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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 
ProteomicsA microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics
Mass spectrometry (MS)-based immunopeptidomics is an attractive antigen discovery method with growing clinical implications, especially for personalized cancer immunotherapies. However, the current experimental approach to extract HLA-I-restricted peptides requires a bulky sample source, which remai...
ORGANISM(S): Homo sapiens (Human) 
2023-05-12 | PXD040858 | Pride
Mass spectrometry Immunopeptidomics Sample preparation Data-independent acquisition Automation Microfluidics 
ProteomicsSensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics
Targeting cancer-specific HLA-peptide complexes is a promising immunotherapy approach, with mutated neoantigens offering high value for their immunogenicity and cancer-specificity. Selecting immunogenic targets requires personalized prioritization of cancer-specific immunopeptides. Mass spectrometry...
ORGANISM(S): Homo sapiens (Human) 
2025-06-20 | PXD059824 | Pride
Immunopeptidomics Real-time searches Antigen discovery 
ProteomicsBiogenesis of HLA ligand presentation in immune cells upon activation reveals changes in peptide length preference
Induction of an effective tumor immunity is a complex process that includes the appropriate presentation of the tumor antigens, activation of specific T cells, and the elimination of malignant cells. Potent and efficient T cell activation is dependent on multiple factors, such as timely expression o...
ORGANISM(S): Homo sapiens (Human) 
2020-09-02 | PXD020011 | Pride
Immunopeptidomics Proteomics Immune cells 
ProteomicsEstimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome
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 ...
ORGANISM(S): Homo sapiens (Human) 
2018-09-03 | PXD010793 | Pride
Lc-msms Immunopeptidomics Proteasomal splicing Hla-i peptides 
ProteomicsImproved sensitivity of immunopeptidomics by leveraging available large-scale pan-HLA spectral libraries and data-independent acquisition
Mass spectrometry is the state-of-the-art methodology for capturing the breadth and depth of the immunopeptidome across HLA allotypes and cell types. The majority of studies in the immunopeptidomics field are discovery-driven and data-dependent tandem mass spectrometry acquisition is commonly used, ...
ORGANISM(S): Homo sapiens (Human) 
2021-04-13 | PXD022950 | Pride
Pan-hla Immunopeptidomics Dia 
Proteomicsthe landscape of phosphorylated HLA-I ligands
The identification and prediction of HLA-I–peptide interactions play an important role in our understanding of antigen recognition in infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-spec...
ORGANISM(S): Homo sapiens (Human) 
2019-12-18 | PXD013831 | Pride
Immunopeptidomics Hla binding peptides Phosphorylations 
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 
ProteomicsFully unsupervised identification of HLA-I motifs
The precise identification of Human Leukocyte Antigen class I (HLA-I) binding motifs plays a central role in our ability to understand and predict (neo-)antigen presentation in infectious diseases and cancer. Here, by exploiting co-occurrence of HLA-I alleles across publicly available as well as ten...
ORGANISM(S): Homo sapiens (Human) 
2017-08-18 | PXD005231 | Pride
Hla peptidome Immunopeptidomics Lc-ms/ms 
ProteomicsHigh-throughput MS-based immunopeptidomics
Comprehensive knowledge of the HLA class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer and other diseases. However methodologies for their extraction for mass-spectrometry analysis have been a major limitation. We designed a novel high-t...
ORGANISM(S): Homo sapiens (Human) 
2017-12-15 | PXD006939 | Pride
Hla-ii Affinity purification Hla-i Hla peptides Lc-ms/ms 
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