Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices
peer-reviewed · Nature Machine Intelligence · 2021
peer-reviewed · Nature Machine Intelligence · 2021. Rui Qiao et al.
| Date | 2021-03-18 |
| Type | peer-reviewed |
| Venue | Nature Machine Intelligence |
| Publisher | Springer Science and Business Media LLC |
| Contribution | algorithm |
| DOI | 10.1038/s42256-021-00304-3 |
| Citations (OpenAlex) | 90 |
| Venue 2-year citedness | 23.00 |
Methods and tools
- PointNovo: Point-set network
Trained on
- ABRF PRG 2018 HeLa DDA (PRG 2018 runs) · 10.5281/zenodo.10405582
- BALF proteomics - In-depth proteomic analysis of human bronchoalveolar lavage fluid towards the biomarker discovery for (as deposited) · PXD012645
- Diabetes causes marked inhibition of mitochondrial metabolism in pancreatic β-cells (as deposited) · PXD012979
- High-resolution spatially-resolved proteome mapping using automated, sacrificial liquid-mediated sample transfer from la (as deposited) · PXD008844
- Low-density lipoprotein receptor-related protein 1 (LRP1)-derived peptides protect against aggregation of LDL and choles (as deposited) · PXD011246
- Nine-species benchmark (original (DeepNovo, 2017)) · MSV000081382, PXD003868 (provenance), PXD004325 (provenance), PXD004424 (provenance), PXD004467 (provenance), PXD004536 (provenance), PXD004565 (provenance), PXD004947 (provenance), PXD004948 (provenance), PXD005025 (provenance)
- Proteome of the rodent malaria parasite Plasmodium berghei liver stage merosomes (as deposited) · PXD010559
- Proteomic analysis of six different tissues from the Atlantic bottlenose dolphin (Tursiops truncatus) (as deposited) · PXD008808
Evaluated on
- ABRF PRG 2018 HeLa DDA (PRG 2018 runs) · 10.5281/zenodo.10405582
- HeLa proteome of 12,250 protein-coding genes (as deposited) · PXD004452
- High-resolution spatially-resolved proteome mapping using automated, sacrificial liquid-mediated sample transfer from la (as deposited) · PXD008844
- Nine-species benchmark (original (DeepNovo, 2017)) · MSV000081382, PXD003868 (provenance), PXD004325 (provenance), PXD004424 (provenance), PXD004467 (provenance), PXD004536 (provenance), PXD004565 (provenance), PXD004947 (provenance), PXD004948 (provenance), PXD005025 (provenance)
- Proteome of the rodent malaria parasite Plasmodium berghei liver stage merosomes (as deposited) · PXD010559
Cites (11)
- Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines (2020) crossref
- Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework (2019) 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
- Novor: Real-Time Peptide de Novo Sequencing Software (2015) crossref
- An effective algorithm for peptide de novo sequencing from MS/MS spectra (2005) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
- 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) crossref
- De novo peptide sequencing via tandem mass spectrometry (1999) crossref
Cited by (78)
- MassNet: billion-scale AI-ready mass spectral corpus empowering scalable deep learning in proteomics (2026) crossref
- Learning from tandem mass spectra at scale with a self-supervised foundation model for proteomics (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
- MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing (2026) both
- 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
- Optimizing Mirror-Image Peptide Sequence Design for Data Storage via Peptide Bond Cleavage Prediction (2025) both
- Sequencing of Polyclonal Antibodies by Integrating Intact Mass, Middle–Down, and De Novo Bottom–Up Mass Spectrometry (2025) both
- DyCoNovo: a De Novo Peptide Prediction Model Based on Dynamic Convolution and Phased Contrastive Learning (2025) crossref
- RT-GCTnovo: A Peptide De Novo Sequencing Model Incorporating Gated Multi-scale Features and Dynamic Mass Masks (2025) crossref
- Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (2025) semanticscholar
- Protein Language Model-Aligned Spectra Embeddings for De Novo Peptide Sequencing (2025) both
- Homo-Tag-Assembler Assay for Full-Length Antibody Sequencing (2025) crossref
- pUniFind: a unified large pre-trained deep learning model pushing the limit of mass spectra interpretation (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
- Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra (2025) both
