SMSNet
algorithm · CNN + RNN
SMSNet: algorithm · CNN + RNN. Sequence-Mask-Search seq2seq
Sequence-Mask-Search seq2seq
| Kind | algorithm |
| Deep learning | yes |
| Acquisition | DDA |
| Family | CNN + RNN |
Code
Live stars, open issues and last-push figures are on the Code activity chart.
Data
What the papers describing this method trained it on and reported its results on, as each paper states it. A version is named only where the paper names one.
Trained on
- Nine-species benchmark (version not stated) · 2019 peer-reviewed
- Nine-species benchmark (original (DeepNovo, 2017)) · 2019 preprint
- ProteomeTools (version not stated) · 2019 peer-reviewed
Evaluated on
- High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform (as deposited) · 2019 peer-reviewed, 2019 preprint
- Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction (as deposited) · 2019 peer-reviewed, 2019 preprint
- Nine-species benchmark (version not stated) · 2019 peer-reviewed
- Nine-species benchmark (original (DeepNovo, 2017)) · 2019 preprint
- ProteomeTools (version not stated) · 2019 peer-reviewed, 2019 preprint
Deposited
Benchmarks
- denovo_benchmarks: median peptide-level average precision 0.602 over 86 datasets, median rank 11 of 15 (version bm-1.0.0).
Both are mass-based matches on the tool’s most recent run. What these numbers mean.
Papers describing it (2)
- Uncovering thousands of new HLA antigens and phosphopeptides with deep learning-based sequence-mask-search de novo peptide sequencing framework (2019, bioRxiv, preprint)
- Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework (2019, Molecular & Cellular Proteomics, peer-reviewed)
Papers using it (4)
Applications and evaluations that ran this method. They are not counted among its authors below.
- Identification of Daboia siamensis venome using integrated multi-omics data (2022, Scientific Reports, peer-reviewed)
- Combined proteomic strategies for in-depth venomic analysis of the beaked sea snake (Hydrophis schistosus) from Songkhla Lake, Thailand (2022, Journal of Proteomics, peer-reviewed)
- Unsupervised Mining of HLA-I Peptidomes Reveals New Binding Motifs and Potential False Positives in the Community Database (2022, Frontiers in Immunology, peer-reviewed)
- Unsupervised mining of HLA-I peptidomes reveals new binding motifs and substantial false positives in community database (2021, bioRxiv, preprint)