PXD063593-1

PXD063593 is an original dataset announced via ProteomeXchange.

Title	Pre-analytical Sample Quality Determines Performance of Plasma Proteomics Workflows for Biomarker Discovery part02
Description	This dataset contains mass spectrometry-based proteomic analyses of human plasma samples processed through five distinct proteomics workflows: neat plasma, perchloric acid precipitation with neutralization (PCA-N), and three bead-based enrichment methods (SAX magnetic beads, Sera Sil 700 magnetic beads, and non-magnetic beads). The study systematically evaluates how sample quality affects proteome coverage and quantification performance across these workflows through controlled spike-in experiments. We performed spike-in series of platelets, erythrocytes, and peripheral blood mononuclear cells (PBMCs) to assess workflow-specific susceptibilities to cellular contamination. Additional experiments include yeast protein spike-ins to evaluate detection of low-abundance proteins, buffer-bead combination screening, freeze-thaw cycle effects, and centrifugation condition comparisons. The dataset provides comprehensive evidence for how pre-analytical variables impact plasma proteome characterization and establishes quantitative benchmarks for assessing plasma sample quality in biomarker discovery studies.
HostingRepository	PRIDE
AnnounceDate	2025-08-24
AnnouncementXML	Submission_2025-08-23_20:37:08.568.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-04 18:41:39	ID requested
⏵ 1	2025-08-23 20:37:08	announced

Dataset with its publication pending

submitter keyword: pre-analytical variables, LC-MS,Plasma proteomics, bead-based enrichment, cellular contamination, sample quality

Mario Oroshi
contact affiliation	Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry
contact email	oroshi@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
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/2025/08/PXD063593

PRIDE project URI

• PRIDE
  1. PXD063593
     1. Label: PRIDE project
     2. Name: Pre-analytical Sample Quality Determines Performance of Plasma Proteomics Workflows for Biomarker Discovery part02