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

Bezstarosti, Karel; Lamers, Mart M.; Doff, Wouter; Wever, Peter C.; Thai, Khoa T. D.; Kampen, Jeroen J.A. van; Haagmans, Bart L.; Demmers, Jeroen

doi:10.1371/journal.pone.0259165

Cited by 32 publications

(27 citation statements)

References 15 publications

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“…Notably, LC-MS/MS proteomics has identified specific proteins and protein-protein interactions linked to mild and severe COVID-19 cases. Upregulation of heparin cofactor II and downregulation of cubilin are associated with COVID-19 severity [9]. Differential regulation of 27 proteins discovered through LC-MS/MS was likewise linked to COVID-19 severity [10].…”

Section: Mass Spectrometry and Proteomicsmentioning

confidence: 96%

“Multiomics” Approaches to Understand and Treat COVID-19: Mass Spectrometry and Next-Generation Sequencing

Appiasie

Guerra²,

Tanguay

et al. 2021

BioChem

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In the race against COVID-19 for timely therapeutic developments, mass spectrometry-based high-throughput methods have been valuable. COVID-19 manifests an extremely diverse spectrum of phenotypes from asymptomatic to life-threatening, drastic elevations in immune response or cytokine storm, multiple organ failure and death. These observations warrant a detailed understanding of associated molecular mechanisms to develop therapies. In this direction, high-throughput methods that generate large datasets focusing on changes in protein interactions, lipid metabolism, transcription, and epigenetic regulation of gene expression are extremely beneficial sources of information. Hence, mass spectrometry-based methods have been employed in several studies to detect changes in interactions among host proteins, and between host and viral proteins in COVID-19 patients. The methods have also been used to characterize host and viral proteins, and analyze lipid metabolism in COVID-19 patients. Information obtained using the above methods are complemented by high-throughput analysis of transcriptomic and epigenomic changes associated with COVID-19, coupled with next-generation sequencing. Hence, this review discusses the most recent studies focusing on the methods described above. The results establish the importance of mass spectrometry-based studies towards understanding the infection process, immune imbalance, disease mechanism, and indicate the potential of the methods’ therapeutic developments and biomarker screening against COVID-19 and future outbreaks.

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Section: Mass Spectrometry and Proteomicsmentioning

confidence: 96%

“Multiomics” Approaches to Understand and Treat COVID-19: Mass Spectrometry and Next-Generation Sequencing

Appiasie

Guerra²,

Tanguay

et al. 2021

BioChem

View full text Add to dashboard Cite

show abstract

“…In this context, the results provided by patients’ sputum, complementary to those given by nasopharyngeal and/or throat swabs, allow to better explore the biological factors contributing to COVID-19 severity and to identify potential predictive biomarkers. In a very interesting methodological work, Bezstarosti et al [ 21 ] demonstrated that targeted proteomics has the potential to identify SARS-CoV-2 proteins with sufficient sensitivity for clinical diagnostic labs in which mass spectrometry equipment is available. After assessing, by parallel reaction monitoring (PRM) MS, the limit of detection for several SARS-CoV-2 proteins in infected Vero E6 cells, they estimated that this limit for tryptic peptides of nucleocapsid proteins was in the mid-attomole range.…”

Section: Sputum Proteomics To Investigate Sars-cov2mentioning

confidence: 99%

Proteomic Analysis of Human Sputum for the Diagnosis of Lung Disorders: Where Are We Today?

Iadarola

Viglio

2022

IJMS

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The identification of markers of inflammatory activity at the early stages of pulmonary diseases which share common characteristics that prevent their clear differentiation is of great significance to avoid misdiagnosis, and to understand the intrinsic molecular mechanism of the disorder. The combination of electrophoretic/chromatographic methods with mass spectrometry is currently a promising approach for the identification of candidate biomarkers of a disease. Since the fluid phase of sputum is a rich source of proteins which could provide an early diagnosis of specific lung disorders, it is frequently used in these studies. This report focuses on the state-of-the-art of the application, over the last ten years (2011–2021), of sputum proteomics in the investigation of severe lung disorders such as COPD; asthma; cystic fibrosis; lung cancer and those caused by COVID-19 infection. Analysis of the complete set of proteins found in sputum of patients affected by these disorders has allowed the identification of proteins whose levels change in response to the organism’s condition. Understanding proteome dynamism may help in associating these proteins with alterations in the physiology or progression of diseases investigated.

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“…Among these 14 peptides, two peptides of the N protein were selected as attractive candidates [75]. Interestingly, the same target peptides were confirmed by independent groups using the PRM method [107,108]. However, neither approach could overcome the problems of the low detection rate (approximately 20% of the PCR assay) and low throughput analysis (20 min per sample).…”

Section: Application Of Lc-ms/ms For Covid-19 Diagnosismentioning

confidence: 99%

Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases

Hayoung

Kim

2022

IJMS

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Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography–mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.

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

Cited by 32 publications

References 15 publications

“Multiomics” Approaches to Understand and Treat COVID-19: Mass Spectrometry and Next-Generation Sequencing

“Multiomics” Approaches to Understand and Treat COVID-19: Mass Spectrometry and Next-Generation Sequencing

Proteomic Analysis of Human Sputum for the Diagnosis of Lung Disorders: Where Are We Today?

Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases

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