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ProteomicsCIITA-transduced glioblastoma cells uncover a rich repertoire of clinically relevant tumor-associated HLA-II antigens
CD4+ T cell responses are crucial for inducing and maintaining effective anti-cancer immunity, and the identification of HLA-II cancer-specific epitopes is key to the development of potent cancer immunotherapies. In many tumor types, and especially in glioblastoma (GBM), HLA-II complexes are hardly ...
ORGANISM(S): Homo sapiens (Human) 
2021-02-03 | PXD020079 | Pride
Glioblastoma Immunopeptidomics Antigen presentation Ciita 
ProteomicsDeep motif deconvolution of HLA-II peptidomes
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...
ORGANISM(S): Homo sapiens (Human) 
2019-10-16 | PXD012308 | Pride
Immunopeptidomics Ligand predictions Mass spectrometry Hla class ii Neoantigens 
ProteomicsThe landscape of the SARS-CoV-2 HLA-peptidome
The human leukocyte antigen (HLA)-bound-viral antigens, serve as an immunological signature that can be selectively recognized by T cells. As viruses evolve by acquiring mutations, it is essential to identify a range of viral presented antigens. Utilizing HLA-peptidomics we Identified SARS-CoV-2-der...
ORGANISM(S): Homo sapiens (Human) 
2021-06-28 | PXD025499 | Pride
Sars-cov-2 Immunopeptidomics Hla-peptidomics 
ProteomicsNatural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors.
Atypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive CNS-tumors of infancy and early childhood. Hallmark is the surprisingly simple genomics with a truncating mutation in the SMARCB1 gene as the oncogenic driver. Nevertheless, AT/RTs are infiltrated by immune cells and even clonally expan...
ORGANISM(S): Homo sapiens (Human) 
2022-05-31 | PXD033935 | Pride
Human Primary at/rt tumors Hla-i and hla-ii 
ProteomicsDeep motif deconvolution of HLA-II peptidomes
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...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-10-18 | MSV000096130 | MassIVE
ProteomicsHLA class II peptidome analysis using data-dependent and data-independent acquisition
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.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-11-22 | MSV000081729 | MassIVE
ProteomicsHLA-DO Modulates the Diversity of the MHC-II Self-peptidome
HLA-DR1 bound peptides of five biological replicates of LG2-WT(012916_WT1,022216_WT1, 02080316MHCIIWT1, 080316MHCIIWT2, 080316MHCIIWT3) and DO-KO Clone 1 LG-2 cells (012916_KO1, 022216_DO1, 081216MHCIIKO1, 080416MHCIIKO2, 080416MHCIIKO3) were processed in parallel. Each biological replicate has 3 te...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-07-03 | MSV000082570 | MassIVE
ProteomicsDefining HLA-II ligand processing and binding rules with mass spectrometry enhances cancer epitope prediction
Increasing evidence indicates CD4+ T cells can recognize cancer-specific antigens and control tumor growth. However, it remains difficult to predict the antigens that will be presented by human leukocyte antigen class II molecules (HLA-II) - hindering efforts to optimally target them therapeutically...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2019-06-18 | MSV000083991 | MassIVE
ProteomicsThe landscape of the SARS-CoV-2 HLA-peptidome
The human leukocyte antigen (HLA)-bound-viral antigens, serve as an immunological signature that can be selectively recognized by T cells. As viruses evolve by acquiring mutations, it is essential to identify a range of viral presented antigens. Utilizing HLA-peptidomics we Identified SARS-CoV-2-der...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2021-11-01 | MSV000088298 | MassIVE
ProteomicsProteomeTools – Part III - HLA Class I & II & non-tryptic peptides
The ProteomeTools project aims to derive molecular and digital tools from the human proteome to facilitate biomedical and life science research. Here, we describe the third iteration of the generation and multimodal LC-MS/MS analysis of >305,000 synthetic non-tryptic peptides representing HLA Class ...
ORGANISM(S): Homo sapiens (Human) 
2021-04-26 | PXD021013 | Pride
Hla Aspn Hla class ii Proteometools Reference standards Hla class i Synthetic peptides Lysn 
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