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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 
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 
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 
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 
ProteomicsCervical Cancer Tissue Immunopeptidomics
10 cervical cancer tissue tumour resections were analysed using an immunopeptidomics workflow.
ORGANISM(S): Homo sapiens (Human) 
2024-01-26 | PXD046182 | Pride
Cervical cancer High-risk hpv infection Immunopeptidomics Hla-associated peptides 
ProteomicsBoLA-DRimmunopeptidomics in Theileria parva infected, bovine cell lines
The ability to maintain T.parva-infected cell lines as rapidly proliferating cells in vitro that express high levels of both MHCI and MHCII, makes this a particularly amenable system in which to apply MHCp elution analysis. Furthermore, the ability of T. parva-infected cells to recall antigen-specif...
ORGANISM(S): Bos taurus (Bovine) 
2022-05-19 | PXD024053 | Pride
Immunppeptidomics Bovine leukocyte antigen  theileria parva  mhc 
TranscriptomicsTranscription profiling of yeast to investigate the involvement of Snf7 and Rim101 in regulation of TIR1 and anaerobically up-regulated genes
Despite the scientific and applied interest in anaerobic metabolism of Saccharomyces cerevisiae, not all genes whose transcription is up-regulated under anaerobic conditions have yet been linked to known transcription factors. Experiments with a reporter construct in which the promoter of the anaero...
ORGANISM(S): Saccharomyces cerevisiae 
2009-10-02 | E-GEOD-18128 | biostudies-arrayexpress
TranscriptomicsEngineering topology and kinetics of sucrose metabolism in Saccharomyces cerevisiae for improved ethanol yield
Sucrose is a major carbon source for industrial bioethanol production by Saccharomyces cerevisiae. In yeasts, two modes of sucrose metabolism occur: (i) extracellular hydrolysis by invertase, followed by uptake and metabolism of glucose and fructose, and (ii) uptake via sucrose-H+ symport followed b...
ORGANISM(S): Saccharomyces cerevisiae 
2011-09-05 | E-GEOD-30535 | biostudies-arrayexpress
UnknownEarly microgliosis precedes neuronal loss and behavioural impairment in mice with a frontotemporal dementia-causing CHMP2B mutation.
Not available
S-EPMC5409096 | biostudies-literature
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