PXD063673

PXD063673 is an original dataset announced via ProteomeXchange.

Title	Comparison of deep plasma proteome enrichment methods
Description	Plasma is a complex biological fluid containing extracellular vesicles (EVs), residual platelets, and soluble proteins, all of which can serve as biomarkers for pathological conditions. While conventional plasma proteomics typically identifies hundreds of proteins, recent enrichment strategies have expanded coverage to thousands. It is not clear yet whether these methods enrich preferentially different classes of protein and whether they allow for reliable quantification Here, we compared three common advanced proteomic workflows—Seer Proteograph (nanoparticle-based), MagNET (SCX magnetic beads), and ENRICHplus (PreOmics)—as well as EV enrichment obtained by centrifugation. We aimed to explore the content in soluble proteins, EV cargo, and platelet-derived proteins in platelet-poor plasma (PPP) from healthy donors after the enrichments. Samples were analyzed using timsTOF platforms and quantified with DIA-NN in library-free mode. Functional insights were obtained using Over-Representation Analysis (ORA), Human Protein Atlas annotations, and EV-specific markers. Quantification was evaluated comparing each method to neat plasma using protein coefficient of variation and point-biserial correlation. We quantified an average of ~4500 proteins with EV centrifugation, ~4000 with Seer, ~2800 with ENRICHplus, ~2300 with MagNET, and ~900 with neat plasma. Each method enriched distinct protein signatures: EV markers such as CD81 were predominantly detected in EV preparations; lipoproteins were enriched in ENRICHplus; cytokine and hormone signaling pathways were most evident in Seer. Platelet protein intensity was directly correlated with total protein identifications but did not compromise quantification of low-abundance proteins. Across 50 healthy individuals, Proteograph consistently demonstrated reproducible enrichment and depletion patterns, with notable exceptions for proteins such as FCN3, F11, and FCGBP.
HostingRepository	PRIDE
AnnounceDate	2025-10-17
AnnouncementXML	Submission_2025-10-17_15:58:24.550.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chiara guerrera
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-06 11:41:59	ID requested
⏵ 1	2025-10-17 15:58:25	announced

10.1016/j.jprot.2025.105519;

Roger K, Metatla I, Ceccacci S, Wahbi K, Mott, é L, Chhuon C, Guerrera IC, Mining the plasma proteome: Evaluation of enrichment methods for depth and reproducibility. J Proteomics, 321():105519(2025) [pubmed]

submitter keyword: EnrichPlus, Proteograph, MagNet, timsTOF, enrichment,plasma, EVs, LC-MS/MS

Ida Chiara Guerrera
contact affiliation	Necker Proteomics, Université Paris Cité - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR3633, Paris, France.
contact email	chiara.guerrera@inserm.fr
lab head
Chiara guerrera
contact affiliation	Necker proteomics, INSERM
contact email	chiara.guerrera@inserm.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD063673
     1. Label: PRIDE project
     2. Name: Comparison of deep plasma proteome enrichment methods