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DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients.
J Proteome Res. 2021 08 06; 20(8):4165-4175.JP

Abstract

Since the recent outbreak of COVID-19, there have been intense efforts to understand viral pathogenesis and host immune response to combat SARS-CoV-2. It has become evident that different host alterations can be identified in SARS-CoV-2 infection based on whether infected cells, animal models or clinical samples are studied. Although nasopharyngeal swabs are routinely collected for SARS-CoV-2 detection by RT-PCR testing, host alterations in the nasopharynx at the proteomic level have not been systematically investigated. Thus, we sought to characterize the host response through global proteome profiling of nasopharyngeal swab specimens. A mass spectrometer combining trapped ion mobility spectrometry (TIMS) and high-resolution QTOF mass spectrometer with parallel accumulation-serial fragmentation (PASEF) was deployed for unbiased proteome profiling. First, deep proteome profiling of pooled nasopharyngeal swab samples was performed in the PASEF enabled DDA mode, which identified 7723 proteins that were then used to generate a spectral library. This approach provided peptide level evidence of five missing proteins for which MS/MS spectrum and mobilograms were validated with synthetic peptides. Subsequently, quantitative proteomic profiling was carried out for 90 individual nasopharyngeal swab samples (45 positive and 45 negative) in DIA combined with PASEF, termed as diaPASEF mode, which resulted in a total of 5023 protein identifications. Of these, 577 proteins were found to be upregulated in SARS-CoV-2 positive samples. Functional analysis of these upregulated proteins revealed alterations in several biological processes including innate immune response, viral protein assembly, and exocytosis. To the best of our knowledge, this study is the first to deploy diaPASEF for quantitative proteomic profiling of clinical samples and shows the feasibility of adopting such an approach to understand mechanisms and pathways altered in diseases.

Authors+Show Affiliations

Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905, United States.Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905, United States.Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905, United States. Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore, 560029, Karnataka India. Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka India. Manipal Academy of Higher Education, Manipal, 576104, Karnataka India.Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905, United States. Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka India. Manipal Academy of Higher Education, Manipal, 576104, Karnataka India.Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905, United States.Proteomics Core, Medical Genome Facility, Mayo Clinic, Rochester, Minnesota 55905, United States.Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905, United States. Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka India. Manipal Academy of Higher Education, Manipal, 576104, Karnataka India.Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905, United States. Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore, 560029, Karnataka India. Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States.

Pub Type(s)

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

Language

eng

PubMed ID

34292740

Citation

Mun, Dong-Gi, et al. "DIA-Based Proteome Profiling of Nasopharyngeal Swabs From COVID-19 Patients." Journal of Proteome Research, vol. 20, no. 8, 2021, pp. 4165-4175.
Mun DG, Vanderboom PM, Madugundu AK, et al. DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients. J Proteome Res. 2021;20(8):4165-4175.
Mun, D. G., Vanderboom, P. M., Madugundu, A. K., Garapati, K., Chavan, S., Peterson, J. A., Saraswat, M., & Pandey, A. (2021). DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients. Journal of Proteome Research, 20(8), 4165-4175. https://doi.org/10.1021/acs.jproteome.1c00506
Mun DG, et al. DIA-Based Proteome Profiling of Nasopharyngeal Swabs From COVID-19 Patients. J Proteome Res. 2021 08 6;20(8):4165-4175. PubMed PMID: 34292740.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients. AU - Mun,Dong-Gi, AU - Vanderboom,Patrick M, AU - Madugundu,Anil K, AU - Garapati,Kishore, AU - Chavan,Sandip, AU - Peterson,Jane A, AU - Saraswat,Mayank, AU - Pandey,Akhilesh, Y1 - 2021/07/22/ PY - 2021/7/23/pubmed PY - 2021/8/10/medline PY - 2021/7/22/entrez KW - COVID-19 KW - diaPASEF KW - host response SP - 4165 EP - 4175 JF - Journal of proteome research JO - J Proteome Res VL - 20 IS - 8 N2 - Since the recent outbreak of COVID-19, there have been intense efforts to understand viral pathogenesis and host immune response to combat SARS-CoV-2. It has become evident that different host alterations can be identified in SARS-CoV-2 infection based on whether infected cells, animal models or clinical samples are studied. Although nasopharyngeal swabs are routinely collected for SARS-CoV-2 detection by RT-PCR testing, host alterations in the nasopharynx at the proteomic level have not been systematically investigated. Thus, we sought to characterize the host response through global proteome profiling of nasopharyngeal swab specimens. A mass spectrometer combining trapped ion mobility spectrometry (TIMS) and high-resolution QTOF mass spectrometer with parallel accumulation-serial fragmentation (PASEF) was deployed for unbiased proteome profiling. First, deep proteome profiling of pooled nasopharyngeal swab samples was performed in the PASEF enabled DDA mode, which identified 7723 proteins that were then used to generate a spectral library. This approach provided peptide level evidence of five missing proteins for which MS/MS spectrum and mobilograms were validated with synthetic peptides. Subsequently, quantitative proteomic profiling was carried out for 90 individual nasopharyngeal swab samples (45 positive and 45 negative) in DIA combined with PASEF, termed as diaPASEF mode, which resulted in a total of 5023 protein identifications. Of these, 577 proteins were found to be upregulated in SARS-CoV-2 positive samples. Functional analysis of these upregulated proteins revealed alterations in several biological processes including innate immune response, viral protein assembly, and exocytosis. To the best of our knowledge, this study is the first to deploy diaPASEF for quantitative proteomic profiling of clinical samples and shows the feasibility of adopting such an approach to understand mechanisms and pathways altered in diseases. SN - 1535-3907 UR - https://www.unboundmedicine.com/medline/citation/34292740/DIA-Based_Proteome_Profiling_of_Nasopharyngeal_Swabs_from_COVID-19_Patients. L2 - https://doi.org/10.1021/acs.jproteome.1c00506 DB - PRIME DP - Unbound Medicine ER -