| --- |
| license: other |
| license_name: see-per-file-provenance |
| pretty_name: De Novo Peptide Sequencing Checkpoint Mirror |
| tags: |
| - proteomics |
| - mass-spectrometry |
| - de-novo-peptide-sequencing |
| --- |
| |
| # De novo peptide sequencing: checkpoint mirror |
|
|
| A backup copy of published model checkpoints for *de novo* peptide sequencing, |
| kept because several of the originals live on Google Drive and Dropbox links |
| that carry no DOI, no version and no preservation commitment, and which |
| therefore can disappear without leaving anything to cite. |
|
|
| **These are other people's weights.** Nothing here was trained by this mirror. |
| Every file keeps the name its authors gave it, and the table below records where |
| it came from, which paper it belongs to and what licence its source repository |
| states. If you use a checkpoint, cite the paper, not this mirror. |
|
|
| Every known checkpoint for these methods, mirrored here or not, is listed with |
| its version, training data, licence and link state in |
| [**The weights behind the numbers**](https://jeroen.vangoey.be/awesome_de_novo_peptide_sequencing/#the-weights-behind-the-numbers), |
| part of the [Awesome De Novo Peptide Sequencing](https://jeroen.vangoey.be/awesome_de_novo_peptide_sequencing/) catalog. Each method's |
| own page there carries the same for that method alone. |
|
|
| ## Provenance and licence, per file |
|
|
| | Folder | File | Method | Source | Licence of source repo | |
| | --- | --- | --- | --- | --- | |
| | `contranovo/` | `ControNovo.ckpt` | ContraNovo | [BEAM-Labs/denovo](https://github.com/BEAM-Labs/denovo) (Google Drive) | MIT | |
| | `pi-primenovo/` | `model_massive.ckpt` | π-PrimeNovo | [PHOENIXcenter/pi-PrimeNovo](https://github.com/PHOENIXcenter/pi-PrimeNovo) (Google Drive) | MIT | |
| | `pi-primenovo/` | `PTM_Phosphorylation.ckpt` | π-PrimeNovo (phospho) | [PHOENIXcenter/pi-PrimeNovo/pi-PrimeNovo-PTM](https://github.com/PHOENIXcenter/pi-PrimeNovo/tree/main/pi-PrimeNovo-PTM) (Google Drive) | MIT | |
| | `refinenovo/` | `model_massivekb.ckpt` | RefineNovo-30M | [BEAM-Labs/denovo](https://github.com/BEAM-Labs/denovo) (Google Drive) | MIT | |
| | `ranknovo-crossnovo/` | `model_0.660.ckpt` | RankNovo **and** CrossNovo | [BEAM-Labs/denovo](https://github.com/BEAM-Labs/denovo) (Google Drive) | MIT | |
| | `dianovo/` | `*.pt` | DIANovo | [hearthewind/dianovo](https://github.com/hearthewind/dianovo) (git-LFS) | Apache-2.0 | |
| | `deepnovo/` | `translate.ckpt-48600.*` + `knapsack.npy.zip` | DeepNovo | [nh2tran/DeepNovo](https://github.com/nh2tran/DeepNovo) (Google Drive, **now gated**) | non-commercial use (custom) | |
| | `deepnovo-dia/` | DeepNovo-DIA model | DeepNovo-DIA | [nh2tran/DeepNovo-DIA](https://github.com/nh2tran/DeepNovo-DIA) (Google Drive) | non-commercial use (custom) | |
|
|
| **The two DeepNovo entries carry custom non-commercial licences.** The files |
| say: |
|
|
| > DeepNovo is publicly available for non-commercial uses. Copyright (C) 2017. |
| > Authors. All rights reserved. |
|
|
| > Copyright (C) 2018. Authors. All rights reserved. DeepNovo-DIA is provided |
| > free of charge for academic and non-commercial use. |
|
|
| So use for academic and non-commercial purposes is granted. Redistribution is |
| not *expressly* granted, and this mirror is non-commercial, attributed, and |
| exists because the DeepNovo link is now gated behind a Google sign-in. If you |
| are an author of either and would rather these were not mirrored, open an issue |
| on the catalog repository and they will be removed. |
|
|
| **One file serves two methods.** `BEAM-Labs/denovo` lists the same Google Drive |
| id for RankNovo and for CrossNovo, so either they ship one checkpoint or the |
| README has an error; the file is stored once, under a folder naming both. |
|
|
