ArticleMolecular & cellular proteomics : MCP2023
Sensitive, High-Throughput HLA-I and HLA-II Immunopeptidomics Using Parallel Accumulation-Serial Fragmentation Mass Spectrometry.
Article in Molecular & cellular proteomics : MCP, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed, 46 citations in OpenAlex.
- Post‑translational modification‑governed immune states in cancer immunity: Biomarker implications for checkpoint competence, tumor visibility and immunotherapy resistance (Review).International journal of oncology · 2026Review
- Calibrating T cell responsiveness through interactions with self.Nature reviews. Immunology · 2026Review
- A Platform for High-throughput and Ultrasensitive Immunopeptidomics.Molecular & cellular proteomics : MCP · 2026Article
- Immunopeptidomics of blood coagulation factor IX: a core peptide derived from the protease domain is promiscuously presented on HLA-DR.Research and practice in thrombosis and haemostasis · 2026Article
- Benchmarking Software for DDA-PASEF Immunopeptidomics.Molecular & cellular proteomics : MCP · 2026Article
- Mass spectrometry-based de novo sequencing reveals non-canonical neoantigens with antitumor efficacy in hepatocellular carcinoma.JHEP reports : innovation in hepatology · 2026Article
- Sensitive detection of cancer antigens enabled by user-defined peptide libraries.Nature biotechnology · 2026Article
- A red blood cell-based antigen delivery system to facilitate T cell epitope presentation to promote peripheral tolerance to ADAMTS13 in immune-mediated thrombotic thrombocytopenic purpura.Research and practice in thrombosis and haemostasis · 2026Article
- MHC II MAPPs for High-Confident Immunogenicity Risk Assessment of Biotherapeutics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- From clinical remission to biological stability in psoriasis: an antigen-blood-tissue framework for relapse stratification.Frontiers in immunology · 2026Review
- High-Coverage Immunopeptidomics Using timsTOF Mass Spectrometers with Thunder-DDA-PASEF Boosted by MSMethods in molecular biology (Clifton, N.J.) · 2026Article
- Koina: Democratizing machine learning for proteomics research.Nature communications · 2025Article
- Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2Deep.Analytical chemistry · 2025Article
- Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome.Chemical reviews · 2025Review
- Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring.Journal of proteome research · 2025Article
- TIMSJournal of proteome research · 2025Article
- A Primer on Proteomic Characterization of Intercellular Communication in a Virus Microenvironment.Molecular & cellular proteomics : MCP · 2025Review
- Unlocking the secrets of the immunopeptidome: MHC molecules, ncRNA peptides, and vesicles in immune response.Frontiers in immunology · 2025Review
- An mRNA-based workflow validating neo-epitope presentation through HLA-I/peptide affinity purification.Frontiers in immunology · 2025Article
- The 2024 Report on the Human Proteome from the HUPO Human Proteome Project.Journal of proteome research · 2024Review
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
Comprehensive and in-depth identification of the human leukocyte antigen class I (HLA-I) and class II (HLA-II) tumor immunopeptidome can inform the development of cancer immunotherapies. Mass spectrometry (MS) is a powerful technology for direct identification of HLA peptides from patient-derived tumor samples or cell lines. However, achieving sufficient coverage to detect rare and clinically relevant antigens requires highly sensitive MS-based acquisition methods and large amounts of sample. While immunopeptidome depth can be increased by off-line fractionation prior to MS, its use is impractical when analyzing limited amounts of primary tissue biopsies. To address this challenge, we developed and applied a high-throughput, sensitive, and single-shot MS-based immunopeptidomics workflow that leverages trapped ion mobility time-of-flight MS on the Bruker timsTOF single-cell proteomics system (SCP). We demonstrate greater than twofold improved coverage of HLA immunopeptidomes relative to prior methods with up to 15,000 distinct HLA-I and HLA-II peptides from 4e7 cells. Our optimized single-shot MS acquisition method on the timsTOF SCP maintains high coverage, eliminates the need for off-line fractionation, and reduces input requirements to as few as 1e6 A375 cells for >800 distinct HLA-I peptides. This depth is sufficient to identify HLA-I peptides derived from cancer-testis antigen and noncanonical proteins. We also apply our optimized single-shot SCP acquisition methods to tumor-derived samples, enabling sensitive, high-throughput, and reproducible immunopeptidome profiling with detection of clinically relevant peptides from less than 4e7 cells or 15 mg wet weight 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.