PXD040860

PXD040860 is an original dataset announced via ProteomeXchange.

Title	Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome
Description	HLA-DQ molecules can be formed as both cis and trans variants. So far, the progress for predicting HLA-DQ antigen presentation has been limited. In addition, the contribution of trans-only variants in shaping the HLA-DQ immunopeptidome remains largely unresolved. Here, we address these issues by integrating state-of-the-art immunoinformatics data mining models with large volumes of high-quality HLA-DQ specific immunopeptidomics data. The analysis demonstrated a highly improved predictive power and molecular coverage for models trained with these novel HLA-DQ data and a limited to no contribution for trans-only HLA-DQ variants to the overall HLA-DQ immunopeptidome.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:47:58.973.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD040860
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Hooman Yari
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monosodium salt; acetylated residue; monohydroxylated residue; deamidated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-14 08:58:03	ID requested
1	2023-05-10 15:54:09	announced
⏵ 2	2023-11-14 08:48:07	announced	2023-11-14: Updated project metadata.

Nilsson JB, Kaabinejadian S, Yari H, Peters B, Barra C, Gragert L, Hildebrand W, Nielsen M, Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome. Commun Biol, 6(1):442(2023) [pubmed]

10.6019/PXD040860;

submitter keyword: Machine learning, Immunopeptidome, HLA-DQ

William Hildebrand
contact affiliation	University of Oklahoma Health Sciences Center
contact email	william-hildebrand@ouhsc.edu
lab head
Hooman Yari
contact affiliation	University of Oklahoma Health Sciences Center
contact email	hooman-yari@ouhsc.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD040860
     1. Label: PRIDE project
     2. Name: Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome