PXD039598-1

PXD039598 is an original dataset announced via ProteomeXchange.

Title	Metaproteomic analysis of nasopharyngeal swab samples to identify microbial peptides and potential co-infection status in COVID-19 patients
Description	Respiratory infections disrupt the microbiota in the upper respiratory tract (URT), putting patients at a risk for subsequent infections. During the pandemic, cases of COVID-19 were aggravated by secondary infections because of impaired immunity and medical interventions, which was clearly evident in the second wave of COVID-19 in India. The potential dangers and clinical difficulties of bacterial and fungal secondary infections in COVID-19 patients necessitate microbial exploration of the URT. In this regard, mass spectrometry (MS)-based proteome data of nasopharyngeal swab samples from COVID-19 patients was used to investigate the metaproteome. The MS datasets were searched against a comprehensive protein sequence database of common URT pathogens using multiple search platforms (MaxQuant, MSFragger, and Search GUI/PeptideShaker). Using parallel reaction monitoring (PRM), we validated a few identified microbial peptides in clinical nasopharyngeal swab samples.
HostingRepository	PanoramaPublic
AnnounceDate	2025-11-01
AnnouncementXML	Submission_2025-11-01_09:38:18.374.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	supported by repository but incomplete data and/or metadata
PrimarySubmitter	Dhanush Borishetty
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Label:13C(6)15N(2)
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-22 08:39:39	ID requested
⏵ 1	2025-11-01 09:38:19	announced

Bihani S, Gupta A, Mehta S, Rajczewski AT, Johnson J, Borishetty D, Griffin TJ, Srivastava S, Jagtap PD, Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients. J Proteome Res, 22(8):2608-2619(2023) [pubmed]

submitter keyword: Clinical Metaproteomics, COVID-19, Nasopharyngeal Swab

Sanjeeva Srivastava
contact affiliation	Department of Bioscience and Bioengineering, Indian Institute of Technology, Bombay, India
contact email	sanjeeva@iitb.ac.in
lab head
Dhanush Borishetty
contact affiliation	Department of Bioscience and Bioengineering, Indian Institute of Technology, Bombay, India
contact email	213300001@iitb.ac.in
dataset submitter

Panorama Public dataset URI