Shortlisting SARS‐CoV‐2 Peptides for Targeted Studies from Experimental Data‐Dependent Acquisition Tandem Mass Spectrometry Data

Abstract

Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial tool for fighting the COVID-19 pandemic. This dataset brief presents the exploration of a shotgun proteomics dataset acquired on SARS-CoV-2 infected Vero cells. Proteins from inactivated virus samples were extracted, digested with trypsin, and the resulting peptides were identified by data-dependent acquisition tandem mass spectrometry. The 101 peptides reporting for six viral proteins were specifically analyzed in terms of their analytical characteristics, species specificity and conservation, and their proneness to structural modifications. Based on these results, a shortlist of 14 peptides from the N, S, and M main structural proteins that could be used for targeted mass-spectrometry method development and diagnostic of the new SARS-CoV-2 is proposed and the best candidates are commented.The world is facing a tremendous pandemic caused by the SARS-CoV-2 virus. [1] The mutations naturally-occurring in the viral genome upon its spread may challenge molecular biology diagnostic tests. [2,3] Mass-spectrometry (MS) based detection of organisms could be an alternative for fast deployment of novel detection means in case of emergence of new pathogens. More specifically, proteotyping based on peptide/protein mass measurement can be performed with either a targeted strategy or without any a priori. [4,5] For such purpose sample preparation, acquisition modes and parameters should be optimized depending on the nature of the samples and the target. Targeted mass spectrometry approaches can be applied for the routine detection of pathogens with high sensitivity. [6] Previous knowledge of

Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window

“…We recently published a data set from a shotgun LC–MS/MS experiment performed with SARS-CoV-2 infected cells and proposed a list of specific viral peptides that could be used for the development of targeted approaches. 3 Interestingly, we observed that some SARS-CoV-2 specific peptides eluted from the LC column at narrow windows of retention time. Here, we used LC–MS/MS with an Orbitrap instrument (Q Exactive HF) for analyzing the peptidome from nasal swabs spiked with different quantities of viral material.…”

“…A window of 20 min of acquisition within a 30 min LC gradient was adjusted to target the region of elution of five previously identified virus-specific peptides. 3 The rationale for focusing the mass spectrometry measurements on these peptides was their remarkable sequence conservation among the numerous SARS-CoV-2 strains sequenced to date or their specificity to the novel coronavirus. 3 These peptides were the following: EITVATSR, GFYAEGSR, HTPINLVR, IAGHHLGR, and ADETQALPQR.…”

“… 3 The rationale for focusing the mass spectrometry measurements on these peptides was their remarkable sequence conservation among the numerous SARS-CoV-2 strains sequenced to date or their specificity to the novel coronavirus. 3 These peptides were the following: EITVATSR, GFYAEGSR, HTPINLVR, IAGHHLGR, and ADETQALPQR. While known variants exist for the latter, the other four peptides are conserved along the several SARS-CoV-2 sequenced genomes.…”

“…Of note, the peptide identified in the condition with 2 ng of viral proteins (2 PFU) is a miss-cleaved version of the ADETQALPQR peptide: KADETQALPQR. Peptide ASANLAATK, that had not been previously selected among the “best” candidates for SARS-CoV-2 proteotyping, 3 was detected in the dilution with 17 ng of viral proteins (20 PFU) and was the most sensitive peptide from protein S.…”

A comprehensive overview of proteomics approach for COVID 19: new perspectives in target therapy strategies

“…SARS-CoV-2-specific peptides have also been reported and shortlisted for targeted mass spectrometric studies by Gouveia et al They used infected cell lysate to identify these peptides and validated these peptides in a nasopharyngeal swab. (Gouveia et al 2020a , b ). Another study using a gargle solution of three patients reported a peptide from nucleoprotein using a 180 min gradient.…”