Description
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 demonstrates substantial improvements in the definition of HLA-II binding motifs and enhanced accuracy in HLA-II ligand and class II epitope predictions.
[dataset license: CC0 1.0 Universal (CC0 1.0)]
Keywords: Immunopeptidomics ; Ligand predictions ; Mass spectrometry ; Hla class ii ; Neoantigens ; DatasetType:Proteomics
Contact
Principal Investigators:
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Michal Bassani-Sternberg, Dr Michal BASSANI-STERNBERG � Group leader Laboratory Hi-TIDe: Immunopeptidomics Head of clinical Mass spectrometry unit Center of experimental therapeutics Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Biop�le 3 Chemin des Boveresses 155, CH-1066 Lausanne, N/A
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Submitting User: |
ccms
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Publications
Racle J, Michaux J, Rockinger GA, Arnaud M, Bobisse S, Chong C, Guillaume P, Coukos G, Harari A, Jandus C, Bassani-Sternberg M, Gfeller D.
Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes.
Nat Biotechnol. 2019 Nov;37(11):1283-1286. Epub 2019 Oct 14.
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Number of distinct biological replicates across all analyses (original submission and reanalyses)
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Distinct replicate labels are counted across all files submitted in the "Metadata" category
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The technical replicate count is defined as the maximum number of times any one distinct
combination of condition and biological replicate was analyzed across all files submitted in the
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"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically
remapped by MassIVE to proteins in the
SwissProt
human reference database.
"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and
reanalyses) associated with this dataset.
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Number of distinct unmodified peptide sequences reported across all analyses (original
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Number of distinct peptide sequences (including modified variants or peptidoforms) reported
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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all
analyses (original submission and reanalyses) associated with this dataset.
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Number of distinct proteins quantified across all analyses (original submission and reanalyses)
associated with this dataset.
Distinct protein accessions are counted across all files submitted in the "Statistical Analysis
of Quantified Analytes" category having a "Protein" column in this dataset.
"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison
across all analyses (original submission and reanalyses) associated with this dataset.
A protein is differentially abundant if its change in abundance across conditions is found
to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated
with statistical tests for differential abundance.
Distinct protein accessions are counted across all files submitted in the "Statistical Analysis
of Quantified Analytes" category having a "Protein" column in this dataset.
"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE.
It has been imported to MassIVE for reanalysis purposes, so its spectra data here may
consist solely of processed peak lists suitable for reanalysis with most software.