, this strategy is universal and flexible and could be quickly adjusted to detect and discriminate different mutants and pathogens.
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Affiliation(s)
- Wen Zhou
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jianhui Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yingyun He
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huiming Yuan
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yue Sun
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kaiguang Yang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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9
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Declercq A, Bouwmeester R, Chiva C, Sabidó E, Hirschler A, Carapito C, Martens L, Degroeve S, Gabriels R. Updated MS²PIP web server supports cutting-edge proteomics applications. Nucleic Acids Res 2023:7151340. [PMID: 37140039 DOI: 10.1093/nar/gkad335] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/04/2023] [Accepted: 04/25/2023] [Indexed: 05/05/2023] Open
Abstract
Interest in the use of machine learning for peptide fragmentation spectrum prediction has been strongly on the rise over the past years, especially for applications in challenging proteomics identification workflows such as immunopeptidomics and the full-proteome identification of data independent acquisition spectra. Since its inception, the MS²PIP peptide spectrum predictor has been widely used for various downstream applications, mostly thanks to its accuracy, ease-of-use, and broad applicability. We here present a thoroughly updated version of the MS²PIP web server, which includes new and more performant prediction models for both tryptic- and non-tryptic peptides, for immunopeptides, and for CID-fragmented TMT-labeled peptides. Additionally, we have also added new functionality to greatly facilitate the generation of proteome-wide predicted spectral libraries, requiring only a FASTA protein file as input. These libraries also include retention time predictions from DeepLC. Moreover, we now provide pre-built and ready-to-download spectral libraries for various model organisms in multiple DIA-compatible spectral library formats. Besides upgrading the back-end models, the user experience on the MS²PIP web server is thus also greatly enhanced, extending its applicability to new domains, including immunopeptidomics and MS3-based TMT quantification experiments. MS²PIP is freely available at https://iomics.ugent.be/ms2pip/.
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Affiliation(s)
- Arthur Declercq
- VIB-UGent Center for Medical Biotechnology, VIB, Belgium
- Department of Biomolecular Medicine, Ghent University, Belgium
| | - Robbin Bouwmeester
- VIB-UGent Center for Medical Biotechnology, VIB, Belgium
- Department of Biomolecular Medicine, Ghent University, Belgium
| | - Cristina Chiva
- Proteomics Unit, Universitat Pompeu Fabra, 08003, Barcelona, Spain
- Proteomics Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Universitat Pompeu Fabra, 08003, Barcelona, Spain
- Proteomics Unit, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
| | - Aurélie Hirschler
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, France
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Belgium
- Department of Biomolecular Medicine, Ghent University, Belgium
| | - Sven Degroeve
- VIB-UGent Center for Medical Biotechnology, VIB, Belgium
- Department of Biomolecular Medicine, Ghent University, Belgium
| | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, Belgium
- Department of Biomolecular Medicine, Ghent University, Belgium
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10
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Hällqvist J, Lane D, Shapanis A, Davis K, Heywood WE, Doykov I, Śpiewak J, Ghansah N, Keevil B, Gupta P, Jukes-Jones R, Singh R, Foley D, Vissers JPC, Pattison R, Ferries S, Wardle R, Bartlett A, Calton LJ, Anderson L, Razavi M, Pearson T, Pope M, Yip R, Ng LL, Nicholas BI, Bailey A, Noel D, Dalton RN, Heales S, Hopley C, Pitt AR, Barran P, Jones DJL, Mills K, Skipp P, Carling RS. Operation Moonshot: rapid translation of a SARS-CoV-2 targeted peptide immunoaffinity liquid chromatography-tandem mass spectrometry test from research into routine clinical use. Clin Chem Lab Med 2023; 61:302-310. [PMID: 36395058 DOI: 10.1515/cclm-2022-1000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022]
Abstract
OBJECTIVES During 2020, the UK's Department of Health and Social Care (DHSC) established the Moonshot programme to fund various diagnostic approaches for the detection of SARS-CoV-2, the pathogen behind the COVID-19 pandemic. Mass spectrometry was one of the technologies proposed to increase testing capacity. METHODS Moonshot funded a multi-phase development programme, bringing together experts from academia, industry and the NHS to develop a state-of-the-art targeted protein assay utilising enrichment and liquid chromatography tandem mass spectrometry (LC-MS/MS) to capture and detect low levels of tryptic peptides derived from SARS-CoV-2 virus. The assay relies on detection of target peptides, ADETQALPQRK (ADE) and AYNVTQAFGR (AYN), derived from the nucleocapsid protein of SARS-CoV-2, measurement of which allowed the specific, sensitive, and robust detection of the virus from nasopharyngeal (NP) swabs. The diagnostic sensitivity and specificity of LC-MS/MS was compared with reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) via a prospective study. RESULTS Analysis of NP swabs (n=361) with a median RT-qPCR quantification cycle (Cq) of 27 (range 16.7-39.1) demonstrated diagnostic sensitivity of 92.4% (87.4-95.5), specificity of 97.4% (94.0-98.9) and near total concordance with RT-qPCR (Cohen's Kappa 0.90). Excluding Cq>32 samples, sensitivity was 97.9% (94.1-99.3), specificity 97.4% (94.0-98.9) and Cohen's Kappa 0.95. CONCLUSIONS This unique collaboration between academia, industry and the NHS enabled development, translation, and validation of a SARS-CoV-2 method in NP swabs to be achieved in 5 months. This pilot provides a model and pipeline for future accelerated development and implementation of LC-MS/MS protein/peptide assays into the routine clinical laboratory.
