TY  - JOUR
AU  - Wacker, Marcel
AU  - Bauer, Jens
AU  - Wessling, Laura
AU  - Dubbelaar, Marissa
AU  - Nelde, Annika
AU  - Rammensee, Hans-Georg
AU  - Walz, Juliane S
TI  - Immunoprecipitation methods impact the peptide repertoire in immunopeptidomics.
JO  - Frontiers in immunology
VL  - 14
SN  - 1664-3224
CY  - Lausanne
PB  - Frontiers Media
M1  - DKFZ-2023-01599
SP  - 1219720
PY  - 2023
AB  - 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
KW  - HLA peptides (Other)
KW  - hydrophobicity (Other)
KW  - immunogenicity (Other)
KW  - immunopeptidomics (Other)
KW  - immunoprecipitation (Other)
KW  - immunotherapies (Other)
KW  - mass spectrometry (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:37545538
C2  - pmc:PMC10400765
DO  - DOI:10.3389/fimmu.2023.1219720
UR  - https://inrepo02.dkfz.de/record/278342
ER  -