bioRxiv
35 papers in the catalog
35 de novo peptide sequencing papers published in bioRxiv, catalogued with authors, methods and citation counts.
Papers
- Learning from tandem mass spectra at scale with a self-supervised foundation model for proteomics (2026, preprint)
- Reference-free protein sequencing by consensus assembly of redundant de novo peptide reads (2026, preprint)
- CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo (2026, preprint)
- False discovery rate control for trustworthy AI-based de novo peptide sequencing (2026, preprint)
- Learning Fragmentation Physics or Exploiting Sequence Priors? Benchmarking Bias in Deep Learning Models for De Novo Peptide Sequencing (2026, preprint)
- DLDN-Bench: A Benchmark Framework for Deep Learning de Novo Peptide Sequencing in Proteomics (2026, preprint)
- π-MSNet: A billion-scale, AI-ready living proteomics data portal (2026, preprint)
- AbNovoBench: a resource and benchmarking platform for monoclonal antibody de novo sequencing (2026, preprint)
- Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides (2025, preprint)
- Limitations of de novo sequencing in resolving sequence ambiguity (2025, preprint)
- Improvements to CasaNovo, a deep learning de novo peptide sequencer (2025, preprint)
- Generalizable direct protein sequencing with InstaNexus (2025, preprint)
- MassNet: billion-scale AI-friendly mass spectral corpus enables robust de novo peptide sequencing (2025, preprint)
- MARLOWE: Taxonomic Characterization of Unknown Samples for Forensics Using De Novo Peptide Identification (2025, preprint)
- PSMtags improve peptide sequencing and throughput in sensitive proteomics (2025, preprint)
- InstaNovo-P: A de novo peptide sequencing model for phosphoproteomics (2025, preprint)
- Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra (2025, preprint)
- DiNovo: high-coverage, high-confidence de novo peptide sequencing using mirror proteases and deep learning (2025, preprint)
- PepGo: a deep learning and tree search-based model for de novo peptide sequencing (2025, preprint)
- Orthrus: an AI-powered, cloud-ready, and open-source hybrid approach for metaproteomics (2024, preprint)
- BiATNovo: An Attention-based Bidirectional De Novo Sequencing Framework for Data-Independent-Acquisition Mass Spectrometry (2024, preprint)
- Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo (2024, preprint)
- A transformer model for de novo sequencing of data independent acquisition mass spectrometry data (2024, preprint)
- π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing (2024, preprint)
- NovoBoard: a comprehensive framework for evaluating the false discovery rate and accuracy of de novo peptide sequencing (2024, preprint)
- A learned score function improves the power of mass spectrometry database search (2024, preprint)
- Multi-Modal Mass Spectrometry Identifies a Conserved Protective Epitope in S. pyogenes Streptolysin O (2023, preprint)
- De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments (2023, preprint)
- Introducing PandaNovo for practical large-scale de novo peptide sequencing (2023, preprint)
- BiATNovo: A Self-Attention based Bidirectional Peptide Sequencing Method (2023, preprint)
- Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing (2023, preprint)
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2023, preprint)
- De novo mass spectrometry peptide sequencing with a transformer model (2022, preprint)
- Spectrum graph-based de-novo sequencing algorithm MaxNovo achieves high peptide identification rates in collisional dissociation MS/MS spectra (2021, preprint)
- Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines (2019, preprint)