Mass Spectrometry-based Proteomics and Glycoproteomics in COVID-19 Biomarkers Identification: A Mini-review

Abstract

The first corona-pandemic, coronavirus disease 2019 (COVID-19) caused a huge health crisis and incalculable damage worldwide. Knowledge of how to cure the disease is urgently needed. Emerging immune escaping mutants of the virus suggested that it may be potentially persistent in human society as a regular health threat as the flu virus. Therefore, it is imperative to identify appropriate biomarkers to indicate pathological and physiological states, and more importantly, clinic outcomes. Proteins are the performers of life functions, and their abundance and modification status can directly reflect the immune status. Protein glycosylation serves a great impact in modulating protein function. The use of both unmodified and glycosylated proteins as biomarkers has also been proved feasible in the studies of SARS, Zika virus, influenza, etc. In recent years, mass spectrometry-based glycoproteomics, as well as proteomics approaches, advanced significantly due to the evolution of mass spectrometry. We focus on the current development of the mass spectrometry-based strategy for COVID-19 biomarkers’ investigation. Potential application of glycoproteomics approaches and challenges in biomarkers identification are also discussed.

Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma

“…Among these were two types of N-linked glycosylation: HexNAc(1)dHex (2) [N] was up in control (Figure 4, middle), and HexNAc [N], was up in bottom). Notably, changes in glycosylation were previously observed on the viral SARS-CoV-2 proteins during COVID-19 (Praissman and Wells, 2021;Reis et al, 2021;Shajahan et al, 2021;Zhong et al, 2021), even though such changes in the host organism, to the best of our knowledge, were not previously reported. Additional modifications on this list were detected at very low levels.…”

Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma

“…Among these were three types of glycosylation (N-linked up in controls, and S-linked and N-terminal up in COVID-19). Notably, changes in glycosylation were previously observed on the viral SARS-CoV-2 proteins during COVID-19 [26][27][28][29] , even though such changes in the host organism, to the best of our knowledge, were not previously reported. Additional modifications on this list were detected at very low levels.…”

Identification of SARS-CoV-2 Proteins from Nasopharyngeal Swabs Probed by Multiple Reaction Monitoring Tandem Mass Spectrometry

“…The in silico data of the selected peptides were then compared with the literature data. 16 , 21 , 22 , 29 Peptides defined by Skyline analysis monitored for each protein are reported in the Supporting Information Table ST2 . This method contained a total of 77 peptides and 407 precursor ion–daughter ions transitions associated with the peptides selected from the defined target proteins that constitute the protein signature of CoV-2 as reported in Table ST2 .…”

“…A number of unique peptides belonging to each target protein were then defined on the basis of their mass spectrometric behavior together with their specific precursor ion–product ion transitions as defined by their unique amino acid sequence by in silico analysis using the Skyline software. The in silico data of the selected peptides were then compared with the literature data. ,,, Peptides defined by Skyline analysis monitored for each protein are reported in the Supporting Information Table ST2. This method contained a total of 77 peptides and 407 precursor ion–daughter ions transitions associated with the peptides selected from the defined target proteins that constitute the protein signature of CoV-2 as reported in Table ST2.…”