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Affiliation(s)
- Jenny Hällqvist
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
- UCL Queen Square Institute of Neurology, London, UK
| | - Dan Lane
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Leicester, UK
- Leicester Diabetes Centre, University of Leicester, Leicester General Hospital, Leicester, UK
| | - Andrew Shapanis
- Centre for Proteomic Research, University of Southampton, Southampton, UK
- Biological Sciences, University of Southampton, Southampton, UK
| | - Kayleigh Davis
- Biochemical Sciences, Synnovis, Guys & St Thomas' NHSFT, London, UK
| | - Wendy E Heywood
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Ivan Doykov
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Justyna Śpiewak
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Nana Ghansah
- Neurometabolic Unit, National Hospital, London, UK
| | - Brian Keevil
- Department of Biochemistry, Manchester University NHS Trust, Manchester, UK
| | - Pankaj Gupta
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Rebekah Jukes-Jones
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Raj Singh
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Dominic Foley
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | | | - Rebecca Pattison
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Samantha Ferries
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Robert Wardle
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Amy Bartlett
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Lisa J Calton
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Leigh Anderson
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Morteza Razavi
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Terry Pearson
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Matt Pope
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Richard Yip
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Leong L Ng
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | | | - Alistair Bailey
- Centre for Proteomic Research, University of Southampton, Southampton, UK
| | - Dan Noel
- Biological Sciences, University of Southampton, Southampton, UK
| | - R Neil Dalton
- WellChild Laboratory, Evelina London Children's Hospital, London, UK
| | - Simon Heales
- Neurometabolic Unit, National Hospital, London, UK
| | | | - Andrew R Pitt
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Perdita Barran
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Donald J L Jones
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Kevin Mills
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Paul Skipp
- Centre for Proteomic Research, University of Southampton, Southampton, UK
- Biological Sciences, University of Southampton, Southampton, UK
| | - Rachel S Carling
- Biochemical Sciences, Synnovis, Guys & St Thomas' NHSFT, London, UK
- GKT School Medical Education, Kings College London, London, UK
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11
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Van Puyvelde B, Van Uytfanghe K, Van Oudenhove L, Gabriels R, Van Royen T, Matthys A, Razavi M, Yip R, Pearson T, Drouin N, Claereboudt J, Foley D, Wardle R, Wyndham K, Hankemeier T, Jones D, Saelens X, Martens G, Stove CP, Deforce D, Martens L, Vissers JPC, Anderson NL, Dhaenens M. Cov 2MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein. Anal Chem 2022; 94:17379-17387. [PMID: 36490367 PMCID: PMC9773173 DOI: 10.1021/acs.analchem.2c01610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The pandemic readiness toolbox needs to be extended, targeting different biomolecules, using orthogonal experimental set-ups. Here, we build on our Cov-MS effort using LC-MS, adding SISCAPA technology to enrich proteotypic peptides of the SARS-CoV-2 nucleocapsid (N) protein from trypsin-digested patient samples. The Cov2MS assay is compatible with most matrices including nasopharyngeal swabs, saliva, and plasma and has increased sensitivity into the attomole range, a 1000-fold improvement compared to direct detection in a matrix. A strong positive correlation was observed with qPCR detection beyond a quantification cycle of 30-31, the level where no live virus can be cultured. The automatable sample preparation and reduced LC dependency allow analysis of up to 500 samples per day per instrument. Importantly, peptide enrichment allows detection of the N protein in pooled samples without sensitivity loss. Easily multiplexed, we detect variants and propose targets for Influenza A and B detection. Thus, the Cov2MS assay can be adapted to test for many different pathogens in pooled samples, providing longitudinal epidemiological monitoring of large numbers of pathogens within a population as an early warning system.
