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@ARTICLE{GmezZepeda:288978,
      author       = {D. Gómez-Zepeda$^*$ and D. Arnold-Schild and J. Beyrle$^*$
                      and A. Declercq and R. Gabriels and E. Kumm and A.
                      Preikschat and M. K. Łącki and A. Hirschler and J. B.
                      Rijal and C. Carapito and L. Martens and U. Distler and H.
                      Schild and S. Tenzer$^*$},
      title        = {{T}hunder-{DDA}-{PASEF} enables high-coverage
                      immunopeptidomics and is boosted by {MS}2{R}escore with
                      {MS}2{PIP} tims{TOF} fragmentation prediction model.},
      journal      = {Nature Communications},
      volume       = {15},
      number       = {1},
      issn         = {2041-1723},
      address      = {[London]},
      publisher    = {Nature Publishing Group UK},
      reportid     = {DKFZ-2024-00530},
      pages        = {2288},
      year         = {2024},
      note         = {#EA:D191#LA:D191# / HI-TRON},
      abstract     = {Human leukocyte antigen (HLA) class I peptide ligands
                      (HLAIps) are key targets for developing vaccines and
                      immunotherapies against infectious pathogens or cancer
                      cells. Identifying HLAIps is challenging due to their high
                      diversity, low abundance, and patient individuality. Here,
                      we develop a highly sensitive method for identifying HLAIps
                      using liquid chromatography-ion mobility-tandem mass
                      spectrometry (LC-IMS-MS/MS). In addition, we train a
                      timsTOF-specific peak intensity MS2PIP model for tryptic and
                      non-tryptic peptides and implement it in MS2Rescore (v3)
                      together with the CCS predictor from ionmob. The optimized
                      method, Thunder-DDA-PASEF, semi-selectively fragments singly
                      and multiply charged HLAIps based on their IMS and m/z.
                      Moreover, the method employs the high sensitivity mode and
                      extended IMS resolution with fewer MS/MS frames (300 ms TIMS
                      ramp, 3 MS/MS frames), doubling the coverage of
                      immunopeptidomics analyses, compared to the
                      proteomics-tailored DDA-PASEF (100 ms TIMS ramp, 10 MS/MS
                      frames). Additionally, rescoring boosts the HLAIps
                      identification by $41.7\%$ to $33\%,$ resulting in 5738
                      HLAIps from as little as one million JY cell equivalents,
                      and 14,516 HLAIps from 20 million. This enables in-depth
                      profiling of HLAIps from diverse human cell lines and human
                      plasma. Finally, profiling JY and Raji cells transfected to
                      express the SARS-CoV-2 spike protein results in 16 spike
                      HLAIps, thirteen of which have been reported to elicit
                      immune responses in human patients.},
      cin          = {D191},
      ddc          = {500},
      cid          = {I:(DE-He78)D191-20160331},
      pnm          = {314 - Immunologie und Krebs (POF4-314)},
      pid          = {G:(DE-HGF)POF4-314},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:38480730},
      doi          = {10.1038/s41467-024-46380-y},
      url          = {https://inrepo02.dkfz.de/record/288978},
}