PXD061608

PXD061608 is an original dataset announced via ProteomeXchange.

Title	Precision-Engineered Nano-Electrospray Emitters Enhance Ionization Efficiency for Trap-Assisted Direct Infusion Mass Spectrometry: Application in Plasma Alzheimer’s Disease Proteomics
Description	Shotgun direct infusion mass spectrometry (DI-MS) enables high-throughput proteomics. Yet, its performance critically depends on nanospray emitter quality. We present here precision-engineered nanospray emitters with an optimized 4-degree emitter tip angle, designed for sensitive, reproducible, user friendly, and compatible across mass spectrometry platforms that demonstrated enhanced ionization efficiency and spray stability, showing a 21-fold improvement in protein identification rates compared to commercial designs. Using both digested HeLa cell protein extracts and plasma samples from Alzheimer's disease (AD) patients, and controls, where the 14 most high-abundant proteins were depleted, we performed a comprehensive DI-MS protein identification and precise quantification using both Orbitrap Exploris 480 (OE480) and Orbitrap Astral mass spectrometers. We consistently identified and quantified over 160 proteins in AD plasma samples in 4 min DI-MS runs, with superior reproducibility (CV < 15%) and sensitivity on the Orbitrap Astral. Our analysis revealed several unreported disease-associated protein signatures, while confirming known AD biomarkers, with C5, C4BPA, and FAM135B as the protein combination with the highest potential as AD plasma biomarkers for the detection of the disease. The enhanced performance of these standardized engineered nanospray emitters over the established DI-MS workflow establishes a robust and scalable platform for high-throughput clinical proteomics.
HostingRepository	PRIDE
AnnounceDate	2025-07-21
AnnouncementXML	Submission_2025-07-20_16:04:20.485.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ana Montero Calle
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-08 10:35:57	ID requested
⏵ 1	2025-07-20 16:04:20	announced

10.1021/ACS.JPROTEOME.5C00218;

submitter keyword: direct infusion mass spectrometry,Alzheimer’s disease, emitters, DI-MS, plasma, plasma proteomics

Rodrigo Barderas
contact affiliation	Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, Majadahonda, E-28220 Madrid, Spain.
contact email	r.barderasm@isciii.es
lab head
Ana Montero Calle
contact affiliation	Instituto de Salud Carlos III
contact email	ana.monteroc@isciii.es
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/2025/07/PXD061608

PRIDE project URI

• PRIDE
  1. PXD061608
     1. Label: PRIDE project
     2. Name: Precision-Engineered Nano-Electrospray Emitters Enhance Ionization Efficiency for Trap-Assisted Direct Infusion Mass Spectrometry: Application in Plasma Alzheimer’s Disease Proteomics