PXD054097-1

PXD054097 is an original dataset announced via ProteomeXchange.

Title	SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor-treated and resistant tumor cells
Description	The immunopeptidome is constantly monitored by T cells to detect foreign or aberrant HLA peptides. It is highly dynamic and reflects the current cellular state, enabling the immune system to recognize abnormal cellular conditions, such as those present in cancer cells. To precisely determine how changes in cellular processes, such as those induced by drug treatment, affect the immunopeptidome, quantitative immunopeptidomics approaches are essential. To meet this need, we developed a pulsed SILAC-based method for quantitative immunopeptidomics. Metabolic labeling with lysine, arginine, and leucine enabled isotopic labeling of nearly all HLA peptides across all HLA allotypes (> 90% on average). We established a data analysis workflow that integrates the de novo sequencing-based tool Peptide-PRISM for comprehensive HLA peptide identification with MaxQuant for accurate quantification. We employed this strategy to explore the modulation of the immunopeptidome upon MAPK pathway inhibition and to investigate alterations associated with acquired resistance to BRAF and MEK inhibitors. Our analyses demonstrated significant changes in the immunopeptidome following MAPK pathway inhibition, as well as in cells resistant to BRAF/MEK inhibitors. Moreover, we identified putative tumor-specific cryptic HLA peptides linked to these processes.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-06_22:02:12.471.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Melissa Bernhardt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-22 01:48:52	ID requested
⏵ 1	2025-05-06 22:02:13	announced

Bernhardt M, Rech A, Berthold M, Lappe M, Herbel JN, Erhard F, Paschen A, Schilling B, Schlosser A, SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells. Front Immunol, 15():1490821(2024) [pubmed]

10.3389/fimmu.2024.1490821;

ProteomeXchange project tag: Cancer (B/D-HPP), Human Immuno-Peptidome Project (HUPO-HIPP) (B/D-HPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

submitter keyword: kinase inhibitor resistance,Immunopeptidomics, cancer, mass-spectrometry, cryptic peptides, MAPK signaling, melanoma, LC-MS/MS

Andreas Schlosser
contact affiliation	Rudolf-Virchow Center Julius-Maximilians-Universität Würzburg Josef-Schneider Straße 2/D15 97080 Würzburg
contact email	andreas.schlosser@uni-wuerzburg.de
lab head
Melissa Bernhardt
contact affiliation	mass spectrometry
contact email	melissa.bernhardt@uni-wuerzburg.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/2025/05/PXD054097

PRIDE project URI

• PRIDE
  1. PXD054097
     1. Label: PRIDE project
     2. Name: SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor-treated and resistant tumor cells