MHC1-TIP: scalable multimodal immunopeptidome profiling of low-input samples

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Melanocyte, Epithelial Cell, Cell Culture, Colon, Kidney

DISEASE(S): Colon Cancer,Melanoma,Renal Cell Carcinoma

SUBMITTER: Rik Lindeboom  

LAB HEAD: Rik Gerrit Hendrik Lindeboom

PROVIDER: PXD065279 | Pride | 2025-12-18

REPOSITORIES: Pride