PXD043542-1

PXD043542 is an original dataset announced via ProteomeXchange.

Title	optiPRM: A targeted immunopeptidomics LC-MS workflow with ultra-high sensitivity for the detection of mutation-derived tumor neoepitopes from limited input material
Description	Personalized cancer immunotherapies such as vaccines and 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. For their detection by liquid chromatography mass spectrometry (LC-MS), 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 for 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, we here present optiPRM, a targeted MS workflow reaching ultra-high sensitivity by per peptide parameter optimization, which allowed for the identification of actionable neoepitopes from sample sizes usually available in the clinic.
HostingRepository	PRIDE
AnnounceDate	2024-08-09
AnnouncementXML	Submission_2024-08-09_02:17:40.039.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD043542
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jonas D. Förster
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-04 17:25:58	ID requested
⏵ 1	2024-08-09 02:17:40	announced
2	2024-10-22 06:53:30	announced	2024-10-22: Updated project metadata.

10.6019/PXD043542;

Salek M, F, ö, rster JD, Becker JP, Meyer M, Charoentong P, Lyu Y, Lindner K, Lotsch C, Volkmar M, Momburg F, Poschke I, Fr, ö, hling S, Schmitz M, Offringa R, Platten M, J, ä, ger D, Z, ö, rnig I, Riemer AB, optiPRM: A Targeted Immunopeptidomics LC-MS Workflow With Ultra-High Sensitivity for the Detection of Mutation-Derived Tumor Neoepitopes From Limited Input Material. Mol Cell Proteomics, 23(9):100825(2024) [pubmed]

10.1016/j.mcpro.2024.100825;

submitter keyword: Immunopeptidomics, PRM, LC-MS, Targeted MS

Angelika B. Riemer
contact affiliation	German Cancer Reseach Center (DKFZ)
contact email	anglika.riemer@dkfz.de
lab head
Jonas D. Förster
contact affiliation	German Cancer Reseach Center (DKFZ)
contact email	jonas.foerster@dkfz.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD043542

PRIDE project URI

• PRIDE
  1. PXD043542
     1. Label: PRIDE project
     2. Name: optiPRM: A targeted immunopeptidomics LC-MS workflow with ultra-high sensitivity for the detection of mutation-derived tumor neoepitopes from limited input material