Winnow
post-processor
Winnow: post-processor. NN rescoring + decoy-free FDR
NN rescoring + decoy-free FDR
| Kind | post-processor |
| Deep learning | yes |
| Acquisition | both |
Code
Live stars, open issues and last-push figures are on the Code activity chart.
Checkpoints
| Version | Trained on | Host | Licence | Size | Checked |
|---|---|---|---|---|---|
| hold-one-out calibrators | each training set minus the held-out one | figshare archival | CC-BY-4.0 | 167 KB | live 2026-10-03 |
| HeLa QC model | — | Hugging Face | CC-BY-NC-SA-4.0 | — | live 2026-10-02 |
A host marked archival has a DOI and keeps what it is given. The others can move or disappear, which is why they are checked rather than merely listed. verified means the bytes were fetched and hashed on the date shown; live means only that the host answered when last asked.
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
- High-throughput MS-based immunopeptidomics (as deposited)
- High-throughput proteomics of the 26 medically most important elapids and vipers from sub-Saharan Africa (as deposited)
- InstaNovo enables diffusion-powered de novo peptide identification in large scale proteomics experiments (as deposited)
- Longitudinal evaluation of biomarkers in wound fluids of venous leg ulcers treated with a protease-modulating wound dressing (as deposited)
- Supplementary Data for “Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly” (as deposited)
- The Proteome Landscape of the Kingdoms of Life (as deposited)
- Winnow MS datasets (version not stated)
Evaluated on
- High-throughput MS-based immunopeptidomics (as deposited)
- High-throughput proteomics of the 26 medically most important elapids and vipers from sub-Saharan Africa (as deposited)
- InstaNovo enables diffusion-powered de novo peptide identification in large scale proteomics experiments (as deposited)
- Longitudinal evaluation of biomarkers in wound fluids of venous leg ulcers treated with a protease-modulating wound dressing (as deposited)
- Supplementary Data for “Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly” (as deposited)
- Systematic HLA Epitope Ranking Pan Algorithm (SHERPA) (as deposited)
- The Proteome Landscape of the Kingdoms of Life (as deposited)
- Winnow MS datasets (version not stated)
Also used, purpose not recorded
- Analysis outputs (as deposited)
Paper describing it
- De novo peptide sequencing rescoring and FDR estimation with Winnow (2025, arXiv, preprint)
Paper using it
An application or evaluation that ran this method. It is not counted among its authors below.
- Generalizable Direct Protein Sequencing With InstaNexus (2026, Molecular & Cellular Proteomics, peer-reviewed)