PXD065279-1

PXD065279 is an original dataset announced via ProteomeXchange.

Title	MHC1-TIP: scalable multimodal immunopeptidome profiling of low-input samples
Description	We developed MHC1-TIP: an optimized mild acid elution-based immunopeptidomics workflow that leverages data independent acquisition and the Astral mass analyzer to enable scalable, single-tube and cost-effective MHC-I ligandome profiling. This dataset includes immunopeptidomics and proteomics data from the A375 melanoma cell line, colorectal cancer patient-derived organoids, and renal cell carcinoma tumour fragments. We show the effects of TGF-beta treatment on the proteome and immunopeptidome of A375 cells and interferon-gamma treatment on patient-derived organoids. We also explore immunopeptidome and proteome heterogeneity in patient-derived tumour fragments. MB_30: A375 immunopeptidomes in DDA (wildtype and B2M knockout); MB_38: Proteomes with and without mild acid treatment with A375 cells; MB_39: Proteomes and immunopeptidomes from TGFb treated A375 cells; MB_41: MHC1-TIP and MHC-I immunoprecipitation data from different A375 cell input numbers; MB_43: immunopeptidomes of A375 cells treated with different doses of interferon-gamma; MB_45: immunopeptidomes of A375 cells with MHC1-TIP and immunoprecipitation after mild acid elution to identify intracellular peptides; MB_46: Proteomics and immunopeptidomics data from 15 ex-vivo cultured patient-derived tumour fragments; MB_49: Proteomics and immunopeptidomics data from 3 patient-derived organoid lines.
HostingRepository	PRIDE
AnnounceDate	2025-12-19
AnnouncementXML	Submission_2025-12-18_23:36:15.508.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rik Lindeboom
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Astral; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-20 15:59:59	ID requested
⏵ 1	2025-12-18 23:36:16	announced

Dataset with its publication pending

submitter keyword: tumours, organoids, proteomics, heterogeneity, melanoma,immunopeptidomics

Rik Gerrit Hendrik Lindeboom
contact affiliation	Division of Molecular Genetics, the Netherlands Cancer Institute, the Netherlands
contact email	r.lindeboom@nki.nl
lab head
Rik Lindeboom
contact affiliation	Netherlands Cancer Institute
contact email	r.lindeboom@nki.nl
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/2025/12/PXD065279

PRIDE project URI

• PRIDE
  1. PXD065279
     1. Label: PRIDE project
     2. Name: MHC1-TIP: scalable multimodal immunopeptidome profiling of low-input samples