Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: Detection of viral proteins and host's biological processes altered by the infection

Rivera, Bernardina; Leyva, Alejandro; Portela, María Magdalena; Moratorio, Gonzalo; Moreno, Pilar; Durán, Rosario; Lima, Analı́a

doi:10.1016/j.dib.2020.106121

Cited by 27 publications

(43 citation statements)

References 5 publications

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“…Several studies propose to use mass spectrometry for diagnostic testing to detect SARS-CoV-2 infection as an alternative to reverse transcription polymerase chain reaction (RT-PCR) (figure 1A) [8,17,18,41,42,55,56,84,95,99,107,136,142]. Often peptides from the abundant nucleocapsid protein are used as markers of SARS-CoV-2 infection.…”

Section: Introductionmentioning

confidence: 99%

Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2

et al. 2021

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The SARS-CoV-2 virus is the causative agent of the 2020 pandemic leading to the COVID-19 respiratory disease. With many scientific and humanitarian efforts ongoing to develop diagnostic tests, vaccines, and treatments for COVID-19, and to prevent the spread of SARS-CoV-2, mass spectrometry research, including proteomics, is playing a role in determining the biology of this viral infection. Proteomics studies are starting to lead to an understanding of the roles of viral and host proteins during SARS-CoV-2 infection, their protein-protein interactions, and post-translational modifications. This is beginning to provide insights into potential therapeutic targets or diagnostic strategies that can be used to reduce the long-term burden of the pandemic. However, the extraordinary situation caused by the global pandemic is also highlighting the need to improve mass spectrometry data and workflow sharing. We therefore describe freely available data and computational resources that can facilitate and assist the mass spectrometry-based analysis of SARS-CoV-2. We exemplify this by reanalyzing a virus-host interactome dataset to detect protein-protein interactions and identify host proteins that could potentially be used as targets for drug repurposing.

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Section: Introductionmentioning

confidence: 99%

Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2

et al. 2021

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“…A different study from oro- and NPS samples detected three proteins to be present exclusively in COVID-19 patients, namely tapasin, MHC II DRβ chain, and guanylate-binding protein 1 (GBP1). 65 Both tapasin and MHC II DRβ are the major components of the innate immune system, and GBP1 inhibits endothelial cell proliferation during chronic inflammation. 66 This result supports the idea that SARS CoV2 triggers the innate immune system in a multitude of ways.…”

Section: Application Of “Omics” Technologies In Disease Diagnosis Andmentioning

confidence: 99%

Role of Multiomics Data to Understand Host–Pathogen Interactions in COVID-19 Pathogenesis

et al. 2021

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Human infectious diseases are contributed equally by the host immune system’s efficiency and any pathogens’ infectivity. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the coronavirus strain causing the respiratory pandemic coronavirus disease 2019 (COVID-19). To understand the pathobiology of SARS-CoV-2, one needs to unravel the intricacies of host immune response to the virus, the viral pathogen’s mode of transmission, and alterations in specific biological pathways in the host allowing viral survival. This review critically analyzes recent research using high-throughput “omics” technologies (including proteomics and metabolomics) on various biospecimens that allow an increased understanding of the pathobiology of SARS-CoV-2 in humans. The altered biomolecule profile facilitates an understanding of altered biological pathways. Further, we have performed a meta-analysis of significantly altered biomolecular profiles in COVID-19 patients using bioinformatics tools. Our analysis deciphered alterations in the immune response, fatty acid, and amino acid metabolism and other pathways that cumulatively result in COVID-19 disease, including symptoms such as hyperglycemic and hypoxic sequelae.

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“…For establishing workflows to evaluate virus-specific peptides, three published cell culture datasets [22][23][24] which used SARS-COV2 infected Vero cell lines were chosen, along with five clinical datasets [25][26][27][28][29] .…”

Section: Case Studymentioning

confidence: 99%

“…In order to evaluate the most robustly detectable SARS-CoV-2 peptides, and make the detection of these viral peptides in human samples in a clinical setting all the more feasible, we set out to examine proteomic datasets from three cell culture-based studies [22][23][24] and five clinical studies [25][26][27][28][29] . We utilized automated workflows implemented in the Galaxy platform and made accessible via the European Galaxy public instance to first identify as many SARS-CoV-2 peptides possible in all samples, creating a master list of SARS-CoV-2 peptides identified across the samples.…”

Section: Introductionmentioning

confidence: 99%

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)

Rajczewski

Mehta

Nguyen

et al. 2021

Preprint

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The Coronavirus Disease 2019 (COVID19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 636 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Through stringent p-value cutoff combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.

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Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: Detection of viral proteins and host's biological processes altered by the infection

Cited by 27 publications

References 5 publications

Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2

Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2

Role of Multiomics Data to Understand Host–Pathogen Interactions in COVID-19 Pathogenesis

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)

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