PXD067986

PXD067986 is an original dataset announced via ProteomeXchange.

Title	Comparative proteomics of human naso-oropharyngeal swabs from COVID19 patients for identification of potential biomarker candidates
Description	Background: COVID-19 has been a global pandemic affecting millions since March 2020. Both as a disease and as a syndrome, COVID19 mimics a number of other clinical entities. Also, current set of investigations such as RT-PCR and antibody based assays are not that efficient in diagnosis of the disease. This necessitates newer platforms such as proteomics to identify potential biomarker candidates that can assist in diagnosis as well as help to understand molecular eitio-pathogenesis. Methods: Proteins from Naso-oro-pharyngeal samples of healthy Control and COVID-19 subjects were trypsin digested and subjected to liquid chromatography assisted mass spectrometry analysis on Orbitrap Fusion Lumos (ThermoFisher). Proteomic analysis was carried using Proteome Discoverer 2.4 (ThermoFisher) using human and SARS-CoV-2 FASTA databases from UniProtKB. Proteins with fold Change ≤ 0.5, or ≥ 2 were designated as differentially expressed and taken up for interactomic analysis and using STRING and Cytoscape, and pathway analysis using KEGG, Reactome, and Wiki pathway. Area under curve for receiver operating characteristic was done in MetaboAnalyst (v6.0) to estimate diagnostic parameters of sensitivity and specificity. Results: Proteomic analysis of naso-oropharyngeal swabs from COVID-19 patients helped to identify 26 differentially expressed human proteins of which 11 are potential biomarker candidate proteins. In addition, 29 SARS-CoV-2 specific peptides from spike protein, nucleocapsid, membrane, ORF1ab, ORF6, ORF7a, ORF8 and ORF9b proteins have been identified of which 6 were mutated. These SARS-CoV-2 proteins make an array of interactions with the identified human proteins establishing their roles in pathogenesis of viral infection. Human biomarker candidate proteins are primarily associated with alterations in glycolytic pathways and immune dysregulation, which are known to facilitate viral invasion, replication, and contribute to disease severity. Additionally, identified human proteins directly interact with viral proteins, indicating a potential coordinated role in SARS-CoV-2 pathogenesis. Conclusions: Label-free proteomics is an ideal platform for identification of biomarker candidates and understand their possible roles in pathogenesis of COVID19. Identified biomarker candidates have a minimum of 70% and a maximum of 100%, sensitivity and specificity thereby having translational value in developing diagnostics for COVID-19.
HostingRepository	PRIDE
AnnounceDate	2026-08-24
AnnouncementXML	Submission_2026-08-23_17:11:06.261.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	GURURAO HARIPRASAD
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-02 05:40:12	ID requested
⏵ 1	2026-08-23 17:11:07	announced

10.1016/j.bbrep.2026.102681;

Bandyopadhyay S, Brijwal M, Haridas A, Choudhary A, Kaur P, Dar L, Hariprasad G, Comparative proteomics of human naso-oropharyngeal swabs from COVID19 patients for identification of potential biomarker candidates. Biochem Biophys Rep, 47():102681(2026) [pubmed]

submitter keyword: SARS-CoV-2 peptides,LC-MS/MS Proteomics, Glycolysis and Immunity dysregulation, COVID-19, Biomarkers

Gururao Hariprasad
contact affiliation	Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
contact email	dr.hariprasadg@gmail.com
lab head
GURURAO HARIPRASAD
contact affiliation	Department of Biophysics All India Institute of Medical Sciences New Delhi India
contact email	dr.hariprasadg@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD067986
     1. Label: PRIDE project
     2. Name: Comparative proteomics of human naso-oropharyngeal swabs from COVID19 patients for identification of potential biomarker candidates