Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model
peer-reviewed · Nature Machine Intelligence · 2023
peer-reviewed · Nature Machine Intelligence · 2023. Zeping Mao et al.
| Date | 2023-10-19 |
| Type | peer-reviewed |
| Venue | Nature Machine Intelligence |
| Publisher | Springer Science and Business Media LLC |
| Contribution | algorithm |
| DOI | 10.1038/s42256-023-00738-x |
| Citations (OpenAlex) | 42 |
| Venue 2-year citedness | 23.00 |
Methods and tools
- GraphNovo: Missing fragments
Trained on
Evaluated on
- GraphNovo dataset and checkpoint (as deposited) · 10.5281/zenodo.8000316
- NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin (as deposited) · PXD013233
- Predictive signatures of 19 antibiotics-induced Escherichia coli proteomes (as deposited) · PXD016001
- The beta subunit of nascent polypeptide associated complex plays a role in flowers and siliques development of Arabidops (as deposited) · PXD016315
Cites (25)
- The impact of noise and missing fragmentation cleavages on de novo peptide identification algorithms (2022) both
- 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
- Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines (2020) both
- De novo sequencing of proteins by mass spectrometry (2020) both
- pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework (2019) both
- De novo peptide sequencing by deep learning (2017) both
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) both
- Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications (2017) both
- Complete De Novo Assembly of Monoclonal Antibody Sequences (2016) both
- Novor: Real-Time Peptide de Novo Sequencing Software (2015) both
- pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) both
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) both
- Peptide Fragment Ion Analyser (PFIA): a simple and versatile tool for the interpretation of tandem mass spectrometric data and de novo sequencing of peptides (2007) both
- MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007) both
- NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing (2005) both
- AUDENS: A Tool for Automated Peptide de Novo Sequencing (2005) both
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) both
- A Hidden Markov Model for de Novo Peptide Sequencing (2004) semanticscholar
- Algorithms for de novo peptide sequencing using tandem mass spectrometry (2004) both
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001) both
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) both
- De novo peptide sequencing via tandem mass spectrometry (1999) both
- Automated interpretation of high-energy collision-induced dissociation spectra of singly protonated peptides by ‘seqms’, a software aid forde novo sequencing by tandem mass spectrometry (1998) both
Cited by (32)
- MassNet: billion-scale AI-ready mass spectral corpus empowering scalable deep learning in proteomics (2026) crossref
- False discovery rate control for trustworthy AI-based de novo peptide sequencing (2026) crossref
- LIPNovo+: Self-Reflective Latent Imputation for Robust De Novo Peptide Sequencing (2026) crossref
- A large-scale unified deep learning model for peptide mass spectrum interpretation trained on multimodal data (2026) crossref
- Zero-shot de novo peptide sequencing with open posttranslational modification discovery (2026) crossref
- Mass Spectrometry-based Antibody Sequencing Technologies (2026) both
- Regressor-guided Diffusion Model for De Novo Peptide Sequencing with Explicit Mass Control (2026) semanticscholar
- DiNovo enables high-coverage and high-confidence de novo peptide sequencing via mirror proteases and deep learning (2026) both
- AbNovoBench: a resource and benchmarking platform for monoclonal antibody de novo sequencing (2026) crossref
- Protein Language Model-Aligned Spectra Embeddings for De Novo Peptide Sequencing (2025) both
- Framework for de novo sequencing of peptide mixtures via network analysis and two-dimensional tandem mass spectrometry (2025) crossref
- TF-GCNNovo: A Peptide Sequence Prediction Model Integrating Transformer and Graph Convolutional Network (2025) crossref
- Diffusion Decoding for Peptide De Novo Sequencing (2025) semanticscholar
- MassNet: billion-scale AI-friendly mass spectral corpus enables robust de novo peptide sequencing (2025) crossref
- Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing (2025) semanticscholar
- Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing (2025) semanticscholar
- Latent Imputation before Prediction: A New Computational Paradigm for De Novo Peptide Sequencing (2025) semanticscholar
- De Novo Peptide Sequencing for Data-independent Acquisition (DIA) Using Deep Learning (2025) crossref
- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments (2025) both
- DiNovo: high-coverage, high-confidence de novo peptide sequencing using mirror proteases and deep learning (2025) crossref
- Integration of proteomics profiling data to facilitate discovery of cancer neoantigens: a survey (2025) both
- Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing (2025) crossref
- π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing (2025) both
- Deep Learning Methods for De Novo Peptide Sequencing (2024) crossref
- Disentangling the Complex Multiplexed DIA Spectra in De Novo Peptide Sequencing (2024) semanticscholar
- NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing (2024) crossref
- Transforming de novo peptide sequencing by explainable AI (2024) crossref
- 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
- NovoBoard: a comprehensive framework for evaluating the false discovery rate and accuracy of de novo peptide sequencing (2024) crossref
- Bidirectional de novo peptide sequencing using a transformer model (2024) both