PXD058436-1

PXD058436 is an original dataset announced via ProteomeXchange.

Title	MHCquant2 refines immunopeptidomics tumor antigen discovery
Description	The identification of human leukocyte antigen (HLA)-presented peptides as targets of anti-cancer T cell response is pivotal for the development of novel immunotherapies. Mass spectrometry (MS)-based immunopeptidomics enables the detection of these peptides, yet confident identifications and thus implementation in immunotherapy design are hampered by the high diversity and low abundance of naturally presented HLA peptides. Here, we introduce MHCquant2, a Nextflow-based open-source pipeline that leverages OpenMS tools and peptide property predictors (DeepLC, MS2PIP) for highly sensitive and scalable HLA peptide identification and quantification across various MS platforms. MHCquant2 increased peptide identifications up to 27% with significant expansion of low-abundant peptides, outperforming state-of-the-art pipelines. Using MHCquant2 we build a comprehensive benign tissue repository comprising re-analyzed data from available benign immunopeptidomes and a novel benignMHCquant2 dataset, adding more than 160,000 novel naturally presented HLA peptides. First applications of this benign repository and the MHCquant2 pipeline enabled (i) the refinement of tumor-associated antigens, (ii) as well as the detection of novel, high-frequent tumor-exclusive peptide antigens for multiple tumor entities, and (iii) the identification and quantification of mutation-derived low-abundant neoepitopes. MHCquant2 refines tumor antigen discovery in immunopeptidomics, paving the way for the implementation of off-the-shelf and personalized immunotherapy design.
HostingRepository	PRIDE
AnnounceDate	2025-08-25
AnnouncementXML	Submission_2025-08-25_09:37:23.920.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jonas Scheid
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-30 14:04:42	ID requested
⏵ 1	2025-08-25 09:37:24	announced

Dataset with its publication pending

submitter keyword: Immunopeptidomics, Nf-core, MHCquant, Pipeline, DDA

Juliane Sarah
contact affiliation	Department of Peptide-based Immunotherapy, University and University Hospital Tuebingen, Germany
contact email	juliane.walz@med.uni-tuebingen.de
lab head
Jonas Scheid
contact affiliation	Department of Peptide-based Immunotherapy, University and Universityhospital of Tübingen Quantitative Biology Center, University of Tübingen
contact email	jonas.scheid@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/2025/08/PXD058436

PRIDE project URI

• PRIDE
  1. PXD058436
     1. Label: PRIDE project
     2. Name: MHCquant2 refines immunopeptidomics tumor antigen discovery