Monoclonal antibody de novo assembly
deposit · DDA · 1 version · 14 papers
Multi-protease runs of monoclonal antibodies deposited as the result of a complete de novo assembly study, and reused since as an antibody-sequencing test set.
| Kind | deposit |
| Acquisition | DDA |
| Organisms | Homo sapiens, Mus musculus |
Multi-protease runs of monoclonal antibodies deposited as the result of a complete de novo assembly study, and reused since as an antibody-sequencing test set.
Versions
as deposited
IgG1-Human and WIgG1-Mouse Herceptin runs.
introduced by Complete De Novo Assembly of Monoclonal Antibody Sequences
Where it lives:
- MassIVE · MSV000079801
Deposited by (1)
- Complete De Novo Assembly of Monoclonal Antibody Sequences (2016) peer-reviewed as deposited
Evaluated on by (11)
- PepPr: De Novo peptide sequencing with peptide priors (2026) preprint as deposited
- π-HelixNovo2: Making Accurate Online De Novo Peptide Sequencing Available to All (2026) peer-reviewed as deposited
- Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (2025) ML conference as deposited
- Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (2025) preprint as deposited
- Distilling Non-Autoregressive Model Knowledge for Autoregressive De Novo Peptide Sequencing (2025) preprint as deposited
- π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing (2025) peer-reviewed as deposited
- BERT model for de novo protein sequencing using tandem mass spectra (2024) abstract as deposited
- PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models (2024) peer-reviewed as deposited
- π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing (2024) preprint as deposited
- Introducing π-HelixNovo for practical large-scale de novo peptide sequencing (2024) peer-reviewed as deposited
- De novo peptide sequencing by deep learning (2017) peer-reviewed as deposited
Used by (2)
Papers that ran on it where the catalog has not recorded whether for training or for evaluation.
- A living proteomics benchmark for comprehensive evaluation of deep learning-based de novo peptide sequencing tools (2026) preprint as deposited
- Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly (2023) peer-reviewed as deposited
Methods on these papers (10)
- ALPS post-processor
- CrossNovo algorithm
- De novo evaluation for monoclonal-antibody assembly benchmark
- DeepNovo algorithm
- Living proteomics benchmark benchmark
- PepPr algorithm
- PowerNovo algorithm
- π-HelixNovo algorithm
- π-HelixNovo2 algorithm
- π-PrimeNovo algorithm
Taken from the describing links only, so a paper that merely ran a tool on this data does not make that tool a method of it.