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The Impact of Mass Spectrometry-Based Omics Approaches in the Fight...
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The Impact of Mass Spectrometry-Based Omics Approaches in the Fight against COVID-19: From the Diagnosis to Therapies

A special issue of BioChem (ISSN 2673-6411).

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 17642

Special Issue Editor

Prof. Dr. Rosa Terracciano

E-Mail Website
Guest Editor
Department of Experimental and Clinical Medicine, Laboratory of Mass Spectrometry and Proteomics, University “Magna Græcia”, Catanzaro, Italy
Interests: proteomics; clinical proteomics; mass spectrometry; biomarker discovery; analytical chemistry; MALDI-TOF MS, proteins; peptides; proteome; organic chemistry

Special Issue Information

Dear colleagues,

There is an urgent need to better understand the molecular mechanisms involved in the SARS-CoV-2 life cycle and in its variants in order to fight the pandemic with appropriate diagnostic and therapeutic interventions. Mass-spectrometry-based proteomics has addressed and could further impressively address important issues including how to increase testing capacity, how the virus causes disease, which key regulators are implicated in the host response, what the cellular and systemic processes or pathways involved in the human immune system are, and many others. In the actual efforts to overcome COVID-19, however, additional studies are mandatory. This Special Issue will include articles and reviews that contribute through the means of proteomics and other integrated omics approaches to answer the various research questions around this pandemic.

Prof. Dr. Rosa Terracciano
Guest Editor

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Keywords

  • mass spectrometry
  • proteomics
  • omics
  • metabolomics
  • lipidomics
  • glycomics
  • SARS-CoV-2
  • COVID-19
  • antiviral agents
  • pharmacotherapy
  • drug discovery
  • protein–protein interactions
  • virus–host interaction
  • vaccine
  • virus diagnosis

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Published Papers (3 papers)

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Research

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19 pages, 41997 KiB  
Article
Untargeted Mass Spectrometry Approach to Study SARS-CoV-2 Proteins in Human Plasma and Saliva Proteome
by Lisa Pagani, Clizia Chinello, Allia Mahajneh, Francesca Clerici, Lucrezia Criscuolo, Andrea Favalli, Paola Gruarin, Renata Grifantini, Alessandra Bandera, Andrea Lombardi, Riccardo Ungaro, Antonio Muscatello, Francesco Blasi, Andrea Gori and Fulvio Magni
BioChem 2022, 2(1), 64-82; https://doi.org/10.3390/biochem2010005 - 8 Feb 2022
Cited by 3 | Viewed by 5185
Abstract
Since the start of the COVID-19 outbreak, more than four million people have died of this disease. Given its ability to provide a precise response, mass spectrometry-based proteomics could represent a useful tool to study this pathology. To this end, an untargeted nLC-ESI-MS/MS-based [...] Read more.
Since the start of the COVID-19 outbreak, more than four million people have died of this disease. Given its ability to provide a precise response, mass spectrometry-based proteomics could represent a useful tool to study this pathology. To this end, an untargeted nLC-ESI-MS/MS-based method to characterise SARS-CoV-2 proteins, including possible variants, and investigate human saliva and plasma proteome in a single analysis was developed for further application in patients. Four SARS-CoV-2 recombinant proteins, three (S1–S2–RBD) belonging to the spike glycoprotein (S) and one corresponding to the nucleoprotein (N), were prepared and analysed with nLC-UHRTOF by injecting decreasing amounts to establish the limit of detection (LOD) of the method. This was determined as 10 pg for all the components of the S protein and for N (71 amol and 213 amol, respectively). Various viral inactivation strategies plus deglycosylation and digestion approaches were then tested in saliva and plasma spiked with different quantities of SARS-CoV-2 recombinant proteins. The limit of characterisation (LOC) in saliva for the N and S proteins was observed at 100 pg (coverage of 20% and 3%, respectively); instead, in plasma, it was 33 pg for N and 330 pg for the S protein, with a coverage of 4% for both. About 300 and 800 human proteins were identified in plasma and saliva, respectively, including several key effectors and pathways that are known to be altered in COVID-19 patients. In conclusion, this approach allows SARS-CoV-2 proteins and the human proteome to be simultaneously explored, both for plasma and saliva, showing a high relevant potential for retrospective studies aimed at investigating possible virus variants and for patient stratification. Full article
(This article belongs to the Special Issue The Impact of Mass Spectrometry-Based Omics Approaches in the Fight against COVID-19: From the Diagnosis to Therapies)
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Review

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29 pages, 1413 KiB  
Review
MALDI MS-Based Investigations for SARS-CoV-2 Detection
by Mariaimmacolata Preianò, Serena Correnti, Corrado Pelaia, Rocco Savino and Rosa Terracciano
BioChem 2021, 1(3), 250-278; https://doi.org/10.3390/biochem1030018 - 1 Dec 2021
Cited by 11 | Viewed by 6639
Abstract
The urgent need to fight the COVID-19 pandemic has impressively stimulated the efforts of the international scientific community, providing an extraordinary wealth of studies. After the sequence of the virus became available in early January 2020, safe and effective vaccines were developed in [...] Read more.
The urgent need to fight the COVID-19 pandemic has impressively stimulated the efforts of the international scientific community, providing an extraordinary wealth of studies. After the sequence of the virus became available in early January 2020, safe and effective vaccines were developed in a time frame much shorter than everybody expected. However, additional studies are required since viral mutations have the potential of facilitating viral transmission, thus reducing the efficacy of developed vaccines. Therefore, improving the current laboratory testing methods and developing new rapid and reliable diagnostic approaches might be useful in managing contact tracing in the fight against both the original SARS-CoV-2 strain and the new, potentially fast-spreading CoV-2 variants. Mass Spectrometry (MS)-based testing methods are being explored, with the challenging promise to overcome the many limitations arising from currently used laboratory testing assays. More specifically, MALDI-MS, since its advent in the mid 1980s, has demonstrated without any doubt the great potential to overcome many unresolved analytical challenges, becoming an effective proteomic tool in several applications, including pathogen identification. With the aim of highlighting the challenges and opportunities that derive from MALDI-based approaches for the detection of SARS-CoV-2 and its variants, we extensively examined the most promising proofs of concept for MALDI studies related to the COVID-19 outbreak. Full article
(This article belongs to the Special Issue The Impact of Mass Spectrometry-Based Omics Approaches in the Fight against COVID-19: From the Diagnosis to Therapies)
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28 pages, 1424 KiB  
Review
“Multiomics” Approaches to Understand and Treat COVID-19: Mass Spectrometry and Next-Generation Sequencing
by Diane Appiasie, Daniel J. Guerra, Kyle Tanguay, Steven Jelinek, Damian D. Guerra and Rwik Sen
BioChem 2021, 1(3), 210-237; https://doi.org/10.3390/biochem1030016 - 14 Nov 2021
Cited by 3 | Viewed by 4691
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue The Impact of Mass Spectrometry-Based Omics Approaches in the Fight against COVID-19: From the Diagnosis to Therapies)
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