PXD007860

PXD007860 is an original dataset announced via ProteomeXchange.

Title	Characterizing T-cell immunopeptidomes
Description	Imunopeptidomes promise novel surface markers as ideal targets for immunotherapies, but their characterization by mass spectrometry (MS) remains challenging. Until recently, cell numbers exceeding 1.0xE9 were needed for reasonably deep immunopeptidome surveys of at least 1,000 HLA ligands. Such limitation in analytical sensitivity necessarily constrains the types of clinical specimens that can evaluated. To evaluate the feasibility of immunopeptidome profiling from limiting cell amounts, primary purified human regulatory (Treg) and conventional T cells (Tconv) were compared, evaluating the relative immunopeptide recovery from T cells isolated from individual healthy donors (N=5) versus pools (N=2 pools from 13 donors). Two donors’ Tconv were subsequently stimulated with CD3/CD28 and IL-2 and compared to resting Tconv. The combined T-cell immunopeptide dataset reported here contains over 13,000 unique peptides derived from over 5,000 proteins. In comparison to protein expression, T cell immunopeptidomes revealed complementary aspects of T cell biology, while pointing to HLA ligands specific for distinct T cell subsets (e.g., FOXP3, CD5 and WNK1). Taken together, these findings have implications for understanding conditions required to induce therapeutic immune responses and may open up new avenues for tuning Treg suppressive functions to treat cancer.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:40:46.278.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	Orbitrap Fusion Lumos; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2017-09-28 01:17:59	ID requested
1	2018-03-08 06:09:23	announced
⏵ 2	2024-10-22 04:40:51	announced	2024-10-22: Updated project metadata.

Olsson N, Schultz LM, Zhang L, Khodadoust MS, Narayan R, Czerwinski DK, Levy R, Elias JE, T-Cell Immunopeptidomes Reveal Cell Subtype Surface Markers Derived From Intracellular Proteins. Proteomics, 18(12):e1700410(2018) [pubmed]

10.1002/pmic.201700410;

curator keyword: Biological, Biomedical

submitter keyword: Human, Antigen presentation, T cell, MHC, Orbitrap

Joshua E Elias
contact affiliation	Department of Chemical & Systems Biology, Stanford University, USA
contact email	josh.elias@stanford.edu
lab head
Niclas Olsson
contact affiliation	Calico Life Sciences
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/2018/03/PXD007860

PRIDE project URI

• PRIDE
  1. PXD007860
     1. Label: PRIDE project
     2. Name: Characterizing T-cell immunopeptidomes