Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HLA-I and HLA-II peptidomes for NESSIE

ABSTRACT: MS data of HLA class I and HLA class II ligandome of human colon tissue and LCLs

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Takayuki Kanaseki

PROVIDER: PXD047303 | JPOST Repository | Thu Aug 08 00:00:00 BST 2024

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ST679_CRC135normal_A2_1.mgf	Mgf
	ST679_CRC135normal_A2_1.raw	Raw
	ST679_CRC135normal_A2_2.mgf	Mgf
	ST679_CRC135normal_A2_2.raw	Raw
	ST679_CRC135normal_A2_3.mgf	Mgf

Items per page:

1 - 5 of 20

Similar Datasets

HLA class II ligandome of colon cancer tissues for neoantigen identification

Project description:MS data of HLA class II ligandome of human colon cancer tissues

2024-09-25 | PXD054060 | JPOST Repository

Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation

Project description:Immunopeptidome analysis of colorectal adenocarcinoma tissues as well as adjacent benign tissues was performed to characterize the natural HLA class I and class II presented ligandome represented in the context of malignancy as well as in benign tissue of the colon.

2019-03-12 | PXD009602 | Pride

HLA class I ligandome of colon cancer tissues for neoantigen identification

Project description:MS data of HLA class I ligandome of human colon cancer tissues

2021-07-26 | PXD026573 | JPOST Repository

HLA class I ligandome of colon cancer tissues for lncRNA antigen identification

Project description:MS data of HLA class I ligandome of human colon cancer tissues

2021-09-27 | PXD024533 | JPOST Repository

Improved prediction of endogenous HLA-associated epitopes based on mono-allelic mass spectrometry profiling

Project description:LC-MS/MS-based identification of HLA-peptides is poised to provide a deep understanding of the rules underlying antigen presentation. However, a key obstacle limiting the utility of MS data is the ambiguity arising from the co-expression of multiple HLA alleles. Here, we introduce a strategy for profiling the HLA ligandome one allele at a time. By using cell lines expressing a single HLA allele, optimizing immunopurifications, and developing a novel spectral search algorithm, we identified thousands of peptides bound to 16 different HLA class I alleles. These data enabled the discovery of novel binding motifs, and an integrative analysis quantifying the contribution of factors critical to epitope presentation, such as protein cleavage and gene expression. We trained neural network prediction algorithms with our large dataset (>24,000 peptides) and outperformed algorithms trained on datasets of peptides with measured affinities. We thus demonstrate a scalable strategy for systematically learning the rules of endogenous antigen presentation.

2017-02-21 | GSE93315 | GEO

Full-length HLA class II sequences

Project description:Full-length HLA class II sequences

| PRJEB42469 | ENA

Deep motif deconvolution of HLA-II peptidomes

Project description:CD4 T cells are key for priming and regulating immune recognition of infected and cancer cells, but predictions of class II epitopes have limited accuracy. We profiled over 100’000 HLA-II ligands by Mass Spectrometry and developed a novel motif deconvolution algorithm to analyze these data. Our work demonstrates substantial improvements in the definition of HLA-II binding motifs and enhanced accuracy in HLA-II ligand and class II epitope predictions.

2019-10-16 | PXD012308 | Pride

Tuning DO:DM ratios modulates HLA class II immunopeptidomes

Project 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.

2023-10-24 | PXD024392 | Pride

HLA Class II analysis of human pancreatic beta cells

Project description:We interrogated the transcriptome from bulk-sorted T1D donor β-cells as compared to non-diabetic donors. We found β-cells also expressed mRNA for HLA Class II and Class II antigen presentation pathway components, but not a macrophage marker.

2019-03-01 | GSE121863 | GEO

Sampling from proteome to HLA-DR ligandome

Project description:Comprehensive analysis of the complex nature of the Human Leukocyte Antigen (HLA) class II ligandome is of utmost importance to understand the basis for CD4+ T cell mediated immunity and tolerance. Here, we implemented important improvements in the analysis of the repertoire of HLA-DR-presented peptides, using hybrid mass spectrometry-based peptide fragmentation techniques on a ligandome sample isolated from matured human monocyte-derived dendritic cells (DC). The reported data set constitutes nearly 14 thousand unique high-confident peptides, i.e. the largest single inventory of human DC derived HLA-DR ligands to date. From a technical viewpoint the most prominent finding is that no single peptide fragmentation technique could elucidate the majority of HLA-DR ligands, due to the wide range of physical chemical properties displayed by the HLA-DR ligandome. Our in-depth profiling allowed us to reveal a strikingly modest correlation between the abundance levels of surface-presented peptides and the cellular expression of their source proteins. Important selective sieving from the sampled proteome to the ligandome, was evidenced by specificity in the sequences of the core regions both at their N- and C- termini, hence not only reflecting binding motifs but also dominant protease activity associated to the endolysosomal compartments. Moreover, we demonstrate that the HLA-DR ligandome reflects a surface representation of cell-compartments specific for biological events linked to the maturation of monocytes into antigen presenting cells. Our results present new perspectives into the complex nature of the HLA class II system and will aid future immunological studies in characterizing the full breadth of potential CD4+ T cell epitopes relevant in health and disease.

2016-01-25 | PXD002951 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data