Introducing PandaNovo for practical large-scale de novo peptide sequencing
preprint · bioRxiv · 2023
preprint · bioRxiv · 2023. Tingpeng Yang et al. De novo peptide sequencing is a promising approach for novel peptide discovery. We use a novel concept of…
| Date | 2023-07-15 |
| Type | preprint |
| Venue | bioRxiv |
| Publisher | Cold Spring Harbor Laboratory |
| Contribution | algorithm |
| DOI | 10.1101/2023.07.15.549133 |
| Citations (OpenAlex) | 5 |
Peer-reviewed version: Introducing π-HelixNovo for practical large-scale de novo peptide sequencing (2024-02-10, Briefings in Bioinformatics)
Abstract
De novo peptide sequencing is a promising approach for novel peptide discovery. We use a novel concept of complementary spectra to enhance ion information and propose a de novo sequencing model{pi} -HelixNovo based on Transformer architecture.{pi} -HelixNovo outperforms other state-of-the-art models and enhances the taxonomic resolution of gut metaproteome, taking a significant step forward in de novo sequencing.
Methods and tools
- π-HelixNovo: Complementary spectra
Cites (7)
- Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly (2023) semanticscholar
- De novo mass spectrometry peptide sequencing with a transformer model (2022) both
- Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices (2021) both
- De novo peptide sequencing by deep learning (2017) both
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) both
- De novo sequencing of peptides by MS/MS (2010) semanticscholar
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
Cited by (15)
- π-MSNet: A billion-scale, AI-ready living proteomics data portal (2026) semanticscholar
- Regressor-guided Diffusion Model for De Novo Peptide Sequencing with Explicit Mass Control (2026) semanticscholar
- Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (2025) semanticscholar
- Limitations of de novo sequencing in resolving sequence ambiguity (2025) semanticscholar
- MassNet: billion-scale AI-friendly mass spectral corpus enables robust de novo peptide sequencing (2025) semanticscholar
- Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing (2025) semanticscholar
- Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra (2025) semanticscholar
- Latent Imputation before Prediction: A New Computational Paradigm for De Novo Peptide Sequencing (2025) semanticscholar
- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments (2025) semanticscholar
- A transformer-based semi-autoregressive framework for high-speed and accurate de novo peptide sequencing (2025) semanticscholar
- π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing (2025) semanticscholar
- A multi-species benchmark for training and validating mass spectrometry proteomics machine learning models (2024) semanticscholar
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2024) semanticscholar
- NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics (2024) semanticscholar
- π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing (2024) crossref