ArticleMolecular & cellular proteomics : MCP2021
Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples.
Article in Molecular & cellular proteomics : MCP, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- LC-MS/MS-based peptide identification, molecular simulations, and biological validation for targeted discovery of antioxidant peptides from large yellow croaker.Food chemistry: X · 2026Article
- Discovery of CD4+ T cell-recognized B. pertussis antigens that reduce airway colonization.JCI insight · 2026Article
- Central T cell tolerance from sparse peptide sampling.Science advances · 2026Article
- Beyond Sequence: Posttranslational Remodeling of Antigens in Autoimmunity.Immunological reviews · 2026Review
- Sensitive detection of cancer antigens enabled by user-defined peptide libraries.Nature biotechnology · 2026Article
- Ribosome Profiling for Novel Antigen Discovery.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Employing complementary fractionation-based N-terminomics approaches enhances the identification of legumain cleavage events in naïve and inflamed colon tissue.Protein science : a publication of the Protein Society · 2025Article
- Deciphering the MHC immunopeptidome of human cancers with Ligand.MHC atlas.Briefings in bioinformatics · 2025Article
- Systematic identification of minor histocompatibility antigens predicts outcomes of allogeneic hematopoietic cell transplantation.Nature biotechnology · 2025Article
- Pancreatic cancer-restricted cryptic antigens are targets for T cell recognition.Science (New York, N.Y.) · 2025Article
- Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome.Chemical reviews · 2025Review
- HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy.Cell · 2025Article
- Leveraging mRNA technology for antigen based immuno-oncology therapies.Journal for immunotherapy of cancer · 2025Review
- Immunopeptidomics for autoimmunity: unlocking the chamber of immune secrets.NPJ systems biology and applications · 2025Review
- Improvement of Tumor Neoantigen Detection by High-Field Asymmetric Waveform Ion Mobility Mass Spectrometry.Cancer immunology research · 2024Article
- Emerging potential of immunopeptidomics by mass spectrometry in cancer immunotherapy.Cancer science · 2024Review
- Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MSNature communications · 2024Article
- Immunopeptidomics in the Era of Single-Cell Proteomics.Biology · 2023Article
- TOFNature communications · 2023Article
- Contribution of an Asian-prevalent HLA haplotype to the risk of HBV-related hepatocellular carcinoma.Scientific reports · 2023Article
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Authors and funding
17 authors.
Funding
Abstract
MS is the most effective method to directly identify peptides presented on human leukocyte antigen (HLA) molecules. However, current standard approaches often use 500 million or more cells as input to achieve high coverage of the immunopeptidome, and therefore, these methods are not compatible with the often limited amounts of tissue available from clinical tumor samples. Here, we evaluated microscaled basic reversed-phase fractionation to separate HLA peptide samples offline followed by ion mobility coupled to LC-MS/MS for analysis. The combination of these two separation methods enabled identification of 20% to 50% more peptides compared with samples analyzed without either prior fractionation or use of ion mobility alone. We demonstrate coverage of HLA immunopeptidomes with up to 8107 distinct peptides starting with as few as 100 million cells. The increased sensitivity obtained using our methods can provide data useful to improve HLA-binding prediction algorithms as well as to enable detection of clinically relevant epitopes such as neoantigens.
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