Proteomics

Dataset Information

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MHCquant: Automated and reproducible data analysis for immunopeptidomics


ABSTRACT: Personalized multi-peptide vaccines are currently being discussed intensively for tumor immunotherapy. In order to find epitopes - short, immunogenic peptides - suitable to elicit an immune response, human leukocyte antigen-presented peptides from cancer tissue samples are purified using immunoaffinity purification and analyzed by high performance liquid chromatography coupled to mass spectrometry. Here we report on a novel computational pipeline to identify peptides from large-scale immunopeptidomics raw data sets. In the conducted experiments we benchmarked our workflow to other existing mass spectrometry analysis software and achieved higher sensitivity. A dataset of 38 HLA immunopeptidomics raw files of peripheral blood mononuclear cells (PBMCs) from 10 healthy volunteers and 4 JY cell lines was used to assess the performance of the pipeline at each processing step. In addition, 66 isotope labeled known HLA-presented peptides were spiked into the JY cell extracts decreasing in concentration by log10 steps from 100 fmol to 0.1 fmol.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Blood Plasma, Peripheral Blood Mononuclear Cell, Blood

SUBMITTER: Leon Bichmann  

LAB HEAD: Professor Oliver Kohlbacher

PROVIDER: PXD011628 | Pride | 2019-10-14

REPOSITORIES: Pride

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Publications


Although mutations may represent attractive targets for immunotherapy, direct identification of mutated peptide ligands isolated from human leucocyte antigens (HLA) on the surface of native tumour tissue has so far not been successful. Using advanced mass spectrometry (MS) analysis, we survey the melanoma-associated immunopeptidome to a depth of 95,500 patient-presented peptides. We thereby discover a large spectrum of attractive target antigen candidates including cancer testis antigens and pho  ...[more]

Publication: 1/2

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