PXD004233

PXD004233 is an original dataset announced via ProteomeXchange.

Title	Arginine (di)methylated Human Leukocyte Antigen class I peptides are favorably presented by HLA-B*07
Description	Specific alterations in protein post-translational modification (PTMs) are recognized hallmarks of diseases. These modifications potentially provide a unique disease-related source of Human Leukocyte Antigen (HLA) class I-presented peptide antigens that can elicit specific immune responses. Although, phosphorylated HLA peptides have received already some attention, the frequency and characteristics of arginine methylated HLA class I peptide presentation have not been explored in detail. In a model human B-cell line we detected by mass spectrometry (MS) 149 HLA class I peptides harboring mono- and/or di-methylated arginine residues. The source proteins of these antigens play important roles in signal transduction, gene transcription and DNA repair. A striking preference was observed in presentation of arginine (di)methylated peptides predicted to bind HLA-B*07 molecules, most likely because the binding motifs of this allele resemble the substrates for arginine methyl-transferases. The HLA-B*07 peptides were preferentially di-methylated at the P3 position in the sequence, thus consecutively to the proline anchor residue at position P2. Such a proline-arginine sequnce has been associated with the arginine methyl-transferases CARM1 and PRMT5. Making use of the specific neutral losses in the MS/MS spectra we could further assign most of the peptides to be asymmetrically di-methylated, most likely by CARM1. The here presented data expand our knowledge of processing and presentation of arginine (di)methylated HLA class I peptides, indicating that this type of modification is frequently presented for recognition by T-cells and might thus present a potential target for immunotherapy.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:29:53.166.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fabio Marino
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	asymmetric dimethyl-L-arginine; symmetric dimethyl-L-arginine; monohydroxylated residue; N5-methyl-L-arginine
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2016-05-26 03:23:29	ID requested
1	2016-08-15 01:51:21	announced
2	2016-10-27 04:00:51	announced	Updated project metadata.
⏵ 3	2024-10-22 04:30:04	announced	2024-10-22: Updated project metadata.

Marino F, Mommen GP, Jeko A, Meiring HD, van Gaans-van den Brink JA, Scheltema RA, van Els CA, Heck AJ, Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07. J Proteome Res, 16(1):34-44(2017) [pubmed]

Mommen GP, Frese CK, Meiring HD, van Gaans-van den Brink J, de Jong AP, van Els CA, Heck AJ, Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD). Proc Natl Acad Sci U S A, 111(12):4507-12(2014) [pubmed]

10.1073/pnas.1321458111;

ProteomeXchange project tag: Human Brain Proteome Project (HUPO_HBPP) (B/D-HPP), Human Immuno-Peptidome Project (HUPO-HIPP), Human Proteome Project

curator keyword: Biomedical

submitter keyword: methylation, dimethylation, EThcD,HLA-class I

Albert J.R. Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics
contact email	a.j.r.heck@uu.nl
lab head
Fabio Marino
contact affiliation	Utrecht University
contact email	F.Marino@uu.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD004233
     1. Label: PRIDE project
     2. Name: Arginine (di)methylated Human Leukocyte Antigen class I peptides are favorably presented by HLA-B*07