ArticleNature communications2024
MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 18 citations in OpenAlex.
- TIPs: a deep learning-guided proteogenomic framework to expand the landscape of transposable element-derived antigens with immunopeptidomics.Genome biology · 2026Article
- Micropeptide colorectal neoplasia differentially expressed (CRNDE) 84aa encoded by CRNDE elicits a T-cell immune response to breast cancer.Translational cancer research · 2026Article
- AI-Driven Drug Discovery: Focus on Targets for Solid Tumors.Pharmaceutics · 2026Review
- Sensitive detection of cancer antigens enabled by user-defined peptide libraries.Nature biotechnology · 2026Article
- Efficient and effective identification of cancer neoantigens from tumor only RNA-seq.NAR genomics and bioinformatics · 2025Article
- Deciphering the MHC immunopeptidome of human cancers with Ligand.MHC atlas.Briefings in bioinformatics · 2025Article
- A Primer on Proteomic Characterization of Intercellular Communication in a Virus Microenvironment.Molecular & cellular proteomics : MCP · 2025Review
- Interferon-α promotes HLA-B-restricted presentation of conventional and alternative antigens in human pancreatic β-cells.Nature communications · 2025Article
- The 2024 Report on the Human Proteome from the HUPO Human Proteome Project.Journal of proteome research · 2024Review
- Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines.Nature communications · 2024Article
- Mapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes.Nature communications · 2024Article
- The 2023 Report on the Proteome from the HUPO Human Proteome Project.Journal of proteome research · 2024Review
- Interferon-α promotes neo-antigen formation and preferential HLA-B-restricted antigen presentation in pancreatic β-cells.bioRxiv : the preprint server for biology · 2023Article
- Exploring the dynamic landscape of immunopeptidomics: Unravelling posttranslational modifications and navigating bioinformatics terrain.Mass spectrometry reviewsReview
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Authors and funding
15 authors at 5 institutions in 5 countries.
Funding
Abstract
Understanding the nature and extent of non-canonical human leukocyte antigen (HLA) presentation in tumour cells is a priority for target antigen discovery for the development of next generation immunotherapies in cancer. We here employ a de novo mass spectrometric sequencing approach with a refined, MHC-centric analysis strategy to detect non-canonical MHC-associated peptides specific to cancer without any prior knowledge of the target sequence from genomic or RNA sequencing data. Our strategy integrates MHC binding rank, Average local confidence scores, and peptide Retention time prediction for improved de novo candidate Selection; culminating in the machine learning model MARS. We benchmark our model on a large synthetic peptide library dataset and reanalysis of a published dataset of high-quality non-canonical MHC-associated peptide identifications in human cancer. We achieve almost 2-fold improvement for high quality spectral assignments in comparison to de novo sequencing alone with an estimated accuracy of above 85.7% when integrated with a stepwise peptide sequence mapping strategy. Finally, we utilize MARS to detect and validate lncRNA-derived peptides in human cervical tumour resections, demonstrating its suitability to discover novel, immunogenic, non-canonical peptide sequences in primary tumour tissue.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.