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Affiliation(s)
- Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Katleen Van Uytfanghe
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | | | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Tessa Van Royen
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Arne Matthys
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Morteza Razavi
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Richard Yip
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Terry Pearson
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Nicolas Drouin
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | | | - Dominic Foley
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Robert Wardle
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Kevin Wyndham
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | - Donald Jones
- Leicester Cancer Research Centre, RKCSB, Cardiovascular Research Centre, Glenfield Hospital, University of Leicester, Leicester LE1 7RH, United Kingdom.,John and Lucille van Geest Biomarker Facility, Leicester LE3 9QP, United Kingdom.,The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Level 4, Sandringham Building, Leicester LE1 7RH, United Kingdom
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Geert Martens
- AZ Delta Medical Laboratories, AZ Delta General Hospital, 8800 Roeselare, Belgium
| | - Christophe P Stove
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Johannes P C Vissers
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - N Leigh Anderson
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
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12
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Wong TF, So PK, Yao ZP. Advances in rapid detection of SARS-CoV-2 by mass spectrometry. Trends Analyt Chem 2022; 157:116759. [PMID: 36035092 PMCID: PMC9391230 DOI: 10.1016/j.trac.2022.116759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/01/2022] [Accepted: 08/14/2022] [Indexed: 12/25/2022]
Abstract
COVID-19 has already been lasting for more than two years and it has been severely affecting the whole world. Still, detection of SARS-CoV-2 remains the frontline approach to combat the pandemic, and the reverse transcription polymerase chain reaction (RT-PCR)-based method is the well recognized detection method for the enormous analytical demands. However, the RT-PCR method typically takes a relatively long time, and can produce false positive and false negative results. Mass spectrometry (MS) is a very commonly used technique with extraordinary sensitivity, specificity and speed, and can produce qualitative and quantitative information of various analytes, which cannot be achieved by RT-PCR. Since the pandemic outbreak, various mass spectrometric approaches have been developed for rapid detection of SARS-CoV-2, including the LC-MS/MS approaches that could allow analysis of several hundred clinical samples per day with one MS system, MALDI-MS approaches that could directly analyze clinical samples for the detection, and efforts for the on-site detection with portable devices. In this review, these mass spectrometric approaches were summarized, and their pros and cons as well as further development were also discussed.
