Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology

Haas, Paige; Muralidharan, Monita; Krogan, Nevan J.; Kaake, Robyn M.; Hüttenhain, Ruth

doi:10.1021/acs.jproteome.0c00764

Cited by 34 publications

(25 citation statements)

References 181 publications

(355 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recent developments in targeted proteomics methods and Orbitrap mass spectrometry such as parallel reaction monitoring (PRM) have shown a substantial sensitivity increase. Although mass spectrometry based approaches have been used in several SARS-CoV-2 studies [ 6 – 10 ] (and reviewed in [ 11 and 12 ]), is not yet clear whether state-of-the-art proteomics technologies could provide the sensitivity and specificity needed in diagnostics.…”

Section: Introductionmentioning

confidence: 99%

Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens

et al. 2021

View full text Add to dashboard Cite

The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry (MS) based proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was estimated to be in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.

show abstract

Section: Introductionmentioning

confidence: 99%

Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens

et al. 2021

View full text Add to dashboard Cite

show abstract

“… 17 , 18 SARS-CoV-2 enters cells in the respiratory tract by binding of its S protein to angiotensin-converting enzyme 2 (ACE2) on the host cell surface, followed by cleavage by serine protease TMPRSS2. 19 , 20 Given that the nasopharynx is the primary site of SARS-CoV-2 exposure, host proteome profiles of nasopharynx would provide the clue that can help understanding pathogenesis and discovering drug targets. The upper respiratory tract including the nasopharyngeal mucosa can be easily sampled using nasopharyngeal swabs (NP swabs), which are the standard sampling for diagnostic testing for COVID-19.…”

Section: Introductionmentioning

confidence: 99%

DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients

et al. 2021

View full text Add to dashboard Cite

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.

show abstract

“…Recent developments in targeted proteomics methods and Orbitrap mass spectrometry such as parallel reaction monitoring (PRM) have shown a substantial sensitivity increase. Although mass spectrometry based approaches have been used in several SARS-CoV-2 studies [6][7][8][9][10] (and reviewed in [11] and [12]), is not yet clear whether state-of-the-art proteomics technologies could provide the sensitivity and specificity needed in diagnostics.…”

Section: Introductionmentioning

confidence: 99%

Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens

Bezstarosti

Lamers

Doff

et al. 2020

Preprint

View full text Add to dashboard Cite

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The rapid, sensitive and specific diagnosis of SARS-CoV-2 by fast and unambiguous testing is widely recognized to be critical in responding the current outbreak. Since the current testing capacity by conventional PCR based methods is insufficient because of shortages of supplies such as RNA extraction kits and PCR reagents, alternative and/or complementary testing assays should be developed. Here, we exploit the potential of targeted mass spectrometry based proteomic technologies to solve the current issue of insufficient SARS-CoV-2 diagnostic testing capacity. We have assessed the limit of detection by parallel reaction monitoring (PRM) on an Orbitrap Eclipse mass spectrometer for target tryptic peptides of several SARS-CoV-2 proteins from a sample of virus infected Vero cells. For Nucleocapsid protein the limit of detection was found to be in the mid-attomole range (0.9 × 10−12 g), which would theoretically correspond to approximately 10,000 SARS-CoV-2 particles, under the assumption that all viral proteins are assembled in macromolecular virus particles. Whether or not this sensitivity is sufficient to play a role in SARS-CoV-2 detection in patient material such as swabs or body fluids largely depends on the amount of viral proteins present in such samples and is subject of further research. If yes, mass spectrometry based methods could serve as a complementary protein based diagnostic tool and further steps should be focused on sample preparation protocols and on improvements in sample throughput.

show abstract

Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology

Cited by 34 publications

References 181 publications

Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens

Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens

DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients

Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens

Contact Info

Product

Resources

About