PXD031813

PXD031813 is an original dataset announced via ProteomeXchange.

Title	Plasma Proteomics Reveal COVID-19 Associated Network and Severity Biomarkers
Description	Coronavirus disease 2019 (COVID-19) has been threatening public health for the last 3 years globally. So far, the pathophysiology of the disease and therapeutic strategies have not clearly known yet. In this project, performing label-free plasma proteomics analysis, we aimed at identifying severity biomarkers for COVID-19 prognosis and proposing potential drugs against the disease symptoms by building the signaling network of significantly regulated proteins and finding the corresponding virus-host interactions. A total of 38 plasma samples from 13 COVID-19 PCR positive individuals and 5 plasma samples from healthy individuals were collected for the analysis. According to the WHO criteria, the severity of our patients was categorized as moderate (n=4), severe (n=3), and critical (n=6). Also, blood samples were collected in different time points after the symptom onset: (1) 1-5 day (± 2 days); early infection, (2) 5-15 days (± 2 days); inflammatory response, and after 15 days (± 2 days); recovery which shows the first PCR negative result from a nasal swab. In summary, we found significantly regulated proteins between COVID-19 patients and uninfected individuals and proposed some critical patient-specific prognostic biomarkers, which can be used as an early predictor of the disease severity. Also, we created a COVID-19 related plasma protein network modulated by SARS-CoV2 viral proteins and indicated clinically significant targets for the disease symptoms.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:42:58.175.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ali Yurtseven
SpeciesList	scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: NCBITaxon:2697049; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-02-21 10:53:36	ID requested
1	2023-03-11 05:35:33	announced
⏵ 2	2023-11-14 08:42:59	announced	2023-11-14: Updated project metadata.

Sahin AT, Yurtseven A, Dadmand S, Ozcan G, Akarlar BA, Kucuk NEO, Senturk A, Ergonul O, Can F, Tuncbag N, Ozlu N, Plasma proteomics identify potential severity biomarkers from COVID-19 associated network. Proteomics Clin Appl, 17(2):e2200070(2023) [pubmed]

ProteomeXchange project tag: Sars-cov-2, Covid-19

submitter keyword: severity biomarkers, COVID-19 associated network, label-free quantification, COVID-19 disease,mass-spectrometry based plasma proteomics

Nurhan Ozlu
contact affiliation	Koc University
contact email	nozlu@ku.edu.tr
lab head
Ali Yurtseven
contact affiliation	Istanbul
contact email	ayurtseven19@ku.edu.tr
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/2023/03/PXD031813

PRIDE project URI

• PRIDE
  1. PXD031813
     1. Label: PRIDE project
     2. Name: Plasma Proteomics Reveal COVID-19 Associated Network and Severity Biomarkers