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Affiliation(s)
- Tsz-Fung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Research Institute for Future Food and Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Pui-Kin So
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Research Institute for Future Food and Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Zhong-Ping Yao
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Research Institute for Future Food and Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
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13
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Adams C, Boonen K, Laukens K, Bittremieux W. Open Modification Searching of SARS-CoV-2-Human Protein Interaction Data Reveals Novel Viral Modification Sites. Mol Cell Proteomics 2022; 21:100425. [PMID: 36241021 PMCID: PMC9554009 DOI: 10.1016/j.mcpro.2022.100425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/18/2022] [Accepted: 10/09/2022] [Indexed: 01/18/2023] Open
Abstract
The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus 2019 disease, has led to an ongoing global pandemic since 2019. Mass spectrometry can be used to understand the molecular mechanisms of viral infection by SARS-CoV-2, for example, by determining virus-host protein-protein interactions through which SARS-CoV-2 hijacks its human hosts during infection, and to study the role of post-translational modifications. We have reanalyzed public affinity purification-mass spectrometry data using open modification searching to investigate the presence of post-translational modifications in the context of the SARS-CoV-2 virus-host protein-protein interaction network. Based on an over twofold increase in identified spectra, our detected protein interactions show a high overlap with independent mass spectrometry-based SARS-CoV-2 studies and virus-host interactions for alternative viruses, as well as previously unknown protein interactions. In addition, we identified several novel modification sites on SARS-CoV-2 proteins that we investigated in relation to their interactions with host proteins. A detailed analysis of relevant modifications, including phosphorylation, ubiquitination, and S-nitrosylation, provides important hypotheses about the functional role of these modifications during viral infection by SARS-CoV-2.
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Affiliation(s)
- Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium,Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium,Sustainable Health Department, Flemish Institute for Technological Research (VITO), Antwerp, Belgium
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,For correspondence: Wout Bittremieux
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14
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Suddhapas K, Choi MH, Shortreed MR, Timperman A. Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern. J Proteome Res 2022; 21:2443-2452. [PMID: 36108102 PMCID: PMC10318299 DOI: 10.1021/acs.jproteome.2c00325] [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] [Indexed: 11/28/2022]
Abstract
The SARS-CoV-2 omicron variant presented significant challenges to the global effort to counter the pandemic. SARS-CoV-2 is predicted to remain prevalent for the foreseeable future, making the ability to identify SARS-CoV-2 variants imperative in understanding and controlling the pandemic. The predominant variant discovery method, genome sequencing, is time-consuming, insensitive, and expensive. Ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) offers an exciting alternative detection modality provided that variant-containing peptide markers are sufficiently detectable from their tandem mass spectra (MS/MS). We have synthesized model tryptic peptides of SARS-CoV-2 variants alpha, beta, gamma, delta, and omicron and evaluated their signal intensity, HCD spectra, and reverse phase retention time. Detection limits of 781, 781, 65, and 65 amol are obtained for the molecular ions of the proteotypic peptides, beta (QIAPGQTGNIADYNYK), gamma (TQLPSAYTNSFTR), delta (VGGNYNYR), and omicron (TLVKQLSSK), from neat solutions. These detection limits are on par with the detection limits of a previously reported proteotypic peptide from the SARS-CoV-2 spike protein, HTPINLVR. This study demonstrates the potential to differentiate SARS-CoV-2 variants through their proteotypic peptides with an approach that is broadly applicable across a wide range of pathogens.
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Affiliation(s)
- Kantaphon Suddhapas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - M Hannah Choi
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - AaronT Timperman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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15
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Gajbhiye A, Nalbant A, Heunis T, Sidgwick F, Porter A, Taha Y, Trost M. A fast and sensitive absolute quantification assay for the detection of SARS-CoV-2 peptides using parallel reaction monitoring mass spectrometry. J Proteomics 2022; 265:104664. [PMID: 35732269 PMCID: PMC9212948 DOI: 10.1016/j.jprot.2022.104664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/12/2022] [Accepted: 06/12/2022] [Indexed: 12/25/2022]
Abstract
The on-going SARS-CoV-2 (COVID-19) pandemic has called for an urgent need for rapid and high-throughput methods for mass testing and early detection, prevention as well as surveillance of the disease. We investigated whether targeted parallel reaction monitoring (PRM) quantification using high resolution Orbitrap instruments can provide the sensitivity and speed required for a high-throughput method that could be used for clinical diagnosis. We developed a high-throughput and sensitive PRM-MS assay that enables absolute quantification of SARS-CoV-2 nucleocapsid peptides with short turn-around times by using isotopically labelled synthetic SARS-CoV-2 concatenated peptides. We established a fast and high-throughput S-trap-based sample preparation method and utilized it for testing 25 positive and 25 negative heat-inactivated clinical nasopharyngeal swab samples for SARS-CoV-2 detection. The method was able to differentiate between negative and some of the positive patients with high viral load. Moreover, based on the absolute quantification calculations, our data show that patients with Ct values as low as 17.8 correspond to NCAP protein amounts of around 7.5 pmol in swab samples. The present high-throughput method could potentially be utilized in specialized clinics as an alternative tool for detection of SARS-CoV-2 but will require enrichment of viral proteins in order to compete with RT-qPCR.
