PXD066304-1

PXD066304 is an original dataset announced via ProteomeXchange.

Title	How blood matrices and sample preparation can influence blood marker discovery
Description	While plasma and serum are increasingly being studied by using high throughput proteomics, it remains largely unexplored how different types of blood materials collected in the routine clinical diagnostics laboratories influence protein marker discovery. We compared the LC-MS/MS proteomic profiles of pooled blood samples from three healthy, voluntary donors in the form of EDTA-, citrate- and heparin-anticoagulated blood as well as serum generated with and without separation gel. Sample preparation was conducted with five different methods. We systematically evaluated the commercially available iST and ENRICH iST kits from Preomics as well as strong-anion exchange (SAX) beads from MagReSyn, the TFA-based approach SPEED and a depletion-based method which uses perchloric acid (perCA) for precipitation of large proteins. Mass-spectrometric measurements were performed on a Q Exactive HF-X and a timsTOF HT in data independent acquisition (DIA) mode. Regarding all possible combinations of sample preparation and matrices, the Q Exactive HF-X MS instrument identified between 250 and 600 protein groups whereas the timsTOF HT identified between 275 and 1100 protein groups. Differences on protein group ID level in the applied sample preparation techniques were evident. Workflows using SAX-beads, ENRICH iST and the perchloric acid precipitation showed highest identification numbers but also highest variability between the different blood matrices. EDTA-plasma and serum exhibited the highest ID numbers while citrated plasma showed the lowest. 116 protein groups overlapped between all 25 sample sets for Q Exactive HF-X and 181 protein groups for timsTOF HT. Importantly, subsets of protein groups were unique for specific combinations of sample preparation and blood matrix. This study shows a systematic approach to determine suitable sample preparation and matrix parameters for the robust identification of individual body fluid marker proteins by mass spectrometry.
HostingRepository	PRIDE
AnnounceDate	2026-01-13
AnnouncementXML	Submission_2026-01-12_22:00:23.628.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thomas Gronauer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF HT; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-18 02:36:35	ID requested
⏵ 1	2026-01-12 22:00:24	announced

10.1021/acs.jproteome.5c00836;

Gronauer TF, Merl-Pham J, von Toerne C, Habler K, Teupser D, Hauck SM, Blood Matrices and Sample Preparation Influence Blood Marker Discovery. J Proteome Res, 25(1):405-417(2026) [pubmed]

submitter keyword: Plasma, SPEED, mass spectrometry, ENRICH-iST, serum, LC−MS, iST, R package mpwR, data-independent acquisition, perCA, Mag-Net

Dr. Stefanie Hauck
contact affiliation	Metabolomics and Proteomics Core (MPC), Helmholtz Zentrum München GmbH German Research Center for Environmental Health, Munich, Germany
contact email	stefanie.hauck@helmholtz-munich.de
lab head
Thomas Gronauer
contact affiliation	Proteomics and Metabolomics Core Facility, Helmholtz Munich, Germany
contact email	thomas.gronauer@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD066304
     1. Label: PRIDE project
     2. Name: How blood matrices and sample preparation can influence blood marker discovery