ArticleNature communications2024
Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Article
- From Neoantigens to Nanocarriers: Modern Methods and Modalities in Using Peptides for Cancer Vaccination.Biochemistry · 2026Review
- Integration of alternative fragmentation techniques into standard LC-MS workflows using a single deep learning model enhances proteome coverage.Nature methods · 2026Article
- Benchmarking Software for DDA-PASEF Immunopeptidomics.Molecular & cellular proteomics : MCP · 2026Article
- Sensitive detection of cancer antigens enabled by user-defined peptide libraries.Nature biotechnology · 2026Article
- Koina: Democratizing machine learning for proteomics research.Nature communications · 2025Article
- MHCquant2 refines immunopeptidomics tumor antigen discovery.Genome biology · 2025Article
- High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.bioRxiv : the preprint server for biology · 2025Article
- Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures.Nature communications · 2025Article
- Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.Journal of proteome research · 2025Article
- Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring.Journal of proteome research · 2025Article
- Cell Storage Conditions Impact Single-Cell Proteomic Landscapes.Journal of proteome research · 2025Article
- TIMSJournal of proteome research · 2025Article
- Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes.Molecular & cellular proteomics : MCP · 2025Article
- Immunopeptidomics for autoimmunity: unlocking the chamber of immune secrets.NPJ systems biology and applications · 2025Review
- Assessment of Data-Independent Acquisition Mass Spectrometry (DIA-MS) for the Identification of Single Amino Acid Variants.Proteomes · 2024Article
- Investigating Antiprotozoal Chemotherapies with Novel Proteomic Tools-Chances and Limitations: A Critical Review.International journal of molecular sciences · 2024Review
- Emerging potential of immunopeptidomics by mass spectrometry in cancer immunotherapy.Cancer science · 2024Review
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Authors and funding
7 authors.
Funding
Abstract
Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence within human leukocyte antigen (HLA) class-specific length restrictions needs to be considered during sequence database searching. This leads to an inflation of the search space and results in lower spectrum annotation rates. Peptide-spectrum match (PSM) rescoring is a powerful enhancement of standard searching that boosts the spectrum annotation performance. We analyze 302,105 unique synthesized non-tryptic peptides from the ProteomeTools project on a timsTOF-Pro to generate a ground-truth dataset containing 93,227 MS/MS spectra of 74,847 unique peptides, that is used to fine-tune the deep learning-based fragment ion intensity prediction model Prosit. We demonstrate up to 3-fold improvement in the identification of immunopeptides, as well as increased detection of immunopeptides from low input samples.
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