PXD070324

PXD070324 is an original dataset announced via ProteomeXchange.

Title	Benchmarking workflows for plasma proteomics
Description	In this project we asses 5 different sample processing workflows for mass spectrometry based plasma proteomics and compare the results with a neat plasma workflow. The workflows evaluated includes protocols for abundant protein depletion (Top14 most abundant protein depletion and protein precipitation by perchloric acid) and enrichment for low abundant proteins (SAX based enrichment of low abundant proteins and ultracentrifugation based enrichment for extracellular vesicles). The assessment comprises two steps: In the first step, each workflow is repeated 8X on the same input material from one donor and focuses on proteomic depth and precision of protein quantifications. In addition, the effect of three different input materials in the form of platelet poor plasma (PPP), platelet rich plasma (PRP) and serum (SER) is evaluated. In the second step, samples from 72 healthy donors is evaluated 1X in SER and in PPP or PRP, and in addition, levels of 10 proteins--commonly measured in clinical practise and spanning 5 orders of magnitude in abundance--is quantified by a clinical rutine measurement performed at a Cobas system. Focus is again proteomic depth obtained by the evaluated methods, and in addition focus is on how well the estimates by the clinical rutine measurements in SER correlate with the mass spectrometry based estimates after sample processing by the 6 assessed workflows in all three input types (PPP. PRP, SER).
HostingRepository	PRIDE
AnnounceDate	2026-05-09
AnnouncementXML	Submission_2026-05-09_10:06:33.055.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ole Østergaard
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-04 16:21:31	ID requested
⏵ 1	2026-05-09 10:06:34	announced

10.1021/acs.jproteome.6c00078;

Kverneland AH, Ø, stergaard O, Schmidt L, Ø, stergaard Johansen M, Ullitz Thorsen S, Frikke Schmidt R, Christoffersen C, Olsen JV, Benchmarking Plasma Proteomics Workflows and Their Correlation to Clinical Routine Protein Assays. J Proteome Res, 25(6):3188-3200(2026) [pubmed]

submitter keyword: data independent acquisition, mass spectrometry, workflow assessment, Astral, extracellular vesicles,Plasma proteomics, enrichment strategies, depletion strategies

Jesper Velgaard Olsen
contact affiliation	Novo Nordisk Foundation, Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Blegdamsvej 3B, DK-2200 Copenhagen N Denmark
contact email	jesper.olsen@cpr.ku.dk
lab head
Ole Østergaard
contact affiliation	Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
contact email	ole.ostergaard@cpr.ku.dk
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/2026/05/PXD070324

PRIDE project URI

• PRIDE
  1. PXD070324
     1. Label: PRIDE project
     2. Name: Benchmarking workflows for plasma proteomics