Proteomics-based Mass Spectrometry Profiling of SARS-CoV-2 Infection from Human Nasopharyngeal Samples

Overview

Journal Mass Spectrom Rev

Publisher Wiley

Specialty Chemistry

Date 2022 Sep 30

PMID 36177493

Authors

Sayantani Chatterjee

Joseph Zaia

Affiliations

Soon will be listed here.

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.

Citing Articles

Measuring N and C Enrichment Levels in Sparsely Labeled Proteins Using High-Resolution and Tandem Mass Spectrometry.

Roberts E, Choi J, Risher J, Kremer P, Barb A, Jonathan Amster I J Am Soc Mass Spectrom. 2024; 35(12):2877-2889.

PMID: 39530698 PMC: 11622383. DOI: 10.1021/jasms.4c00237.

The Impact of Serum/Plasma Proteomics on SARS-CoV-2 Diagnosis and Prognosis.

DAmato M, Grignano M, Iadarola P, Rampino T, Gregorini M, Viglio S Int J Mol Sci. 2024; 25(16).

PMID: 39201322 PMC: 11354567. DOI: 10.3390/ijms25168633.

Application of Proteomics Technology Based on LC-MS Combined with Western Blotting and Co-IP in Antiviral Innate Immunity.

Liang W, Zhu Z, Zheng C Methods Mol Biol. 2024; 2854:93-106.

PMID: 39192122 DOI: 10.1007/978-1-0716-4108-8_11.

Extracellular Vesicle-Based SARS-CoV-2 Vaccine.

Matsuzaka Y, Yashiro R Vaccines (Basel). 2023; 11(3).

PMID: 36992123 PMC: 10058598. DOI: 10.3390/vaccines11030539.

Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples.

Chatterjee S, Zaia J Mass Spectrom Rev. 2022; 43(1):193-229.

PMID: 36177493 PMC: 9538640. DOI: 10.1002/mas.21813.

References

Schuster O, Atiya-Nasagi Y, Rosen O, Zvi A, Glinert I, Ben Shmuel A . Coupling immuno-magnetic capture with LC-MS/MS(MRM) as a sensitive, reliable, and specific assay for SARS-CoV-2 identification from clinical samples. Anal Bioanal Chem. 2022; 414(5):1949-1962. PMC: 8723902. DOI: 10.1007/s00216-021-03831-5. View

Swearingen K, Moritz R . High-field asymmetric waveform ion mobility spectrometry for mass spectrometry-based proteomics. Expert Rev Proteomics. 2012; 9(5):505-17. PMC: 4777519. DOI: 10.1586/epr.12.50. View

Redondo N, Zaldivar-Lopez S, Garrido J, Montoya M . SARS-CoV-2 Accessory Proteins in Viral Pathogenesis: Knowns and Unknowns. Front Immunol. 2021; 12:708264. PMC: 8293742. DOI: 10.3389/fimmu.2021.708264. View

Padhi A, Tripathi T . Can SARS-CoV-2 Accumulate Mutations in the S-Protein to Increase Pathogenicity?. ACS Pharmacol Transl Sci. 2020; 3(5):1023-1026. PMC: 7551720. DOI: 10.1021/acsptsci.0c00113. View

Harvey D . Mass spectrometric analysis of glycosylated viral proteins. Expert Rev Proteomics. 2018; 15(5):391-412. DOI: 10.1080/14789450.2018.1468756. View

Radbel J, Jagpal S, Roy J, Brooks A, Tischfield J, Sheldon M . Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Is Comparable in Clinical Samples Preserved in Saline or Viral Transport Medium. J Mol Diagn. 2020; 22(7):871-875. PMC: 7219422. DOI: 10.1016/j.jmoldx.2020.04.209. View

Terracciano R, Preiano M, Fregola A, Pelaia C, Montalcini T, Savino R . Mapping the SARS-CoV-2-Host Protein-Protein Interactome by Affinity Purification Mass Spectrometry and Proximity-Dependent Biotin Labeling: A Rational and Straightforward Route to Discover Host-Directed Anti-SARS-CoV-2 Therapeutics. Int J Mol Sci. 2021; 22(2). PMC: 7825748. DOI: 10.3390/ijms22020532. View

