PXD035348

PXD035348 is an original dataset announced via ProteomeXchange.

Title	A comprehensive comparison of Rapid and Deep Plasma Proteomics workflows to identify and quantify biomarkers of Sickle Cell Anaemia
Description	Plasma serves as a rich source of protein biomarkers but in-depth proteomic analysis is challenging due to the vast dynamic range of protein abundance. Pre-fractionation of plasma proteins is commonly practiced to improve the proteome coverage but the protocols are time-expensive, suffer from flowchart complexity, and often less reproducible. Here, we explore multiple strategies of shotgun proteomics to optimize biomarker discovery workflows for Sickle Cell Anaemia (SCA) patients from remote India. A deep proteomics workflow via off-line reverse phase Ultra High-Pressure Liquid Chromatography based fractionation of tryptic digested plasma peptides followed by optimized pooling of peptides based on charge and hydrophobicity yielded the best depth of plasma proteome with a trade-off of significantly long experimental time. Alternatively, a rapid analysis of tryptic digested plasma peptides via a shorter gradient mass spectrometry run saves time but quantifies only ~ 50% of the proteins than the deep workflow. Intriguingly, despite the difference in proteome coverage, more than 80% of known FDA and SCA biomarkers quantified in the deep workflow are also quantified in the rapid workflow. Given the practical difficulties of sample collection and plasma preservation in rural India, we propose the deep proteomics workflow for biomarker discovery in smaller cohorts and the rapid workflow for biomarker validations in larger cohorts. Additional targeted proteomics based strategies may be designed for the validation of missing biomarkers in the rapid workflow.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:35:12.108.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Swasti Raychaudhuri
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-14 07:34:46	ID requested
1	2024-04-04 07:20:05	announced
⏵ 2	2024-10-22 06:35:12	announced	2024-10-22: Updated project metadata.

10.1007/S42485-022-00096-Z;

submitter keyword: Plasma proteomics, low abundant proteins,Sickle Cell Anaemia, Biomarkers, high abundant proteins

Dr. Swasti Raychaudhuri
contact affiliation	Principal Scientist CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad - 500007, India
contact email	rcswasti@ccmb.res.in
lab head
Swasti Raychaudhuri
contact affiliation	CSIR-Centre for Cellular and Molecular Biology
contact email	rcswasti@ccmb.res.in
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/2024/04/PXD035348

PRIDE project URI

• PRIDE
  1. PXD035348
     1. Label: PRIDE project
     2. Name: A comprehensive comparison of Rapid and Deep Plasma Proteomics workflows to identify and quantify biomarkers of Sickle Cell Anaemia