PXD054360

PXD054360 is an original dataset announced via ProteomeXchange.

Title	Deep Exploration of the Immunopeptidome of a Pancreatic Cancer Cell Line Panc1: Implications for Clinical Immunopeptidomics and Immunotherapy (DDA datasets)
Description	Pancreatic ductal adenocarcinoma (PDAC), with its devastating prognosis and limited treatment options, necessitates innovative therapeutic strategies. T-cell-based immunotherapy has shown promise for various cancers, including PDAC. Thus, a comprehensive understanding of the HLA-peptidome in PDAC is essential to pave the way for the effective design of immunotherapy and other interventions. In this study, we employed off-line high-pH reverse-phase (HPH-RP) fractionation of peptides extracted from immunoaffinity purified HLA class I molecules isolated from the surface of Panc1 cells in the absence and presence of cytokine stimulation. We demonstrate that this strategy is a relatively simple and rapid technique that significantly expands the depth of coverage of the PDAC immunopeptidome using data-dependent acquisition strategies and allowing the identification of more potentially actionable peptide antigens. Whilst cell lines provide an abundant source of material for immunopeptidomics analysis, clinical samples and biopsies from pancreatic cancer patients typically involve much smaller amounts of material. Thus, we performed a proof of concept study and demonstrated that immunopeptidome characterization was feasible from cell pellets of only 1 million cells (equivalent to approximately 1mg of tissue), using a spectral library generated from the HPH-RP fractionated material and the ZenoSWATH DIA-MS workflow on the SCIEX 7600 ZenoToF system. These studies form the basis for future clinical translational immunopeptidomics approaches to screen tumor antigen presentation in PDAC biopsies and provide new opportunities for immune-based therapies.
HostingRepository	PRIDE
AnnounceDate	2025-07-14
AnnouncementXML	Submission_2025-07-13_16:38:13.985.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mohammadreza Dorvash
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	cysteinylation (disulfide with free L-cysteine); acetylated residue; monohydroxylated residue; deamidated residue
Instrument	ZenoTOF 7600

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-29 22:42:46	ID requested
⏵ 1	2025-07-13 16:38:14	announced

Dorvash M, Illing PT, Croft NP, Ramarathinam SH, Purcell AW, Deep Exploration of the Immunopeptidome of a Pancreatic Cancer Cell Line: Implications for Clinical Immunopeptidomics and Immunotherapy. Mol Cell Proteomics, ():101030(2025) [pubmed]

10.1016/j.mcpro.2025.101030;

submitter keyword: Tumor-Associated Antigens, HLA, variable window ZenoSWATH DIA,Pancreatic Cancer, Immunopeptidome, PDAC

Anthony Purcell
contact affiliation	Department of Biochemistry and Molecular Biology and the Biomedicine Discovery Institute; Monash University; Clayton 3800; Victoria; Australia
contact email	anthony.purcell@monash.edu
lab head
Mohammadreza Dorvash
contact affiliation	Department of Biochemistry and Molecular Biology and the Biomedicine Discovery Institute; Monash University; Clayton 3800; Victoria; Australia
contact email	mohammadreza.dorvash@monash.edu
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/PXD054360

PRIDE project URI

• PRIDE
  1. PXD054360
     1. Label: PRIDE project
     2. Name: Deep Exploration of the Immunopeptidome of a Pancreatic Cancer Cell Line Panc1: Implications for Clinical Immunopeptidomics and Immunotherapy (DDA datasets)