PXD043057 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | LC-MSMS of the MHC-I immunopeptidome of human NSCLC samples |
Description | While immune checkpoint blockade (ICB) therapy has significantly improved the outcome of metastatic melanoma and non-small cell lung cancer (NSCLC), most patients do not derive long-term benefits. Previous studies suggest that treatment failure is partly due to insufficient immune recognition of tumor antigens (TAs). Notably, immune targeting of TAs has focused on TAs derived from non-synonymous genomic mutations. We used a proteogenomic approach combining RNA-sequencing and mass spectrometry to study the MHC I-immunopeptidome of cutaneous melanoma and NSCLC samples. The RNA-sequencing of each sample was used to construct sample-specific databases for the mass spectrometry-based identification of MHC I-associated peptides (MAPs). MAPs were then filtered based on their RNA expression in the respective cancer types from The Cancer Genome Atlas (TCGA-SKCM for melanoma MAPs, or TCGA-LUSC and TCGA-LUAD for NSCLC MAPs) vs. benign tissues (from the Genotype-Tissue Expression (GTEx) Project, medullary thymic epithelial cells, purified blood and bone marrow cells, and normal melanocytes for melanoma or bronchial brushing samples for NSCLC). MAPs were classified as mutated tumor-specific antigens (mTSAs, derived from non-synonymous mutations expressed in the sample of origin), or unmutated tumor antigens: aberrantly expressed tumor-specific antigens (aeTSAs, no/low expression in benign tissues and at least two times higher expression in TCGA), tumor-associated antigens (TAAs, significant expression in benign tissues and at least two times higher expression in TCGA), lineage-associated antigens (LSAs, specific expression to cancer and normal tissue of origin, i.e., lung and bronchial brushing samples for NSCLC or skin and melanocytes for melanoma). The tumor antigens described here represent attractive targets for immunotherapy of melanoma and NSCLC. |
HostingRepository | PRIDE |
AnnounceDate | 2025-02-19 |
AnnouncementXML | Submission_2025-02-19_11:15:39.143.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD043057 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Courcelles Mathieu |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; deamidated residue |
Instrument | orbitrap |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-06-16 06:31:55 | ID requested | |
⏵ 1 | 2025-02-19 11:15:39 | announced | |
Publication List
Keyword List
submitter keyword: non-small cell lung cancer, LC-MSMS, immunopeptidome, MHC class I |
Contact List
Pierre Thibault |
contact affiliation | Institute for Research in Immunology and Cancer, Department of Biochemistry, Department of Chemistry, Université de Montréal, Québec, Canada H3T 1J4 |
contact email | pierre.thibault@umontreal.ca |
lab head | |
Courcelles Mathieu |
contact affiliation | IRIC |
contact email | mathieu.courcelles@umontreal.ca |
dataset submitter | |
Full Dataset Link List
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/2025/02/PXD043057 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD043057
- Label: PRIDE project
- Name: LC-MSMS of the MHC-I immunopeptidome of human NSCLC samples