PXD065103-1

PXD065103 is an original dataset announced via ProteomeXchange.

Title	Evaluation of nanoparticle-based plasma enrichment on individuals with primary and metastatic pancreatic cancer
Description	Using nanoparticles based plasma enrichment strategies on plasma samples, we were able to achieve a huge increase of identified plasma proteins from around 700 to more than 5000 proteins as compared to neat plasma digest. The substantial increase in depth allowed us to perform in-depth analysis and we were able to apply this to a small cohort of plasma samples from pancreatic cancer (PC) patients with primary tumor, tumor that had metastases vs healthy controls. Majority of identified proteins were part of the Human Plasma Proteome Project (HPPP) database, and more than 300 proteins are on the list of FDA approved drug targets. We showed a large and significant increase in ribosomal proteins in plasma of PC that metastasized. ADH1C and ADH1B, both members of the alcohol dehydrogenase family, had one of the largest increase and potentially correlated with liver metastasis. We further highlighted 15 different potentially secreted and/or cell surface proteins that were otherwise not identified in neat, digested plasma and have potential to be useful markers due to their cancer associations. Lastly, we compared different mass spectrometer (Orbitrap Astral and Orbitrap Ascend) and column (depth and throughput) setups on the same dataset and showed similar conclusions potentially can be achieved, although the depth approach on the newer instrumentations can reveal additional insights in the plasma proteome.
HostingRepository	PRIDE
AnnounceDate	2025-12-04
AnnouncementXML	Submission_2025-12-04_01:01:49.803.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ching-Seng Ang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Astral; Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-17 02:19:36	ID requested
⏵ 1	2025-12-04 01:01:50	announced

10.3390/CANCERS17233765;

submitter keyword: nanoparticles, comparative proteomics, pancreatic cancer

Ching-Seng Ang
contact affiliation	Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052, Australia
contact email	ching-seng.ang@unimelb.edu.au
lab head
Ching-Seng Ang
contact affiliation	University of Melbourne
contact email	cang@unimelb.edu.au
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/2025/12/PXD065103

PRIDE project URI

• PRIDE
  1. PXD065103
     1. Label: PRIDE project
     2. Name: Evaluation of nanoparticle-based plasma enrichment on individuals with primary and metastatic pancreatic cancer