ReviewJournal for immunotherapy of cancer2023
Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery.
Review in Journal for immunotherapy of cancer, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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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.
The trial behind it
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
25 citing papers in PubMed, 33 citations in OpenAlex.
- Immunoediting and precision biomarkers in prostate cancer: The emerging role of liquid biopsy, immune contexture and HLA genotype (Review).International journal of oncology · 2026Review
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- Technical review of artificial intelligence in TCR-T therapy.Journal of the National Cancer Center · 2026Review
- A Platform for High-throughput and Ultrasensitive Immunopeptidomics.Molecular & cellular proteomics : MCP · 2026Article
- Benchmarking Software for DDA-PASEF Immunopeptidomics.Molecular & cellular proteomics : MCP · 2026Article
- Review
- Identification of molecularly targeted therapy-induced immunopeptidome in diffuse midline glioma (DMG).Neoplasia (New York, N.Y.) · 2026Article
- Assessing the Performance of Mass Spectrometry Search Strategies in Identifying Translational Errors Using PDX Proteomics Data.Molecular & cellular proteomics : MCP · 2026Article
- Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics.Nature communications · 2026Article
- Review
- A Novel Machine Learning Post-processing Filter for Mass Spectrometry-Based Proteogenomics Leveraging Retention Time Deviation and Peptide Physicochemical Properties.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A proposal of good manufacturing practices (GMP) laboratory for CAR T-cell therapy in Latin America and the Caribbean: challenges and opportunities.Frontiers in public health · 2026Review
- PepQueryMHC: rapid and comprehensive tumor antigen prioritization from immunopeptidomics data.Genome biology · 2025Article
- CTG-Initiated Cryptic Peptide Translation Up- and Downstream of a Canonical ATG Start Codon Is Enhanced by TLR Stimulation and Induces Tumor Regression in Mice.Cancer immunology research · 2025Article
- Isoforms of Phosphorylated Tau as Potential Biomarkers for Alzheimer's Disease: The Contribution of Mass Spectrometry-Based Proteomics.NeuroSci · 2025Review
- Immunogenic cryptic peptides dominate the antigenic landscape of ovarian cancer.Science advances · 2025Article
- Unlocking the secrets of the immunopeptidome: MHC molecules, ncRNA peptides, and vesicles in immune response.Frontiers in immunology · 2025Review
- Immunolyser 2.0: An advanced computational pipeline for comprehensive analysis of immunopeptidomic data.Computational and structural biotechnology journal · 2025Article
- Unlocking cancer vaccine potential: What are the key factors?Human vaccines & immunotherapeutics · 2024Review
- Tumor-associated antigen prediction using a single-sample gene expression state inference algorithm.Cell reports methods · 2024Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
Identification of tumor antigens presented by the human leucocyte antigen (HLA) molecules is essential for the design of effective and safe cancer immunotherapies that rely on T cell recognition and killing of tumor cells. Mass spectrometry (MS)-based immunopeptidomics enables high-throughput, direct identification of HLA-bound peptides from a variety of cell lines, tumor tissues, and healthy tissues. It involves immunoaffinity purification of HLA complexes followed by MS profiling of the extracted peptides using data-dependent acquisition, data-independent acquisition, or targeted approaches. By incorporating DNA, RNA, and ribosome sequencing data into immunopeptidomics data analysis, the proteogenomic approach provides a powerful means for identifying tumor antigens encoded within the canonical open reading frames of annotated coding genes and non-canonical tumor antigens derived from presumably non-coding regions of our genome. We discuss emerging computational challenges in immunopeptidomics data analysis and tumor antigen identification, highlighting key considerations in the proteogenomics-based approach, including accurate DNA, RNA and ribosomal sequencing data analysis, careful incorporation of predicted novel protein sequences into reference protein database, special quality control in MS data analysis due to the expanded and heterogeneous search space, cancer-specificity determination, and immunogenicity prediction. The advancements in technology and computation is continually enabling us to identify tumor antigens with higher sensitivity and accuracy, paving the way toward the development of more effective cancer immunotherapies.
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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 Socratic graph.