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Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing.
Mol Cell Proteomics. 2020 09; 19(9):1503-1522.MC

Abstract

As the COVID-19 pandemic continues to spread, thousands of scientists around the globe have changed research direction to understand better how the virus works and to find out how it may be tackled. The number of manuscripts on preprint servers is soaring and peer-reviewed publications using MS-based proteomics are beginning to emerge. To facilitate proteomic research on SARS-CoV-2, the virus that causes COVID-19, this report presents deep-scale proteomes (10,000 proteins; >130,000 peptides) of common cell line models, notably Vero E6, Calu-3, Caco-2, and ACE2-A549 that characterize their protein expression profiles including viral entry factors such as ACE2 or TMPRSS2. Using the 9 kDa protein SRP9 and the breast cancer oncogene BRCA1 as examples, we show how the proteome expression data can be used to refine the annotation of protein-coding regions of the African green monkey and the Vero cell line genomes. Monitoring changes of the proteome on viral infection revealed widespread expression changes including transcriptional regulators, protease inhibitors, and proteins involved in innate immunity. Based on a library of 98 stable-isotope labeled synthetic peptides representing 11 SARS-CoV-2 proteins, we developed PRM (parallel reaction monitoring) assays for nano-flow and micro-flow LC-MS/MS. We assessed the merits of these PRM assays using supernatants of virus-infected Vero E6 cells and challenged the assays by analyzing two diagnostic cohorts of 24 (+30) SARS-CoV-2 positive and 28 (+9) negative cases. In light of the results obtained and including recent publications or manuscripts on preprint servers, we critically discuss the merits of MS-based proteomics for SARS-CoV-2 research and testing.

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Authors+Show Affiliations

Zecha J
Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
Lee CY
Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
Bayer FP
Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
Meng C
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany.
Grass V
Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany; German Center for Infection Research (DZIF), Munich partner site, Germany.
Zerweck J
JPT Peptide Technologies GmbH, Berlin, Germany.
Schnatbaum K
JPT Peptide Technologies GmbH, Berlin, Germany.
Michler T
Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany.
Pichlmair A
Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany; German Center for Infection Research (DZIF), Munich partner site, Germany.
Ludwig C
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany. Electronic address: tina.ludwig@tum.de.
Kuster B
Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany. Electronic address: kuster@tum.de.

MeSH

A549 CellsAmino Acid SequenceAngiotensin-Converting Enzyme 2AnimalsBRCA1 ProteinBetacoronavirusCOVID-19Caco-2 CellsCase-Control StudiesChlorocebus aethiopsCoronavirus InfectionsGene Expression RegulationGene OntologyHost-Pathogen InteractionsHumansIndicators and ReagentsMolecular Sequence AnnotationOpen Reading FramesPandemicsPeptidyl-Dipeptidase APneumonia, ViralProteomicsSARS-CoV-2Serine EndopeptidasesSignal Recognition ParticleSignal TransductionVero CellsViral ProteinsVirus Internalization

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32591346

Citation

Zecha, Jana, et al. "Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing." Molecular & Cellular Proteomics : MCP, vol. 19, no. 9, 2020, pp. 1503-1522.
Zecha J, Lee CY, Bayer FP, et al. Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing. Mol Cell Proteomics. 2020;19(9):1503-1522.
Zecha, J., Lee, C. Y., Bayer, F. P., Meng, C., Grass, V., Zerweck, J., Schnatbaum, K., Michler, T., Pichlmair, A., Ludwig, C., & Kuster, B. (2020). Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing. Molecular & Cellular Proteomics : MCP, 19(9), 1503-1522. https://doi.org/10.1074/mcp.RA120.002164
Zecha J, et al. Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing. Mol Cell Proteomics. 2020;19(9):1503-1522. PubMed PMID: 32591346.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing. AU - Zecha,Jana, AU - Lee,Chien-Yun, AU - Bayer,Florian P, AU - Meng,Chen, AU - Grass,Vincent, AU - Zerweck,Johannes, AU - Schnatbaum,Karsten, AU - Michler,Thomas, AU - Pichlmair,Andreas, AU - Ludwig,Christina, AU - Kuster,Bernhard, Y1 - 2020/06/26/ PY - 2020/06/09/received PY - 2020/06/26/revised PY - 2020/6/28/pubmed PY - 2020/9/17/medline PY - 2020/6/28/entrez KW - ACE2 KW - COVID-19 KW - SARS-CoV-2 KW - Vero E6 KW - clinical proteomics KW - label-free quantification KW - mass spectrometry KW - parallel reaction monitoring KW - stable-isotope labeling KW - targeted mass spectrometry SP - 1503 EP - 1522 JF - Molecular & cellular proteomics : MCP JO - Mol Cell Proteomics VL - 19 IS - 9 N2 - As the COVID-19 pandemic continues to spread, thousands of scientists around the globe have changed research direction to understand better how the virus works and to find out how it may be tackled. The number of manuscripts on preprint servers is soaring and peer-reviewed publications using MS-based proteomics are beginning to emerge. To facilitate proteomic research on SARS-CoV-2, the virus that causes COVID-19, this report presents deep-scale proteomes (10,000 proteins; >130,000 peptides) of common cell line models, notably Vero E6, Calu-3, Caco-2, and ACE2-A549 that characterize their protein expression profiles including viral entry factors such as ACE2 or TMPRSS2. Using the 9 kDa protein SRP9 and the breast cancer oncogene BRCA1 as examples, we show how the proteome expression data can be used to refine the annotation of protein-coding regions of the African green monkey and the Vero cell line genomes. Monitoring changes of the proteome on viral infection revealed widespread expression changes including transcriptional regulators, protease inhibitors, and proteins involved in innate immunity. Based on a library of 98 stable-isotope labeled synthetic peptides representing 11 SARS-CoV-2 proteins, we developed PRM (parallel reaction monitoring) assays for nano-flow and micro-flow LC-MS/MS. We assessed the merits of these PRM assays using supernatants of virus-infected Vero E6 cells and challenged the assays by analyzing two diagnostic cohorts of 24 (+30) SARS-CoV-2 positive and 28 (+9) negative cases. In light of the results obtained and including recent publications or manuscripts on preprint servers, we critically discuss the merits of MS-based proteomics for SARS-CoV-2 research and testing. SN - 1535-9484 UR - https://www.unboundmedicine.com/medline/citation/32591346/Data_Reagents_Assays_and_Merits_of_Proteomics_for_SARS_CoV_2_Research_and_Testing_ DB - PRIME DP - Unbound Medicine ER -