Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HLA-DQ8 Immunopeptidomics, Type 1 Diabetes

ABSTRACT: In this project we will investigate the peptides present by HLA-DQ8. We will identify linear, spliced and PTM peptides from one cell line.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Cell Suspension Culture

DISEASE(S): Disease Free

SUBMITTER: Pouya Faridi

LAB HEAD: Anthony Purcell

PROVIDER: PXD019466 | Pride | 2021-07-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	F120190614_PF_9033_WT__SPV-L3_p1.mgf	Mgf
	F120190614_PF_9033_WT__SPV-L3_p1.pride.mgf.gz	Mgf
	F120190614_PF_9033_WT__SPV-L3_p1.raw	Raw
	F120190614_PF_9033_WT__SPV-L3_p2.mgf	Mgf
	F120190614_PF_9033_WT__SPV-L3_p2.pride.mgf.gz	Mgf

Items per page:

1 - 5 of 23

Similar Datasets

Trans-splicing of class I HLA bound peptides diversifies the immunopeptidome

Project description:The diversity of peptides displayed by class I HLA plays an essential role in T cell immunity. The peptide repertoire is extended by various post-translational modifications, including cis-splicing of peptides from the same protein. Here, we have applied a novel bioinformatic workflow and demonstrate that spliced-peptides are also generated through trans-splicing (fusion of peptide segments from distinct antigens) and their abundance challenges current models of proteasomal-splicing that predict cis-splicing as the most probable outcome. These trans-spliced peptides display canonical HLA binding motif sequence features. These results highlight the unanticipated diversity of the immunopeptidome and have important implications for autoimmunity, vaccine design and immunotherapy.

2018-10-16 | PXD009660 | Pride

Trans-splicing of class I HLA bound peptides diversifies the immunopeptidome

2021-12-06 | PXD017922 | Pride

HLA-DR ligands from BLCLs 9022 and 9087

Project description:HLA-DR-bound peptides eluted from B-lymphoblastoid cell lines 9022 and 9087.

2020-03-11 | PXD017682 | Pride

Identification of HLA-B*57:01-restricted endogenous and HIV epitopes

Project description:A novel modified HLA-B*57:01-restricted epitope was identified in one of the reversed-phase fractions following immunoaffinity purification of HLA-peptide complexes from C1R cells expressing HIV envelope protein. Also includes six immunopeptidome datasets from several B57 and env transfected cell lysates.

2018-02-19 | PXD004471 | Pride

Melanoma spliced and linear HLA-I peptides

Project description:In this project we have identifed and linear and spliced HLA-I bound peptides to LM-MEl-44, 53 and 33 cell lines in two different condition, treated and not treated with interferone gamma.

2020-09-25 | PXD014397 | Pride

Large-Scale Immuno-Peptidome Analysis Reveals Recurrent Post-Translational Splicing of Cancer and Immune-Associated Genes

Project description:Post translational spliced peptides bound to the HLA are unique type of peptides, shown in cancer, for HLA-class-I. Thus far, no consensus has been reached on the extent to which post-translational spliced peptides (PTSPs) occur, stirring significant debate. Furthermore, the role of the HLA-class-II pathway has been studied only in diabetes. Here, we exploit our large-scale cancer peptidomics database and devise a pipeline to filter spliced peptide predictions, to identify recurring spliced peptides, both for HLA-class-I and -II. Our results indicate that HLA-Class-I spliced peptides account for a low percentage (4.4%) of the immunopeptidome, yet are larger in number relative to other types of identified aberrant peptides. Therefore, spliced peptides contribute significantly to the repertoire of presented peptides in cancer cells. In addition, HLA-class-II bound spliced peptides were identified as well, but to a lower extent (0.6%).