Grossegesse M, Hartkopf F, Nitsche A, Schaade L, Doellinger J, Muth T . Perspective on Proteomics for Virus Detection in Clinical Samples. J Proteome Res. 2020; 19(11):4380-4388. DOI: 10.1021/acs.jproteome.0c00674. View

Zhang Y, Kutateladze T . Molecular structure analyses suggest strategies to therapeutically target SARS-CoV-2. Nat Commun. 2020; 11(1):2920. PMC: 7286911. DOI: 10.1038/s41467-020-16779-4. View

10.

Grant O, Montgomery D, Ito K, Woods R . Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition. Sci Rep. 2020; 10(1):14991. PMC: 7490396. DOI: 10.1038/s41598-020-71748-7. View

11.

Ke Z, Oton J, Qu K, Cortese M, Zila V, McKeane L . Structures and distributions of SARS-CoV-2 spike proteins on intact virions. Nature. 2020; 588(7838):498-502. PMC: 7116492. DOI: 10.1038/s41586-020-2665-2. View

12.

Eldrid C, Allen J, Newby M, Crispin M . Suppression of O-Linked Glycosylation of the SARS-CoV-2 Spike by Quaternary Structural Restraints. Anal Chem. 2021; 93(43):14392-14400. PMC: 8547167. DOI: 10.1021/acs.analchem.1c01772. View

13.

Wrapp D, Wang N, Corbett K, Goldsmith J, Hsieh C, Abiona O . Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020; 367(6483):1260-1263. PMC: 7164637. DOI: 10.1126/science.abb2507. View

14.

Cipollo J, Parsons L . Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure-function relationships. Mass Spectrom Rev. 2020; 39(4):371-409. PMC: 7318305. DOI: 10.1002/mas.21629. View

15.

Sheng Y, Vinjamuri A, Alvarez M, Xie Y, McGrath M, Chen S . Host Cell Glycocalyx Remodeling Reveals SARS-CoV-2 Spike Protein Glycomic Binding Sites. Front Mol Biosci. 2022; 9:799703. PMC: 8964299. DOI: 10.3389/fmolb.2022.799703. View

16.

Rosenbalm K, Tiemeyer M, Wells L, Aoki K, Zhao P . Glycomics-informed glycoproteomic analysis of site-specific glycosylation for SARS-CoV-2 spike protein. STAR Protoc. 2020; 1(3):100214. PMC: 7757665. DOI: 10.1016/j.xpro.2020.100214. View

17.

Zhang L, Jackson C, Mou H, Ojha A, Peng H, Quinlan B . SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat Commun. 2020; 11(1):6013. PMC: 7693302. DOI: 10.1038/s41467-020-19808-4. View

18.

Zhang H, Rostami M, Leopold P, Mezey J, OBeirne S, Strulovici-Barel Y . Expression of the SARS-CoV-2 Receptor in the Human Airway Epithelium. Am J Respir Crit Care Med. 2020; 202(2):219-229. PMC: 7365377. DOI: 10.1164/rccm.202003-0541OC. View

19.

Wang D, Baudys J, Bundy J, Solano M, Keppel T, Barr J . Comprehensive Analysis of the Glycan Complement of SARS-CoV-2 Spike Proteins Using Signature Ions-Triggered Electron-Transfer/Higher-Energy Collisional Dissociation (EThcD) Mass Spectrometry. Anal Chem. 2020; 92(21):14730-14739. PMC: 7586457. DOI: 10.1021/acs.analchem.0c03301. View

20.

Chatterjee S, Y Lee L, Kawahara R, Abrahams J, Adamczyk B, Anugraham M . Protein Paucimannosylation Is an Enriched N-Glycosylation Signature of Human Cancers. Proteomics. 2019; 19(21-22):e1900010. DOI: 10.1002/pmic.201900010. View