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ProteomicsIDENTIFICATION OF AN UNCONVENTIONAL SUBPEPTIDOME BOUND TO THE BEHÇET’S DISEASE - ASSOCIATED HLA–B*51:01 THAT IS REGULATED BY ENDOPLASMIC RETICULUM AMINOPEPTIDASE 1 (ERAP1)
Human leukocyte antigen (HLA) - B*51:01 and endoplasmic reticulum aminopeptidase 1 (ERAP1) are two strong predisposing genetic factors to Behçet's disease (BD). Previous studies have focused on two subgroups of HLA-B*51 peptidome containing Proline (Pro) or Alanine (Ala) at position 2 (P2). Little i...
ORGANISM(S): Homo sapiens (Human) 
2020-03-18 | PXD013064 | Pride
Erap1  hla–b*51:01  behçet’s disease 
ProteomicsElucidation of the Signatures of Proteasome-Catalyzed Peptide Splicing
Proteasomes catalyze the degradation of endogenous proteins into oligopeptides, but can concurrently create spliced oligopeptides through ligation of previously non-contiguous peptide fragments. Recent studies have uncovered a formerly unappreciated role for proteasome-catalyzed peptide splicing (PC...
ORGANISM(S): Homo sapiens (Human) Human immunodeficiency virus 
2021-05-17 | PXD025893 | Pride
Peptide spliicng Proteasome Antigen processing 
ProteomicsAnalysis of bovine leukocyte antigen (BoLA)-associated peptides by LC-MS
An increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is in general challenging due to the poly-specificity nature of the data. We here outline a general pipeline for dealing with this challenge,...
ORGANISM(S): Bos taurus (Bovine) 
2017-11-20 | PXD008151 | Pride
Immunopeptidomics Bola 
ProteomicsMS-rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments
We propose a new pipeline for the refinement of spectrum-peptide assignment, designed specifically for MHC ligand identification. By modeling the peptidome as a collection of a limited number of specificities, corresponding to the MHC alleles of the cell line, our method achieves increased sequencin...
ORGANISM(S): Homo sapiens (Human) 
2019-01-02 | PXD011723 | Pride
Immunopeptidome  hla  lc-ms/ms  netmhcpan  binding prediction 
ProteomicsMS-rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments, part 2
We propose a new pipeline for the refinement of spectrum-peptide assignment, designed specifically for MHC ligand identification. By modeling the peptidome as a collection of a limited number of specificities, corresponding to the MHC alleles of the cell line, our method achieves increased sequencin...
ORGANISM(S): Mus musculus (Mouse) 
2019-01-02 | PXD011794 | Pride
Mhc Immunopeptidomics Tc-1 
ProteomicsOesophageal Tumour and Normal Oesophageal and Stomach tissue HLA class II Immunopeptidomics
Oesophageal TumOesophageal Tumour and Normal Oesophageal and Stomach tissue were analysed with HLA class II Immunopeptidomics using the L243 antibody
ORGANISM(S): Homo sapiens (Human) 
2026-06-08 | PXD060958 | Pride
Oesphageal tumour Immunopeptidomics Adenocarcinoma Hla class ii 
ProteomicsImmunopeptidomics of Bacillus Calmette-Guérin (BCG)-infected Thp-1 cells
We have immunoprecipitated MHC class-I and class-II complexes from THP-1 macrophages infected with BCG, eluted MHC-bound peptides and analysed them by liquid chromatography tandem mass spectrometry.
ORGANISM(S): Homo sapiens (Human) Mycobacterium 
2020-05-26 | PXD015646 | Pride
Bacillus calmette-guérin Hla Mhc Bcg Immunopeptidome 
ProteomicsNNAlign_MA; MHC peptidome deconvolution for accurate MHC binding motif characterization and improved T cell epitope predictions
Current mass spectrometry technologies allow for identification of MHC-associated peptide ligands. Studies have proven these data to be a rich source of information for learning the rules of MHC-mediated antigen presentation. Such immunopeptidomes are usually poly-specific, containing multiple seque...
ORGANISM(S): Bos taurus (Bovine) 
2019-10-07 | PXD015240 | Pride
Immunopeptidomics Bola ligandome 
ProteomicsElucidation of the signatures of proteasome-catalysed peptide splicing
Proteasomes catalyse the degradation of endogenous proteins into oligopeptides, but can concurrently create spliced oligopeptides through ligation of previously non-contiguous peptide fragments. Recent studies have uncovered a formerly unappreciated role for proteasome-catalysed peptide splicing (PC...
ORGANISM(S): Homo sapiens (Human) 
2020-10-26 | PXD021339 | Pride
Protein splicing Proteasome Splicing mechanism 
ProteomicsPRMT5 links the E2F pathway with a new source of tumour associated antigens
Immunopeptidomics analyses of HCT116 cells +/- PRMT5 inhibition
ORGANISM(S): Homo sapiens (Human) 
2023-02-01 | PXD029613 | Pride
Prmt5 Hct116 Immunopeptidomics Hla 
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