PXD024392-2

PXD024392 is an original dataset announced via ProteomeXchange.

Title	Tuning DO:DM ratios modulates HLA class II immunopeptidomes
Description	Major Histocompatibility Complex Class II antigen presentation underlies a wide range of immune responses in health and disease. Although peptide ligand binding affinity has been the major focus for explaining and predicting class II antigens, we know that the levels and activities of accessory molecules, HLA-DM (DM) and HLA-DO (DO) can have strong effects on peptide repertoires. However, the extent to which these antagonistic proteins’ levels relative to one another shape the identities and properties of peptides selected for presentation remains unclear. Hence, after creating cell line panel with varying DO:DM ratios, of we set out to measure the effects these ratios can have on peptide presentation. Using a combined immunopeptidomic and proteomic discovery strategy, we profiled ligandome differences across this panel. By surveying over 10,000 unique HLA-DR4-presented peptides, we found marked increases in repertoire diversity and altered physical properties of presented peptides that corresponded with increasing DO:DM ratios.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:06:50.926.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Niclas Olsson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; deamidated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-25 22:57:37	ID requested
1	2023-10-24 11:04:30	announced
⏵ 2	2023-11-14 09:06:51	announced	2023-11-14: Updated project metadata.
3	2024-10-22 06:08:31	announced	2024-10-22: Updated project metadata.

Olsson N, Jiang W, Adler LN, Mellins ED, Elias JE, Tuning DO:DM Ratios Modulates MHC Class II Immunopeptidomes. Mol Cell Proteomics, 21(3):100204(2022) [pubmed]

submitter keyword: HLA-II,MHC, DM, antigen presentation, DO, Orbitrap

Joshua E. Elias
contact affiliation	Chan Zuckerberg Biohub, Stanford, CA 94025, USA
contact email	josh.elias@czbiohub.org
lab head
Niclas Olsson
contact affiliation	Stanford University
contact email	nic.e.olsson@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/2023/10/PXD024392

PRIDE project URI

• PRIDE
  1. PXD024392
     1. Label: PRIDE project
     2. Name: Tuning DO:DM ratios modulates HLA class II immunopeptidomes