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@ARTICLE{Wacker:278342,
      author       = {M. Wacker and J. Bauer and L. Wessling and M. Dubbelaar and
                      A. Nelde and H.-G. Rammensee$^*$ and J. S. Walz$^*$},
      title        = {{I}mmunoprecipitation methods impact the peptide repertoire
                      in immunopeptidomics.},
      journal      = {Frontiers in immunology},
      volume       = {14},
      issn         = {1664-3224},
      address      = {Lausanne},
      publisher    = {Frontiers Media},
      reportid     = {DKFZ-2023-01599},
      pages        = {1219720},
      year         = {2023},
      abstract     = {Mass spectrometry-based immunopeptidomics is the only
                      unbiased method to identify naturally presented HLA ligands,
                      which is an indispensable prerequisite for characterizing
                      novel tumor antigens for immunotherapeutic approaches. In
                      recent years, improvements based on devices and methodology
                      have been made to optimize sensitivity and throughput in
                      immunopeptidomics. However, developments in ligand
                      isolation, mass spectrometric analysis, and subsequent data
                      processing can have a marked impact on the quality and
                      quantity of immunopeptidomics data.In this work, we compared
                      the immunopeptidome composition in terms of peptide yields,
                      spectra quality, hydrophobicity, retention time, and
                      immunogenicity of two established immunoprecipitation
                      methods (column-based and 96-well-based) using cell lines as
                      well as primary solid and hematological tumor
                      samples.Although, we identified comparable overall peptide
                      yields, large proportions of method-exclusive peptides were
                      detected with significantly higher hydrophobicity for the
                      column-based method with potential implications for the
                      identification of immunogenic tumor antigens. We showed that
                      column preparation does not lose hydrophilic peptides in the
                      hydrophilic washing step. In contrast, an additional $50\%$
                      acetonitrile elution could partially regain lost hydrophobic
                      peptides during 96-well preparation, suggesting a reduction
                      of the bias towards the column-based method but not
                      completely equalizing it.Together, this work showed how
                      different immunoprecipitation methods and their adaptions
                      can impact the peptide repertoire of immunopeptidomic
                      analysis and therefore the identification of potential
                      tumor-associated antigens.},
      keywords     = {HLA peptides (Other) / hydrophobicity (Other) /
                      immunogenicity (Other) / immunopeptidomics (Other) /
                      immunoprecipitation (Other) / immunotherapies (Other) / mass
                      spectrometry (Other)},
      cin          = {TU01},
      ddc          = {610},
      cid          = {I:(DE-He78)TU01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:37545538},
      pmc          = {pmc:PMC10400765},
      doi          = {10.3389/fimmu.2023.1219720},
      url          = {https://inrepo02.dkfz.de/record/278342},
}