PXD011749-2

PXD011749 is an original dataset announced via ProteomeXchange.

Title	Plasma proteome profiling to detect and avoid sample-related biases in biomarker studies
Description	Blood-based protein tests inform medical decision-making, but despite major investments, few new biomarkers reach the clinic. Plasma and serum are rich sources of information about an individual’s health state and mass spectrometry (MS)-based proteomics now allows highly specific and quantitative read-out of the plasma proteome. Here we employ plasma proteome profiling to define marker panels assessing the quality of plasma and serum samples and the likelihood that suggested biomarkers are instead artifacts related to sample handling and processing. We acquired reference proteomes of erythrocytes, platelets, plasma and whole blood of 20 individuals (>6000 proteins), and compared serum and plasma proteomes. Based on spike-in experiments we defined a panels of contamination-associated proteins, many of which have been reported as biomarker candidates. We provide sample preparation guidelines and an online resource (www.plasmaproteomeprofiling.com) to assess overall sample-related bias in clinical studies and to prevent costly miss-assignment of biomarker candidates.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:50:25.100.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	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-20 01:06:52	ID requested
1	2018-11-23 06:12:54	announced
⏵ 2	2024-10-22 04:50:25	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Plasma, quality, pre-analytics, biomarker, plasma proteome profiling

Matthias Mann
contact affiliation	Proteomics and Signal Transduction Max Planck Institute of Biochemistry Am Klopferspitz 18 D-82152 Martinsried
contact email	mmann@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/2018/11/PXD011749

PRIDE project URI

• PRIDE
  1. PXD011749
     1. Label: PRIDE project
     2. Name: Plasma proteome profiling to detect and avoid sample-related biases in biomarker studies