PXD038782-1

PXD038782 is an original dataset announced via ProteomeXchange.

Title	TOFIMS mass spectrometry-based immunopeptidomics refines tumor antigen identification
Description	T cell recognition of human leukocyte antigen (HLA)-presented tumor-associated peptides is central for cancer immune surveillance. Mass spectrometry (MS)-based immunopeptidomics represents the only unbiased method for directly identifying and characterizing naturally presented tumor-associated peptides, which represent a key prerequisite for the development of T cell-based immunotherapies. This study reports on the de novo implementation of ion mobility separation-based timsTOF MS for next-generation immunopeptidomics, enabling high-speed and sensitive detection of HLA peptides. A direct comparison of timsTOF-based with state-of-the-art immunopeptidomics using orbitrap technology showed significantly increased HLA peptide identifications from benign and malignant primary samples of solid tissue and hematological origin. First application of timsTOF immunopeptidomics for tumor antigen discovery enabled (i) the expansion of benign reference immunopeptidome databases with more than 150,000 HLA peptides from 94 primary benign tissue samples, (ii) the refinement of previously described tumor antigens, and (iii) the identification of a vast array of novel tumor antigens comprising low abundant neoepitopes that might serve as targets for future cancer immunotherapy development.
HostingRepository	PRIDE
AnnounceDate	2023-11-22
AnnouncementXML	Submission_2023-11-21_19:23:47.769.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Naomi Hoenisch Gravel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-12 22:56:57	ID requested
⏵ 1	2023-11-21 19:23:48	announced
2	2024-10-22 06:15:30	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: HLA, benign immunopeptidome, tumor antigen,mass spectrometry, timsTOF, immunopeptidome

Juliane Walz
contact affiliation	Department of Peptid-based Immunotherapy, University and University Hospital Tübingen, Germany
contact email	juliane.walz@med.uni-tuebingen.de
lab head
Naomi Hoenisch Gravel
contact affiliation	Peptid-based Immunotherpay, University and University Clinic Tübingen
contact email	naomi.hoenisch-gravel@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/2023/11/PXD038782

PRIDE project URI

• PRIDE
  1. PXD038782
     1. Label: PRIDE project
     2. Name: TOFIMS mass spectrometry-based immunopeptidomics refines tumor antigen identification