PXD041804-2

PXD041804 is an original dataset announced via ProteomeXchange.

Title	Immunoprecipitation methods impact the peptide repertoire in immunopeptidomics
Description	T cell-based immunotherapies, which have become a promising treatment approach for cancer patients, rely on the identification of human leukocyte antigen (HLA)-presented peptides. Mass spectrometry-based immunopeptidomics is the state-of-the-art method for the identification of clinically relevant naturally presented HLA-restricted tumor-associated antigens. In the last years, different methods for the immunoprecipitation-based isolation of HLA-presented peptides have been developed and are used in the field. Here, we performed a comparison of a column-based with a high-throughput 96-well method by analyzing the immunopeptidome of cell lines as well as primary solid and hematological tumor samples. Whereas no differences in the total number of identified peptides were observed, the column-based method identified method-exclusive peptides that featured higher hydrophobicity and exhibited improved predicted immunogenicity. Adding an additional acetonitrile elution step to the 96-well method could partially reduce this hydrophilic shift. In total, we showed that immunopeptidomics data is affected by the immunoprecipitation method used for isolation, which might have a critical impact on the selection of target antigens and has to be considered when selecting clinically relevant targets for the development of T cell-based immunotherapies.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:52:15.422.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marcel Wacker
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-25 16:04:27	ID requested
1	2023-07-05 06:27:45	announced
⏵ 2	2024-10-22 05:52:15	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: hydrophobicity, mass spectrometry,Immunotherapies, immunopeptidomics, immunoprecipitation, immunogenicity, HLA peptides

Juliane S. Walz
contact affiliation	Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
contact email	juliane.walz@med.uni-tuebingen.de
lab head
Marcel Wacker
contact affiliation	Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
contact email	marcel.wacker@uni-tuebingen.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD041804
     1. Label: PRIDE project
     2. Name: Immunoprecipitation methods impact the peptide repertoire in immunopeptidomics