PXD068107

PXD068107 is an original dataset announced via ProteomeXchange.

Title	Systematic evaluation of blood contamination in nanoparticle-based plasma proteomics
Description	Circulating blood proteomics enables minimally invasive biomarker discovery. Nanoparticle-based circulating plasma proteomics studies have reported varying number of proteins (ca 2000-7000), but it’s unclear whether higher protein number is more informative. Here, we first develop OmniProt – a silica-nanoparticle workflow optimized through systematic evaluation of nanoparticle types and protein corona formation parameters. Next, we present an Astral spectral library for 10,109 protein groups. Using Astral with 60 sample-per-day throughput, OmniProt identifies ca 3000 to 6000 protein groups from human plasma. Notably, platelet/erythrocyte/coagulation-related contamination artificially elevates protein identifications and compromises quantification accuracy in nanoparticle-enriched samples. Through controlled contamination experiments, we identified biomarkers for platelet/erythrocyte/coagulation-related contaminations in nanoparticle-based plasma proteomics. We developed open-access software Baize for contamination assessment. We validated pipeline in 193 patients with CT-indistinct benign nodules or early lung cancers, flagging five contaminated samples. This study reveals contamination alters protein identification/quantification in nanoparticle-based plasma proteomics and presents Baize software to evaluate contamination.
HostingRepository	PRIDE
AnnounceDate	2025-12-20
AnnouncementXML	Submission_2025-12-20_07:18:14.280.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	欢 高
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	carbamoylated residue
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-04 21:22:52	ID requested
⏵ 1	2025-12-20 07:18:14	announced

10.1038/S44321-025-00346-9;

submitter keyword: coagulation contamination, lung cancer

biomarkers, EDTA tube, erythrocyte contamination,nanoparticle, sodium citrate tube, lithium heparin tube, platelet contamination, plasma proteomics

Tiannan Guo
contact affiliation	Westlake University
contact email	guotiannan@westlake.edu.cn
lab head
欢 高
contact affiliation	Westlake University
contact email	gaohuanhuan@westlake.edu.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD068107
     1. Label: PRIDE project
     2. Name: Systematic evaluation of blood contamination in nanoparticle-based plasma proteomics