PXD047901-1

PXD047901 is an original dataset announced via ProteomeXchange.

Title	Deep plasma proteomics with data-independent acquisition: A fastlane towards biomarkers identification
Description	Plasma proteomic is a precious tool in human disease research, but requires extensive sample preparation in order to perform in-depth analysis and biomarker discovery using traditional Data-Dependent Acquisition (DDA). Here, we highlight the efficacy of combining moderate plasma prefractionation and Data-Independent Acquisition (DIA) to significantly improve proteome coverage and depth, while remaining cost- and time-efficient. Using human plasma collected from a 20-patient COVID-19 cohort, our method utilises commonly available solutions for depletion, sample preparation, and fractionation, followed by 3 LC-MS/MS injections for a 360-minutes DIA run time. DIA-NN software was then used for precursor identification, and the QFeatures R package was used for protein aggregation. We detect 1,346 proteins on average per patient, and 2,135 unique proteins across the cohort. Filtering precursors present in under 25% of patients, we still detect 1,231 average proteins and 1,603 unique proteins, indicating robust protein identification. Differential analysis further demonstrates the applicability of this method for plasma proteomic research and clinical biomarker identification. In summary, this study introduces a streamlined, cost- and time-effective approach to deep plasma proteome analysis, expanding its utility beyond classical research environments and enabling larger-scale multi-omics investigations in clinical settings.
HostingRepository	PRIDE
AnnounceDate	2024-09-27
AnnouncementXML	Submission_2024-09-27_07:16:39.390.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Didier Vertommen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-18 06:31:33	ID requested
⏵ 1	2024-09-27 07:16:40	announced

10.1021/acs.jproteome.4c00104;

Ward B, Pyr Dit Ruys S, Balligand JL, Belkhir L, Cani PD, Collet JF, De Greef J, Dewulf JP, Gatto L, Haufroid V, Jodogne S, Kabamba B, Lingurski M, Yombi JC, Vertommen D, Elens L, Deep Plasma Proteomics with Data-Independent Acquisition: Clinical Study Protocol Optimization with a COVID-19 Cohort. J Proteome Res, 23(9):3806-3822(2024) [pubmed]

submitter keyword: DIA-NN, Data-independent acquisition, Deep proteome analysis,Plasma proteomics, Fractionation, Clinical proteomics, COVID-19, Biomarkers

Laure Elens
contact affiliation	Integrated PharmacoMetrics, pharmacoGenomics and pharmacoKinetics (PMGK) research group Louvain Drug Research Institute (LDRI) Université catholique de Louvain Avenue Emmanuel Mounier 72, B1.72.02 1200 Brussels; Belgium
contact email	laure.elens@uclouvain.be
lab head
Didier Vertommen
contact affiliation	UCL - de Duve Institute, Brussels Belgium
contact email	didier.vertommen@uclouvain.be
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/2024/09/PXD047901

PRIDE project URI

• PRIDE
  1. PXD047901
     1. Label: PRIDE project
     2. Name: Deep plasma proteomics with data-independent acquisition: A fastlane towards biomarkers identification