2023-05-10 | PXD034788 | Pride

Contribution of proteasome-catalyzed peptide cis-splicing to viral targeting by CD8+ T cells in HIV-1 infection

Project description:Peptides generated by proteasome-catalyzed splicing of non-contiguous amino acid sequences have been shown to constitute a source of non-templated human leukocyte antigen class I (HLA-I) epitopes, but their role in pathogen-specific immunity remains unknown. CD8+ T cells are key mediators of human immunodeficiency virus type 1 (HIV-1) control, and identification of novel epitopes to enhance targeting of infected cells is a priority for prophylactic and therapeutic strategies. To explore the contribution of proteasome-catalyzed peptide splicing (PCPS) to HIV-1 epitope generation, we developed a broadly-applicable mass spectrometry-based discovery workflow that we employed to identify spliced HLA-I-bound peptides on HIV-infected cells. We demonstrate that HIV-1-derived spliced peptides comprise a novel, but relatively minor, component of the HLA-I-bound viral immunopeptidome. Although spliced HIV-1 peptides may elicit CD8+ T cell responses relatively infrequently during infection, CD8+ T cells primed by partially-overlapping contiguous epitopes in HIV-infected individuals were able to cross-recognize spliced viral peptides, suggesting a potential role for PCPS in restricting HIV-1 escape pathways. Vaccine-mediated priming of responses to spliced HIV-1 epitopes could thus provide a novel means of exploiting epitope targets typically under-utilized during natural infection.

2019-11-25 | PXD015489 | Pride

Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome

Project description:Spliced peptides are short protein fragments spliced together in the proteasome by peptide bond formation. True estimation of the contribution of proteasome-spliced peptides (PSPs) to the global Human Leukocyte Antigen (HLA) ligandome is critical. A recent study suggested that PSPs contribute up to 30% of the HLA ligandome. We performed a thorough reanalysis of the reported results using multiple computational tools and various validation steps and concluded that only a fraction of the proposed PSPs passes the quality filters. To better estimate the actual number of PSPs, we present an alternative workflow. We performed de-novo sequencing of the HLA-peptide spectra and discarded all de-novo sequences found in the UniProt database. We checked whether the remaining de-novo sequences could match spliced peptides from human proteins. The spliced sequences were appended to the UniProt fasta file, which was searched by two search tools at a FDR of 1%. We find that 2-6% of the HLA ligandome could be explained as spliced protein fragments. The majority of these potential PSPs have good peptide-spectrum match properties and are predicted to bind the respective HLA molecules. However, it remains to be shown how many of these potential PSPs actually originate from proteasomal splicing events.

2018-09-03 | PXD010793 | Pride

Immunopeptidome of an acute myeloid leukemia cell line THP1

Project description:We report the use of complementary peptide antigen enrichment and comprehensive mass spectrometric acquisition strategies to provide in-depth immunopeptidome data for AML cell line THP1

2020-05-13 | PXD015039 | Pride

Database search engines and target database features impinge upon the identification of post-translationally cis-spliced peptides in HLA class I immunopeptidomes

Project description:Unconventional epitopes presented by HLA class I complexes are emerging targets for T cell targeted immunotherapies. Their identification by mass spectrometry required development of novel methods to cope with the large number of theoretical candidates. Methods to identify post-translationally spliced peptides led to a broad range of outcomes. We here investigated the impact of three common database search engines – i.e. Mascot, Mascot+Percolator and PEAKS DB – as final identification step, as well as the features of target database on the ability to correctly identify non-spliced and cis-spliced peptides. We used ground truth datasets measured by mass spectrometry to benchmark methods’ performance and extended the analysis to HLA class I immunopeptidomes. PEAKS DB showed better precision and recall of cis-spliced peptides and larger number of identified peptides in HLA class I immunopeptidomes than the other search engine strategies. The better performance of PEAKS DB appears to result from better discrimination between target and decoy hits and hence a more robust FDR estimation, and seems independent to peptide and spectrum features here investigated. Head of the research group Molecular Immunology at King’s College London and the Francis Crick Institute, London (UK). Email: michele.mishto@kcl.ac.uk,

2022-04-06 | PXD031709 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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