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Affiliation(s)
- Akshada Gajbhiye
- Laboratory for Biomedical Mass Spectrometry, Newcastle University, Newcastle upon Tyne, UK
| | - Atakan Nalbant
- Laboratory for Biomedical Mass Spectrometry, Newcastle University, Newcastle upon Tyne, UK
| | - Tiaan Heunis
- Laboratory for Biomedical Mass Spectrometry, Newcastle University, Newcastle upon Tyne, UK
| | - Frances Sidgwick
- Laboratory for Biomedical Mass Spectrometry, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Porter
- Laboratory for Biomedical Mass Spectrometry, Newcastle University, Newcastle upon Tyne, UK
| | - Yusri Taha
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, Newcastle upon Tyne NE1 4LP, UK
| | - Matthias Trost
- Laboratory for Biomedical Mass Spectrometry, Newcastle University, Newcastle upon Tyne, UK.
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16
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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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17
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Zhou X, Zhang W, Ouyang Z. Recent advances in on-site mass spectrometry analysis for clinical applications. Trends Analyt Chem 2022; 149:116548. [PMID: 35125564 PMCID: PMC8802081 DOI: 10.1016/j.trac.2022.116548] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In recent years, mass spectrometry (MS) is increasingly attracting interests for clinical applications, which also calls for technical innovations to make a transfer of MS from conventional analytical laboratories to clinics. The system design and analysis procedure should be friendly for novice users and appliable for on-site clinical diagnosis. In addition, the analysis result should be auto-interpreted and reported in formats much simpler than mass spectra. This motivates new ideas for developments in all the aspects of MS. In this review, we report recent advances of direct sampling ionization and miniature MS system, which have been developed targeting clinical and even point-of-care analysis. We also discuss the trend of the development and provide perspective on the technical challenges raised by diseases such as coronavirus SARS-CoV-2.
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Affiliation(s)
- Xiaoyu Zhou
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Wenpeng Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
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18
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Acharjee A, Stephen Kingsly J, Kamat M, Kurlawala V, Chakraborty A, Vyas P, Vaishnav R, Srivastava S. Rise of the SARS-CoV-2 Variants: can proteomics be the silver bullet? Expert Rev Proteomics 2022; 19:197-212. [PMID: 35655386 DOI: 10.1080/14789450.2022.2085564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The challenges posed by emergent strains of SARS-CoV-2 need to be tackled by contemporary scientific approaches, with proteomics playing a significant role. AREAS COVERED In this review, we provide a brief synthesis of the impact of proteomics technologies in elucidating disease pathogenesis and classifiers for the prognosis of COVID-19 and propose proteomics methodologies that could play a crucial role in understanding emerging variants and their altered disease pathology. From aiding the design of novel drug candidates to facilitating the identification of T cell vaccine targets, we have discussed the impact of proteomics methods in COVID-19 research. Techniques varied as mass spectrometry, single-cell proteomics, multiplexed ELISA arrays, high-density proteome arrays, surface plasmon resonance, immunopeptidomics, and in silico docking studies that have helped augment the fight against existing diseases were useful in preparing us to tackle SARS-CoV-2 variants. We also propose an action plan for a pipeline to combat emerging pandemics using proteomics technology by adopting uniform standard operating procedures and unified data analysis paradigms. EXPERT OPINION The knowledge about the use of diverse proteomics approaches for COVID-19 investigation will provide a framework for future basic research, better infectious disease prevention strategies, improved diagnostics, and targeted therapeutics.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Madhura Kamat
