PXD062275-1

PXD062275 is an original dataset announced via ProteomeXchange.

Title	A simplified perchloric acid workflow with neutralization (PCA N) for democratizing deep plasma proteomics at population scale - Submission02
Description	Large scale plasma proteomics studies offer tremendous potential for biomarker discovery but face significant challenges in balancing analytical depth, throughput and cost effectiveness. We present an optimized perchloric acid based workflow with neutralization – PCA N – that addresses these limitations. By introducing a neutralization step following protein precipitation, PCA N enables direct enzymatic digestion without additional purification steps, reducing sample volume requirements to only 5 µL of plasma while maintaining deep plasma proteome coverage. The streamlined protocol allows preparation of over 10,000 samples per day using 384 well formats at costs comparable to undepleted plasma analysis (NEAT). Rigorous validation according to the recently introduced CLSI C64 guideline demonstrated that despite somewhat higher technical variability compared to NEAT, PCA N maintained excellent biological resolution and reproducibility. We confirmed the workflow’s exceptional stability through analysis of 1,500 quality control samples systematically interspersed among 36,000 plasma samples measured continuously over 311 days. Technical performance remained consistent across multiple instruments, sample preparation batches and nearly a year of measurements. Compared to NEAT plasma proteomics, PCA N doubled the proteomic depth while maintaining comparable reagent costs and throughput. The minimal sample reequipments, operational simplicity while using only common laboratory chemical and exceptional scalability positions PCA N as an attractive approach for population level plasma proteomics, democratizing access to deep plasma proteome analysis.
HostingRepository	PRIDE
AnnounceDate	2025-10-06
AnnouncementXML	Submission_2025-10-06_12:20:41.163.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: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-26 18:39:11	ID requested
⏵ 1	2025-10-06 12:20:41	announced

Dataset with its publication pending

submitter keyword: LC-MSMS,Plasma

Prof. Dr. Matthias Mann
contact affiliation	Dept. Proteomics and Signal Transduction Director at the Max-Planck Institute of Biochemistry
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/2025/09/PXD062275

PRIDE project URI

• PRIDE
  1. PXD062275
     1. Label: PRIDE project
     2. Name: A simplified perchloric acid workflow with neutralization (PCA N) for democratizing deep plasma proteomics at population scale - Submission02