PXD061101-1

PXD061101 is an original dataset announced via ProteomeXchange.

Title	Identification of MHC ligands through allele guided isolation combined with machine learning for specific MHC assignment
Description	Isolation of MHC ligands and subsequent analysis by mass spectrometry is considered the gold standard for defining targets for T cell-based immunotherapies. However, as many targets of high tumor-specificity are only presented at low abundance on the cell surface of tumor cells, the efficient isolation of these peptides is crucial for their successful detection. Furthermore, since multiple MHC alleles can present the same MHC ligand, improving the prediction and assignment to a specific MHC allele is highly desirable. Here, we demonstrate how optimizations of the MHC ligand isolation strategy support the identification of specific MHC ligands and how the hydrophobicity of presented peptides as well as their post-translational modifications need to be considered as exemplified by, the detection of cysteinylated MHC ligands from cancer germline antigens or point-mutated neoepitopes. To further improve the identification and characterization of MHC ligands, we developed a novel MHC class I ligand prediction algorithm (ARDisplay-I) that outperforms the current state-of-the-art. Moreover, ARDisplay-I facilitates the assignment of peptides to the appropriate MHC allele, especially if multiple alleles have to be considered. Implementing these strategies can augment the development of T cell receptor-based therapies by facilitating the identification of novel immunotherapy targets and enriching the resources available in the computational immunology field.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-07_17:10:40.485.xml
DigitalObjectIdentifier	https://doi.org/10.6019/PXD061101
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Martin Klatt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	cysteinylation (disulfide with free L-cysteine); phosphorylated residue; monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-23 15:59:21	ID requested
⏵ 1	2026-06-07 17:10:41	announced

10.1016/j.mcpro.2026.101560;

10.6019/PXD061101;

Mecklenbr, ä, uker S, Skoczylas P, Biernat P, Zaghla BKQ, Atay B, Hossam M, Kr, ó, l-J, ó, zaga B, Jasi, ń, ski M, Pienkowski VM, Sanecka-Duin A, Popp O, Haji M, Szatanek R, Mertins P, Kaczmarczyk J, Keller U, Blum A, Klatt MG, Identification of MHC Ligands Through Allele-Guided Isolation Combined With Machine Learning for Improved MHC Assignment Using ARDisplay-I. Mol Cell Proteomics, 25(5):101560(2026) [pubmed]

submitter keyword: HLA assignment, Machine Learning,Immunopeptidome

Martin Klatt
contact affiliation	Charité-University Medicine Berlin
contact email	martin.klatt@charite.de
lab head
Martin Klatt
contact affiliation	Charite - University Medicine Berlin
contact email	martin.g.klatt@gmail.com
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/2026/06/PXD061101

PRIDE project URI

• PRIDE
  1. PXD061101
     1. Label: PRIDE project
     2. Name: Identification of MHC ligands through allele guided isolation combined with machine learning for specific MHC assignment