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | - Vishakha Kurlawala
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | | | - Priyanka Vyas
- Department of Biotechnology and Botany, Mahila PG Mahavidyalaya, J. N. V University, Jodhpur, India
| | - Radhika Vaishnav
- Department of Life Sciences, Ivy Tech Community College, Indianapolis, Indiana, USA
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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19
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Pinto G, Illiano A, Ferrucci V, Quarantelli F, Fontanarosa C, Siciliano R, Di Domenico C, Izzo B, Pucci P, Marino G, Zollo M, Amoresano A. Identification of SARS-CoV-2 Proteins from Nasopharyngeal Swabs Probed by Multiple Reaction Monitoring Tandem Mass Spectrometry. ACS OMEGA 2021; 6:34945-34953. [PMID: 34926968 PMCID: PMC8672425 DOI: 10.1021/acsomega.1c05587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/02/2021] [Indexed: 05/12/2023]
Abstract
Numerous reverse transcription polymerase chain reaction (RT-PCR) tests have emerged over the past year as the gold standard for detecting millions of cases of SARS-CoV-2 reported daily worldwide. However, problems with critical shortages of key reagents such as PCR primers and RNA extraction kits and unpredictable test reliability related to high viral replication cycles have triggered the need for alternative methodologies to PCR to detect specific COVID-19 proteins. Several authors have developed methods based on liquid chromatography with tandem mass spectrometry (LC-MS/MS) to confirm the potential of the technique to detect two major proteins, the spike and the nucleoprotein, of COVID-19. In the present work, an S-Trap mini spin column digestion protocol was used for sample preparation prodromal to LC-MS/MS analysis in multiple reactions monitoring ion mode (MRM) to obtain a comprehensive method capable of detecting different viral proteins. The developed method was applied to n. 81 oro/nasopharyngeal swabs submitted in parallel to quantitative reverse transcription PCR (RT-qPCR) assays to detect RdRP, the S and N genes specific for COVID-19, and the E gene for all Sarbecoviruses, including SARS-CoV-2 (with cycle negativity threshold set to 40). A total of 23 peptides representative of the six specific viral proteins were detected in the monitoring of 128 transitions found to have good ionic currents extracted in clinical samples that reacted differently to the PCR assay. The best instrumental response came from the FLPFQFGR sequence of spike [558-566] peptide used to test the analytical performance of the method that has good sensitivity with a low false-negative rate. Transition monitoring using a targeted MS approach has the great potential to detect the fragmentation reactions of any peptide molecularly defined by a specific amino acid sequence, offering the extensibility of the approach to any viral sequence including derived variants and thus providing insights into the development of new types of clinical diagnostics.
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Affiliation(s)
- Gabriella Pinto
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Anna Illiano
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Veronica Ferrucci
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | | | - Carolina Fontanarosa
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Roberto Siciliano
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Carmela Di Domenico
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Barbara Izzo
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | - Piero Pucci
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Gennaro Marino
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
| | - Massimo Zollo
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | - Angela Amoresano
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
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Abstract
A new protocol step improves robustness and ease-of-use for mass spectrometry in the clinic, opening the door to mass deployment to monitor infectious agents.
