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HLA class II peptidome analysis using data-dependent and data-independent acquisition

ABSTRACT: HLA class II peptides were purified from Maver-1 and DOHH2 cells and measured on the Q Exactive platform by data-dependent and data-independent acquisition.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Dario Neri

PROVIDER: MSV000081729 | MassIVE | Wed Nov 22 03:03:00 GMT 2017

SECONDARY ACCESSION(S): PXD008264

REPOSITORIES: MassIVE

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Publications

Membranal and Blood-Soluble HLA Class II Peptidome Analyses Using Data-Dependent and Independent Acquisition.

Ritz Danilo D Sani Emiliano E Debiec Hanna H Ronco Pierre P Neri Dario D Fugmann Tim T

Proteomics 20180314 12

The interaction between HLA class II peptide complexes on antigen-presenting cells and CD4<sup>+</sup> T cells is of fundamental importance for anticancer and antipathogen immunity as well as for the maintenance of immunological tolerance. To study CD4<sup>+</sup> T cell reactivities, detailed knowledge of the presented peptides is necessary. In recent years, dramatic advances in the characterization of membranal and soluble HLA class I peptidomes could be observed. However, the same is not true ...[more]

PMID: 29314611

Similar Datasets

Membranal and Blood-Soluble HLA Class II Peptidome Analyses Using Data-Dependent and Independent Acquisition.

Project description:The interaction between HLA class II peptide complexes on antigen-presenting cells and CD4+ T cells is of fundamental importance for anticancer and antipathogen immunity as well as for the maintenance of immunological tolerance. To study CD4+ T cell reactivities, detailed knowledge of the presented peptides is necessary. In recent years, dramatic advances in the characterization of membranal and soluble HLA class I peptidomes could be observed. However, the same is not true for HLA class II peptidomes, where only few studies identify more than hundred peptides. Here we describe a MS-based workflow for the characterization of membranal and soluble HLA class II DR and DQ peptidomes. Using this workflow, we identify a total of 8595 and 3727 HLA class II peptides from Maver-1 and DOHH2 cells, respectively. Based on this data, a motif-based binding predictor is developed and compared to NetMHCIIpan 3.1. We then apply the workflow to human plasma, resulting in the identification of between 34 and 152 HLA-DR and between 100 and 180 HLA-DQ peptides, respectively. Finally, we implement a data-independent acquisition workflow to increase reproducibility and sensitivity of HLA class II peptidome characterizations.

| S-EPMC6003597 | biostudies-literature

HLA class II subs

Project description:HLA class II full-length submissions 30/08/2022

| PRJEB55642 | ENA

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

Project description:Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not trained on high-quality epitope datasets covering a broad range of HLA alleles. To enable prediction of endogenous HLA class I-associated peptides across a large fraction of the human population, we used mass spectrometry to profile >185,000 peptides eluted from 95 HLA-A, -B, -C and -G mono-allelic cell lines. We identified canonical peptide motifs per HLA allele, unique and shared binding submotifs across alleles and distinct motifs associated with different peptide lengths. By integrating these data with transcript abundance and peptide processing, we developed HLAthena, providing allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation. These models predicted endogenous HLA class I-associated ligands with 1.5-fold improvement in positive predictive value compared with existing tools and correctly identified >75% of HLA-bound peptides that were observed experimentally in 11 patient-derived tumor cell lines.

2019-12-16 | GSE131267 | GEO

Data-independent acquisition of HLA class I peptidomes

Project description:HLA class I peptides were purified from Maver-1 and HEK293 cells and measured on the Q Exactive platform by data-dependent and data-independent acquisition.

2017-08-11 | MSV000081439 | MassIVE

HLA Class I/II submissions 240607

Project description:HLA class I/II submissions 240607

| PRJEB76430 | ENA

Full-length HLA class II sequences

Project description:Full-length HLA class II sequences

| PRJEB42469 | ENA

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

HLA Class I submissions 240531

Project description:HLA class I submissions 240531

| PRJEB76242 | ENA

Gene expression analysis of molecules with known function in HLA class II antigen processing and presentation in hematopoietic and (cytokine pre-treated) non-hematopoietic cells.

Project description:Gene expression analysis of molecules with known function in HLA class II antigen processing and presentation. Various hematopoietic cell types and (cytokine pre-treated) non-hematopoietic cells that are targeted in Graft-versus-Leukemia reactivity and Graft-versus-Host Disease were collected. Expression was compared between the different hematopoietic and non-hematopoietic cell types for the Invariant chain, HLA-DMA, HLA-DMB, HLA-DOA and HLA-DOB genes. The data show that the Invariant chain, HLA-DMA, HLA-DMB and HLA-DOA genes are expressed in all or the majority of cell types with HLA class II surface expression, whereas expression of the HLA-DOB gene is restricted to professional antigen presenting B-cells and mature dendritic cells. Total RNA was isolated from various hematopoietic cell types isolated (and cultured) from (G-CSF mobilized) peripheral blood from five different individuals and from (IFN-g pre-treated) fibroblasts cultured from skin biopsies from four different patients transplanted with allogeneic hematopoietic stem cells.

2012-06-18 | E-GEOD-38798 | biostudies-arrayexpress

Gene expression analysis of molecules with known function in HLA class II antigen processing and presentation in hematopoietic and (cytokine pre-treated) non-hematopoietic cells.

2012-06-19 | GSE38798 | GEO