PXD058376

PXD058376 is an original dataset announced via ProteomeXchange.

Title	PCI-DB: A novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development
Description	Various cancer immunotherapies rely on the T cell recognition of peptide antigens presented on human leukocyte antigens (HLA). However, the identification and selection of naturally presented peptide targets for the development of personalized as well as off-the-shelf immunotherapy approaches remains challenging. Here, we introduce the open-access Peptides for Cancer Immunotherapy Database (PCI-DB, https://pci-db.org/), a comprehensive resource of immunopeptidome data originating from various malignant and benign primary tissues that provides the research community with a convenient tool to facilitate the identification of peptide targets for immunotherapy development. The PCI-DB includes > 6.6 million HLA class I and > 3.4 million HLA class II peptides from over 40 tissue types and cancer entities analyzed uniformly using high-sensitive nf-core bioinformatics pipelines and applying a global peptide false discovery rate (FDR) approach. First application of the database provided insights into the representation of cancer-testis antigens (CTA) across malignant and benign tissues and enabled the identification and characterization of the cross-tumor entity and entity-specific tumor-associated antigens as well as naturally presented neoepitopes from frequent cancer mutations. Further, we used the PCI-DB to design personalized peptide vaccines for two patients suffering from metastatic cancer. PCI-DB enabled the composition of both a multi-peptide vaccine comprising non-mutated, highly frequent tumor-associated antigens matching the immunopeptidome of the individual patient´s tumor and a neoepitope-based vaccine matching the mutational profile of the cancer patient. Both vaccine approaches induced potent and long-lasting T-cell responses, accompanied by long-term survival of these advanced cancer patients. In conclusion, the PCI-DB provides a highly versatile tool to broaden the understanding of cancer-related antigen presentation and, ultimately, supports the development of novel immunotherapies.
HostingRepository	PRIDE
AnnounceDate	2025-04-04
AnnouncementXML	Submission_2025-04-04_10:49:20.896.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Steffen Lemke
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF; Orbitrap Fusion Lumos; timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-28 03:20:54	ID requested
⏵ 1	2025-04-04 10:49:21	announced

10.1136/JITC-2024-011366;

ProteomeXchange project tag: Human Immuno-Peptidome Project (HUPO-HIPP) (B/D-HPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

submitter keyword: Human, LC-MSMS, synthetic peptides

Prof. Dr. med. Juliane Walz
contact affiliation	Department of Peptide-based Immunotherapy
contact email	juliane.walz@med.uni-tuebingen.de
lab head
Steffen Lemke
contact affiliation	University of Tübingen
contact email	steffen.lemke@uni-tuebingen.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/2025/04/PXD058376

PRIDE project URI

• PRIDE
  1. PXD058376
     1. Label: PRIDE project
     2. Name: PCI-DB: A novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development