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Affiliation(s)
- Bart Van Puyvelde
- Laboratory of Pharmaceutical Biotechnology, Ghent UniversityGhentBelgium
- ProGenTomicsGhentBelgium
| | - Maarten Dhaenens
- Laboratory of Pharmaceutical Biotechnology, Ghent UniversityGhentBelgium
- ProGenTomicsGhentBelgium
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21
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Hober A, Tran-Minh KH, Foley D, McDonald T, Vissers JPC, Pattison R, Ferries S, Hermansson S, Betner I, Uhlén M, Razavi M, Yip R, Pope ME, Pearson TW, Andersson LN, Bartlett A, Calton L, Alm JJ, Engstrand L, Edfors F. Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis. eLife 2021; 10:e70843. [PMID: 34747696 PMCID: PMC8626084 DOI: 10.7554/elife.70843] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/04/2021] [Indexed: 12/11/2022] Open
Abstract
Reliable, robust, large-scale molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for monitoring the ongoing coronavirus disease 2019 (COVID-19) pandemic. We have developed a scalable analytical approach to detect viral proteins based on peptide immuno-affinity enrichment combined with liquid chromatography-mass spectrometry (LC-MS). This is a multiplexed strategy, based on targeted proteomics analysis and read-out by LC-MS, capable of precisely quantifying and confirming the presence of SARS-CoV-2 in phosphate-buffered saline (PBS) swab media from combined throat/nasopharynx/saliva samples. The results reveal that the levels of SARS-CoV-2 measured by LC-MS correlate well with their correspondingreal-time polymerase chain reaction (RT-PCR) read-out (r = 0.79). The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with a quantitative read-out of viral proteins corresponding to cycle thresholds (Ct) equivalents ranging from 21 to 34. Using RT-PCR as a reference, we demonstrate that the LC-MS-based method has 100% negative percent agreement (estimated specificity) and 95% positive percent agreement (estimated sensitivity) when analyzing clinical samples collected from asymptomatic individuals with a Ct within the limit of detection of the mass spectrometer (Ct ≤ 30). These results suggest that a scalable analytical method based on LC-MS has a place in future pandemic preparedness centers to complement current virus detection technologies.
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Affiliation(s)
| | - Khue Hua Tran-Minh
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
| | | | | | | | | | | | | | | | - Mathias Uhlén
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
| | | | - Richard Yip
- SISCAPA Assay Technologies, IncVictoriaCanada
| | | | | | | | | | | | - Jessica J Alm
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology & National Pandemic Center, Karolinska InstitutetSolnaSweden
| | - Lars Engstrand
- Microbiology, Tumour and Cell Biology, Karolinska InstitutetStockholmSweden
| | - Fredrik Edfors
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
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22
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Jones CW. International Open Access Week and JACS Au. JACS AU 2021; 1:1515. [PMID: 34723255 PMCID: PMC8549041 DOI: 10.1021/jacsau.1c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
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23
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A rapid and reliable liquid chromatography/mass spectrometry method for SARS-CoV-2 analysis from gargle solutions and saliva. Anal Bioanal Chem 2021; 413:6503-6511. [PMID: 34427712 PMCID: PMC8383918 DOI: 10.1007/s00216-021-03614-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/15/2021] [Accepted: 08/09/2021] [Indexed: 10/30/2022]
Abstract
We describe a rapid liquid chromatography/tandem mass spectrometry (LC-MS/MS) method for the direct detection and quantitation of SARS-CoV-2 nucleoprotein in gargle solutions and saliva. The method is based on a multiple-reaction monitoring (MRM) mass spectrometry approach with a total cycle time of 5 min per analysis and allows the detection and accurate quantitation of SARS-CoV-2 nucleoprotein as low as 500 amol/μL. We improved the sample preparation protocol of our recent piloting SARS-CoV-2 LC-MS study regarding sensitivity, reproducibility, and compatibility with a complementary reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) analysis of the same sample. The aim of this work is to promote diagnostic tools that allow identifying and monitoring SARS-CoV-2 infections by LC-MS/MS methods in a routine clinical environment.
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24
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Armengaud J. Unleashing immuno-mass spectrometry superpowers to detect SARS-CoV-2. EBioMedicine 2021; 69:103480. [PMID: 34252697 PMCID: PMC8270654 DOI: 10.1016/j.ebiom.2021.103480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 06/24/2021] [Indexed: 11/20/2022] Open
Abstract
In this article of EBioMedicine, Santosh Renuse and colleagues1 show the relevance of combining immunoaffinity capture with targeted mass spectrometry measurement to detect SARS-CoV-2 nucleocapsid proteins in nasopharyngeal swab samples. The COVID-19 pandemic has confirmed the need to improve the toolbox available to diagnose respiratory infections. Rapid, reliable, and highly specific detection is essential if we are to mount immediate preventive and therapeutic responses. This report stands out from previous studies as it implements immunocapture along with robust validation for a large cohort of subjects. The results presented show that mass spectrometry is definitively at a crossroads for large-scale clinical applications.
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Affiliation(s)
- Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France..
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