PepQueryMHC: Rapid and Comprehensive Tumor Antigen Prioritization from Immunopeptidomics Data

Published December 9, 2025 | Version v4

Dataset Open

Data Description

LUAD_MHC_I_GTEX.tsv: RNA-seq expression of selected class I tumor antigens from a published lung adenocarcinoma immunopeptidomics study (Abelin, J. G. et al., Gillette, M. A. et al., Lonsdale, J. et al.).
LUAD_MHC_II_GTEX.tsv: RNA-seq expression of selected class II tumor antigens from a published lung adenocarcinoma immunopeptidomics study (Abelin, J. G. et al., Gillette, M. A. et al., Lonsdale, J. et al.).
MSK_LUAD_Primary_seurat_object.rds: Seurat object containing the single-cell RNA-seq dataset of eight primary lung adenocarcinoma samples (processed) (Laughney, A. M. et al.).
PepQueryMHC_top10p_result.tsv: Top 10% most abundant peptides expressed in the eight primary lung adenocarcinoma single-cell RNA-seq samples (Laughney, A. M. et al.).
PepQueryMHC.v1.0.5.jar and source code

Files

Name	Size
meta.zip md5:d0f7dc8be47bf307902549d40359313d	2.2 GB	Preview Download
PepQueryMHC-main.zip md5:576206d028a0bd1952a53e2019dce636	150.3 kB	Preview Download
PepQueryMHC.v1.0.5.jar md5:d9fe647d5bacc9a23c1e30c2fef150ab	8.7 MB	Download

Abelin, J. G. et al. Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues. Nat Commun 14, 1851 (2023).
Gillette, M. A. et al. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. Cell 182, 200-225.e35 (2020).
Lonsdale, J. et al. The Genotype-Tissue Expression (GTEx) project. Nat Genet 45, 580–585 (2013).
Laughney, A. M. et al. Regenerative lineages and immune-mediated pruning in lung cancer metastasis. Nat Med 26, 259–269 (2020).