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@ARTICLE{Li:298584,
      author       = {M. J. Li and L. C. Meyer and N. Meier and J. Witte and M.
                      Maldacker and A. Seredynska$^*$ and J. Schueler and O.
                      Schilling$^*$ and M. C. Föll$^*$},
      title        = {{S}patial {P}roteomics by {P}arallel
                      {A}ccumulation-{S}erial {F}ragmentation {S}upported {MALDI}
                      {MS}/{MS} {I}maging: {A} {F}irst {G}lance {I}nto
                      {M}ultiplexed and {S}patial {P}eptide {I}dentification.},
      journal      = {Rapid communications in mass spectrometry},
      volume       = {39},
      number       = {9},
      issn         = {0951-4198},
      address      = {New York, NY},
      publisher    = {Wiley Interscience},
      reportid     = {DKFZ-2025-00301},
      pages        = {e10006},
      year         = {2025},
      abstract     = {In spatial proteomics, matrix-assisted laser
                      desorption/ionization (MALDI) imaging enables rapid and
                      cost-effective peptide measurements. Yet, in situ peptide
                      identification remains challenging. Therefore, this study
                      aims to integrate the trapped ion mobility spectrometry
                      (TIMS)-based parallel accumulation-serial fragmentation
                      (PASEF) into MALDI imaging of tryptic peptides to enable
                      multiplexed MS/MS imaging.An initial MALDI TIMS MS1 survey
                      measurement was performed, followed by a manual generation
                      of a precursor list containing mass over charge values and
                      ion mobility windows. Inside the dual TIMS system, submitted
                      precursors were trapped, separately eluted by their ion
                      mobility and analyzed in a quadrupole time-of-flight device,
                      thereby enabling multiplexed MALDI MS/MS imaging. Finally,
                      precursors were identified by peptide to spectrum
                      matching.This study presents the first multiplexed MALDI
                      TIMS MS/MS imaging (iprm-PASEF) of tryptic peptides. Its
                      applicability was showcased on two histomorphologically
                      distinct tissue specimens in a four-plex and five-plex
                      setup. Precursors were successfully identified by the search
                      engine MASCOT in one single MALDI imaging experiment for
                      each respective tissue. Peptide identifications were
                      corroborated by liquid-chromatography tandem mass
                      spectrometry experiments and fragment colocalization
                      analyses.In this study, we present a novel pipeline, based
                      on iprm-PASEF, that allows the multiplexed and spatial
                      identification of tryptic peptides in MALDI imaging. Hence,
                      it marks a first step towards the integration of MALDI
                      imaging into the emerging field of spatial proteomics.},
      keywords     = {Spectrometry, Mass, Matrix-Assisted Laser
                      Desorption-Ionization: methods / Proteomics: methods /
                      Tandem Mass Spectrometry: methods / Animals / Peptides:
                      chemistry / Peptides: analysis / Ion Mobility Spectrometry:
                      methods / Peptide Fragments: analysis / Peptide Fragments:
                      chemistry / MALDI imaging (Other) / MS/MS imaging (Other) /
                      TIMS (Other) / iprm‐PASEF (Other) / peptide imaging
                      (Other) / spatial proteomics (Other) / Peptides (NLM
                      Chemicals) / Peptide Fragments (NLM Chemicals)},
      cin          = {FR01},
      ddc          = {530},
      cid          = {I:(DE-He78)FR01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:39910729},
      doi          = {10.1002/rcm.10006},
      url          = {https://inrepo02.dkfz.de/record/298584},
}