ArticleMolecular & cellular proteomics : MCP2015
Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation.
Article in Molecular & cellular proteomics : MCP, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 254 papers, 2 of them syntheses that pooled it.
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Who cites it
254 citing papers in PubMed, 2 syntheses or guidelines pooled it, 442 citations in OpenAlex.
- Transformers meets neoantigen detection: a systematic literature review.Journal of integrative bioinformatics · 2024Pooled it
- Challenges targeting cancer neoantigens in 2021: a systematic literature review.Expert review of vaccines · 2021Pooled it
- Immunopeptidomics-Guided Warehouse Design for Peptide-Based Immunotherapy in Chronic Lymphocytic Leukemia.Frontiers in immunology · 2021Trial
- Central T cell tolerance from sparse peptide sampling.Science advances · 2026Article
- Beyond Sequence: Posttranslational Remodeling of Antigens in Autoimmunity.Immunological reviews · 2026Review
- ENO1 as an Immunoregulatory Hub in Cancer: Mechanisms and Translational Implications.Biomolecules · 2026Review
- Immunopeptidomics-guided identification of functional neoantigens in non-small cell lung cancer.NPJ precision oncology · 2026Article
- A Platform for High-throughput and Ultrasensitive Immunopeptidomics.Molecular & cellular proteomics : MCP · 2026Article
- AI-enabled virtual immunopeptidomics links quantitative neoantigen presentation to immunogenicity.bioRxiv : the preprint server for biology · 2026Article
- Advances in predicting T cell epitope recognition for cancer immunotherapy.Nature cancer · 2026Review
- Analysis of MHC class II-bound CyHV-2 peptides inJournal of virology · 2026Article
- Predominant mutated non-canonical tumor-specific antigens identified by proteogenomics demonstrate immunogenicity and tumor suppression in CRC.Cell genomics · 2026Article
- Mechanistic biomarkers for cancer vaccine development: from cancer cell biology to neoantigen-guided precision immunotherapy.Frontiers in cell and developmental biology · 2026Review
- BeitAI-pHLA: Multiallele Peptide-HLA Class I Binding Prediction Using Protein Language Model and Multi-Instance Learning.Computational and structural biotechnology journal · 2026Article
- Head and neck cancer therapeutic vaccines: a review.Frontiers in oncology · 2026Review
- A poxvirus model reveals general correlates of antigen presentation and immunogenicity for viral CD8Science advances · 2025Article
- Identification of TTLL8, POTEE, and PKMYT1 as immunogenic cancer-associated antigens and potential immunotherapy targets in ovarian cancer.Oncoimmunology · 2025Article
- RNA-based cancer vaccines: mechanisms, clinical progress, and translational challenges.Immunologic research · 2025Review
- Immunopeptidome analysis reveals SERPINB3 as an autoantigen driving eczematized psoriasis.Science advances · 2025Article
- Transgenic inducible MHC I overexpression in mouse alveolar type 2 cells.Transgenic research · 2025Article
194 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HLA class I molecules reflect the health state of cells to cytotoxic T cells by presenting a repertoire of endogenously derived peptides. However, the extent to which the proteome shapes the peptidome is still largely unknown. Here we present a high-throughput mass-spectrometry-based workflow that allows stringent and accurate identification of thousands of such peptides and direct determination of binding motifs. Applying the workflow to seven cancer cell lines and primary cells, yielded more than 22,000 unique HLA peptides across different allelic binding specificities. By computing a score representing the HLA-I sampling density, we show a strong link between protein abundance and HLA-presentation (p < 0.0001). When analyzing overpresented proteins - those with at least fivefold higher density score than expected for their abundance - we noticed that they are degraded almost 3 h faster than similar but nonpresented proteins (top 20% abundance class; median half-life 20.8h versus 23.6h, p < 0.0001). This validates protein degradation as an important factor for HLA presentation. Ribosomal, mitochondrial respiratory chain, and nucleosomal proteins are particularly well presented. Taking a set of proteins associated with cancer, we compared the predicted immunogenicity of previously validated T-cell epitopes with other peptides from these proteins in our data set. The validated epitopes indeed tend to have higher immunogenic scores than the other detected HLA peptides. Remarkably, we identified five mutated peptides from a human colon cancer cell line, which have very recently been predicted to be HLA-I binders. Altogether, we demonstrate the usefulness of combining MS-analysis with immunogenesis prediction for identifying, ranking, and selecting peptides for therapeutic use.
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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.