PXD023016-2

PXD023016 is an original dataset announced via ProteomeXchange.

Title	Proteomic Investigation Reveals Dominant Alterations of Neutrophil Degranulation and mRNA Translation Pathways in COVID-19 Patients
Description	The altered molecular proteins and pathways in response to COVID-19 infection are still unclear. Here, we performed a comprehensive proteomics-based investigation of of nasopharyngeal swab samples from COVID-19 patients to identify viral and host peptides by employing simple extraction strategies and also established a panel of host proteins using high-resolution mass spectrometry. The differentially expressed peptides/proteins identified from host and pathogen correlated with the viral load of the host which indicates that these proteins might be good prognostic biomarkers of severity prediction. A few host proteins such as Interleukin-6, L-lactate dehydrogenase, C-reactive protein, Ferritin and Aspartate aminotransferase was found to be upregulated in COVID-19 positive patients using targeted MRM study. Further, the proteins L-lactate dehydrogenase, Aspartate aminotransferase and Alanine aminotransferase was also validated in the clinical settings using immunological assays. We also identified neutrophil degranulation, platelet degranulation, interleukin-12 signaling pathways, mRNA translation of proteins and , co-factor metabolomic process protein metabolism, and stress responses to be key GO enriched pathways, thus altered in the COVID-19 infected patients.providing the detailed investigation of host response in COVID-19 infection , thus providing the landscape of COVID-19 pathophysiology. This study thus also revealed that mass spectrometry-based detected host proteins/peptides has a potential for clinical translation and a few proteins might be routinely monitored in clinics for the disease progression, peptide tests can be used by clinicians for diagnosis as well as identified pathways/ markers as the predictors of disease progression. Furthermore, the identified proteins and their drug binding studies might aid in COVID-19 therapeutic interventions.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:51:40.138.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Avinash singh
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-09 01:35:12	ID requested
1	2021-02-14 22:59:39	announced
⏵ 2	2023-11-14 08:51:41	announced	2023-11-14: Updated project metadata.

Bankar R, Suvarna K, Ghantasala S, Banerjee A, Biswas D, Choudhury M, Palanivel V, Salkar A, Verma A, Singh A, Mukherjee A, Pai MGJ, Roy J, Srivastava A, Badaya A, Agrawal S, Shrivastav O, Shastri J, Srivastava S, Proteomic investigation reveals dominant alterations of neutrophil degranulation and mRNA translation pathways in patients with COVID-19. iScience, 24(3):102135(2021) [pubmed]

ProteomeXchange project tag: Covid-19

submitter keyword: COVID-19, Human, Nasopharyngeal swab, SARS-CoV-2, Mass spectrometry, Proteomics

Sanjeeva Srivastava
contact affiliation	Proteomics Lab, 304, BSBE Department, Indian Institute Technology Bombay, Powai, Mumbai, India-400076
contact email	sanjeeva@iitb.ac.in
lab head
Avinash singh
contact affiliation	PhD student
contact email	singhavi739@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/02/PXD023016

PRIDE project URI

• PRIDE
  1. PXD023016
     1. Label: PRIDE project
     2. Name: Proteomic Investigation Reveals Dominant Alterations of Neutrophil Degranulation and mRNA Translation Pathways in COVID-19 Patients