- Latent Imputation before Prediction: A New Computational Paradigm for De Novo Peptide Sequencing (2025) semanticscholar
- PSMtags improve peptide sequencing and throughput in sensitive proteomics (2025) crossref
- Efficient Screening of Synergistic Antioxidant and AChE Inhibitory Peptides From Sea Cucumber (Stichopus japonicus) Using a Novel Approach Combining De Novo Sequencing and Parallel Peptide Synthesis (2025) crossref
- De Novo Peptide Sequencing for Data-independent Acquisition (DIA) Using Deep Learning (2025) crossref
- MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing (2025) crossref
- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments (2025) both
- Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra (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
- PepGo: a deep learning and tree search-based model for de novo peptide sequencing (2025) semanticscholar
- A transformer-based semi-autoregressive framework for high-speed and accurate de novo peptide sequencing (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
- A multi-species benchmark for training and validating mass spectrometry proteomics machine learning models (2024) both
- NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing (2024) crossref
- BERT model for de novo protein sequencing using tandem mass spectra (2024) crossref
- Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo (2024) both
- Accounting for Digestion Enzyme Bias in Casanovo (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) both
- PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models (2024) crossref
- 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
- AdaNovo: Adaptive De Novo Peptide Sequencing with Conditional Mutual Information (2024) semanticscholar
- Bidirectional de novo peptide sequencing using a transformer model (2024) both
- Transformer-Based De Novo Peptide Sequencing for Data-Independent Acquisition Mass Spectrometry (2024) semanticscholar
- 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
- Multi-Modal Mass Spectrometry Identifies a Conserved Protective Epitope in S. pyogenes Streptolysin O (2023) crossref
- Accurate de novo peptide sequencing using fully convolutional neural networks (2023) both
- Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model (2023) both
- De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments (2023) both
- Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review (2023) crossref
- Novel Proteoform Discovery by Precise Semi-De Novo Sequencing of Novel Junction Peptides (2023) crossref
- Introducing PandaNovo for practical large-scale de novo peptide sequencing (2023) both
- Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics (2023) both
- The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides (2023) both
- BiATNovo: A Self-Attention based Bidirectional Peptide Sequencing Method (2023) both
- PGPointNovo: an efficient neural network-based tool for parallel de novo peptide sequencing (2023) both
- Denovo-GCN: De Novo Peptide Sequencing by Graph Convolutional Neural Networks (2023) both
- Application of a Novel Hybrid CNN-GNN for Peptide Ion Encoding (2023) both
- Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly (2023) both
- Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing (2023) crossref
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2023) crossref
- Critical evaluation of the use of artificial data for machine learning based de novo peptide identification (2023) both
- The Current State-of-the-Art Identification of Unknown Proteins Using Mass Spectrometry Exemplified on De Novo Sequencing of a Venom Protease from Bothrops moojeni (2022) both
- Current state, existing challenges, and promising progress for de novo sequencing and assembly of monoclonal antibodies (2022) both
- De novo mass spectrometry peptide sequencing with a transformer model (2022) semanticscholar
- Discovering and Validating Neoantigens by Mass Spectrometry-based Immunopeptidomics and Deep Learning (2022) crossref
- A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics (2022) both
- DPST: De Novo Peptide Sequencing with Amino-Acid-Aware Transformers (2022) semanticscholar
- De novo mass spectrometry peptide sequencing with a transformer model (2022) both
- Spectrum graph-based de-novo sequencing algorithm MaxNovo achieves high peptide identification rates in collisional dissociation MS/MS spectra (2021) both