A transformer model for de novo sequencing of data independent acquisition mass spectrometry data
peer-reviewed · Nature Methods · 2025
peer-reviewed · Nature Methods · 2025. Justin Sanders et al.
| Date | 2025-07-01 |
| Type | peer-reviewed |
| Venue | Nature Methods |
| Publisher | Springer Nature |
| Contribution | algorithm |
| DOI | 10.1038/s41592-025-02718-y |
| Citations (OpenAlex) | 13 |
| Venue 2-year citedness | 20.00 |
Preprint version: A transformer model for de novo sequencing of data independent acquisition mass spectrometry data (2024-06-03, bioRxiv)
Methods and tools
- Cascadia: Transformer for DIA
Cites (18)
- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments (2025) crossref
- Deep Learning Methods for De Novo Peptide Sequencing (2024) crossref
- Accounting for Digestion Enzyme Bias in Casanovo (2024) crossref
- ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing (2024) crossref
- AdaNovo: Adaptive De Novo Peptide Sequencing with Conditional Mutual Information (2024) crossref
- Bidirectional de novo peptide sequencing using a transformer model (2024) crossref
- Transformer-Based De Novo Peptide Sequencing for Data-Independent Acquisition Mass Spectrometry (2024) crossref
- Introducing π-HelixNovo for practical large-scale de novo peptide sequencing (2024) crossref
- Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing (2024) crossref
- Transformer-Based De Novo Peptide Sequencing for Data-Independent Acquisition Mass Spectrometry (2023) crossref
- Accurate de novo peptide sequencing using fully convolutional neural networks (2023) crossref
- De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments (2023) crossref
- BiATNovo: A Self-Attention based Bidirectional Peptide Sequencing Method (2023) crossref
- DPST: De Novo Peptide Sequencing with Amino-Acid-Aware Transformers (2022) crossref
- De novo mass spectrometry peptide sequencing with a transformer model (2022) crossref
- pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework (2019) crossref
- Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry (2018) crossref
- De novo peptide sequencing by deep learning (2017) crossref
Cited by (3)
- False discovery rate control for trustworthy AI-based de novo peptide sequencing (2026) crossref
- Identification of Species-Specific Peptide Markers in Highly Processed Meat Products Using De Novo Sequencing (2026) crossref
- DiffNovo: A Transformer-Diffusion Model for De Novo Peptide Sequencing (2025) crossref