PXD055242-1

PXD055242 is an original dataset announced via ProteomeXchange.

Title	Meta-Analysis and DIA-MS-based Proteomic Investigation of COPD Patients and Asymptomatic Smokers in the Indian population
Description	Chronic obstructive pulmonary disease (COPD) is India's second largest cause of death and is largely caused by smoking. Asymptomatic smokers develop COPD due to genetic, environmental, and molecular variables, making early screening crucial. Data-independent acquisition mass spectrometry (DIA-MS) proteomics offers an unbiased method to analyze proteomic profiles. This study is the first to use DIA-based proteomics to analyze individual serum samples from three distinct male cohorts: healthy individuals (n=10), asymptomatic smokers (n=10), and COPD patients (n=10). This comprehensive approach identified 667 proteins with a 1% false discovery rate. Differentially expressed proteins included 40 in the normal versus asymptomatic comparison, 88 in the COPD versus normal comparison, and 40 in the COPD versus asymptomatic comparison. Among them, PRDX6, ELANE, PRKCSH, PRTN3, and MNDA could help differentiate COPD from asymptomatic smokers, while ELANE, H3-3A, IGHE, SLC4A1, and SERPINA11 could differentiate COPD from healthy subjects. Pathway enrichment and protein-protein interaction analyses revealed significant alterations in hemostasis, immune system functions, fibrin clot formation, and post-translational protein modifications. Key proteins were validated using a parallel reaction monitoring assay. DIA data are available via ProteomeXchange with identifier PXD055242. Our findings reveal key protein classifiers in COPD patients, asymptomatic smokers, and healthy individuals, helping clinicians understand disease pathobiology and improve disease management and quality of life.
HostingRepository	PRIDE
AnnounceDate	2024-11-13
AnnouncementXML	Submission_2024-11-13_04:02:18.050.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gautam Sharma
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	2024-08-27 06:05:37	ID requested
⏵ 1	2024-11-13 04:02:18	announced

10.1021/acs.jproteome.4c00463;

Sharma G, Gupta DP, Ganguly K, Anand MP, Srivastava S, Meta-Analysis and DIA-MS-Based Proteomic Investigation of COPD Patients and Asymptomatic Smokers in the Indian Population. J Proteome Res, 23(11):4973-4987(2024) [pubmed]

submitter keyword: smokers, healthy subjects, proteomics, DIA, Indian population,: COPD, asymptomatic smokers

Sanjeeva Srivastava
contact affiliation	Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IITB), Powai, Mumbai, Maharashtra - 400076
contact email	sanjeeva@iitb.ac.in
lab head
Gautam Sharma
contact affiliation	Indian Institute of Technology (IIT), Bombay
contact email	graviksharma45@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/2024/11/PXD055242

PRIDE project URI

• PRIDE
  1. PXD055242
     1. Label: PRIDE project
     2. Name: Meta-Analysis and DIA-MS-based Proteomic Investigation of COPD Patients and Asymptomatic Smokers in the Indian population