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@ARTICLE{Salek:292117,
      author       = {M. Salek$^*$ and J. Förster$^*$ and J. Becker$^*$ and M.
                      Meyer$^*$ and P. Charoentong$^*$ and Y. Lyu$^*$ and K.
                      Lindner$^*$ and C. Lotsch$^*$ and M. Volkmar and F.
                      Momburg$^*$ and I. Poschke$^*$ and S. Fröhling$^*$ and M.
                      Schmitz$^*$ and R. Offringa$^*$ and M. Platten$^*$ and D.
                      Jäger$^*$ and I. Zörnig$^*$ and A. Riemer$^*$},
      title        = {opti{PRM}: {A} targeted immunopeptidomics {LC}-{MS}
                      workflow with ultra-high sensitivity for the detection of
                      mutation-derived tumor neoepitopes from limited input
                      material.},
      journal      = {Molecular $\&$ cellular proteomics},
      volume       = {23},
      number       = {9},
      issn         = {1535-9476},
      address      = {Bethesda, Md.},
      publisher    = {The American Society for Biochemistry and Molecular
                      Biology},
      reportid     = {DKFZ-2024-01616},
      pages        = {100825},
      year         = {2024},
      note         = {#EA:D410#LA:D410# / HI-TRON / 2024, 23(9), art. no. 100825},
      abstract     = {Personalized cancer immunotherapies such as therapeutic
                      vaccines and adoptive transfer of T cell receptor
                      (TCR)-transgenic T cells rely on the presentation of
                      tumor-specific peptides by human leukocyte antigen (HLA)
                      class I molecules to cytotoxic T cells. Such neoepitopes can
                      for example arise from somatic mutations and their
                      identification is crucial for the rational design of new
                      therapeutic interventions. Liquid chromatography mass
                      spectrometry (LC-MS)-based immunopeptidomics is the only
                      method to directly prove actual peptide presentation and we
                      have developed a parameter optimization workflow to tune
                      targeted assays for maximum detection sensitivity on a per
                      peptide basis, termed optiPRM. Optimization of collision
                      energy using optiPRM allows for improved detection of low
                      abundant peptides that are very hard to detect using
                      standard parameters. Applying this to immunopeptidomics, we
                      detected a neoepitope in a patient-derived xenograft (PDX)
                      from as little as 2.5×106 cells input. Application of the
                      workflow on small patient tumor samples allowed for the
                      detection of five mutation-derived neoepitopes in three
                      patients. One neoepitope was confirmed to be recognized by
                      patient T cells. In conclusion, optiPRM, a targeted MS
                      workflow reaching ultra-high sensitivity by per peptide
                      parameter optimization, which makes the identification of
                      actionable neoepitopes possible from sample sizes usually
                      available in the clinic.},
      cin          = {D410 / D121 / D120 / HD01 / D170 / B340 / DD01 / D200},
      ddc          = {610},
      cid          = {I:(DE-He78)D410-20160331 / I:(DE-He78)D121-20160331 /
                      I:(DE-He78)D120-20160331 / I:(DE-He78)HD01-20160331 /
                      I:(DE-He78)D170-20160331 / I:(DE-He78)B340-20160331 /
                      I:(DE-He78)DD01-20160331 / I:(DE-He78)D200-20160331},
      pnm          = {314 - Immunologie und Krebs (POF4-314)},
      pid          = {G:(DE-HGF)POF4-314},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:39111711},
      doi          = {10.1016/j.mcpro.2024.100825},
      url          = {https://inrepo02.dkfz.de/record/292117},
}