ArticleJournal of proteome research2019
Pre-fractionation Extends but also Creates a Bias in the Detectable HLA Class Ι Ligandome.
Article in Journal of proteome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 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
- The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I-Associated Peptides.Cancer immunology research · 2023Article
- Differential ion mobility mass spectrometry in immunopeptidomics identifies neoantigens carrying colorectal cancer driver mutations.Communications biology · 2022Article
- Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues.iScience · 2022Article
- Allotype-Specific Glycosylation and Cellular Localization of Human Leukocyte Antigen Class I Proteins.Journal of proteome research · 2021Article
- Article
- HLA-B and cysteinylated ligands distinguish the antigen presentation landscape of extracellular vesicles.Communications biology · 2021Article
- Article
- HLA Class II Presentation Is Specifically Altered at Elevated Temperatures in the B-Lymphoblastic Cell Line JY.Molecular & cellular proteomics : MCP · 2021Article
- Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples.Molecular & cellular proteomics : MCP · 2021Article
- Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction.Molecular & cellular proteomics : MCP · 2021Article
- The HLA Ligandome Comprises a Limited Repertoire of O-GlcNAcylated Antigens Preferentially Associated With HLA-B*07:02.Frontiers in immunology · 2021Article
- Mild Acid Elution and MHC Immunoaffinity Chromatography Reveal Similar Albeit Not Identical Profiles of the HLA Class I Immunopeptidome.Journal of proteome research · 2021Article
- Critical Review of Existing MHC I Immunopeptidome Isolation Methods.Molecules (Basel, Switzerland) · 2020Review
- Single-cell derived tumor organoids display diversity in HLA class I peptide presentation.Nature communications · 2020Article
- Review
- The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases.Molecular & cellular proteomics : MCP · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HLA class Ι molecules can communicate a range of cellular alterations (mutations, changes in protein copy number, aberrant post-translational modifications, or pathogen proteins) to CD8+ T lymphocytes in the form of HLA peptide ligands. At any given moment, tens of thousands of different self and foreign HLA class Ι peptides may be presented on the cell surface by HLA class Ι complexes. Due to the enormous biochemical diversity and low abundance of each of these peptides, HLA ligandome analysis presents unique challenges. Even with advances in enrichment strategies and MS instrumentation and fragmentation, sufficient ligandome depth for identification of viral pathogens and immuno therapeutically important tumor neo-antigens is still not routinely achievable. In this study, we evaluated two pre-fractionation techniques, high-pH reversed-phase and strong cation exchange, for the complementary analyses of HLA class Ι peptide ligands. We observe that pre-fractionation substantially extends the detectable HLA class Ι ligandome but also creates an identification bias. We thus advocate a rational choice between high-pH reversed-phase or strong cation exchange pre-fractionation for deeper HLA class Ι ligandome analysis, depending on the HLA locus, allele, or peptide ligand modification in question.
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