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--- |
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license: cc0-1.0 |
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configs: |
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- config_name: default |
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data_files: |
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- split: train |
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path: data/train-* |
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- split: validation |
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path: data/validation-* |
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- split: test |
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path: data/test-* |
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dataset_info: |
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features: |
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- name: sequence |
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dtype: string |
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- name: modified_sequence |
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dtype: string |
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- name: precursor_mz |
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dtype: float64 |
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- name: precursor_charge |
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dtype: int64 |
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- name: mz_array |
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sequence: float64 |
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- name: intensity_array |
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sequence: float32 |
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splits: |
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- name: train |
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num_bytes: 839098224 |
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num_examples: 499402 |
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- name: validation |
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num_bytes: 49792990 |
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num_examples: 28572 |
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- name: test |
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num_bytes: 300840334 |
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num_examples: 111312 |
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download_size: 1414788031 |
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dataset_size: 1189731548 |
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--- |
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# Dataset Card for Nine-Species excluding Yeast |
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Dataset used for the baseline comparison of InstaNovo to other models. |
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## Dataset Description |
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- **Repository:** [InstaNovo](https://github.com/instadeepai/InstaNovo) |
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- **Paper:** [InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments](https://www.nature.com/articles/s42256-025-01019-5) |
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### Dataset Summary |
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Dataset used in the original [DeepNovo](https://www.pnas.org/doi/full/10.1073/pnas.1705691114) paper. |
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- The training set contains 8 species excluding yeast |
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- The validation/test set contains the yeast species |
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## Dataset Structure |
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The dataset is tabular, where each row corresponds to a labelled MS2 spectra. |
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- `sequence (string)` \ |
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The target peptide sequence excluding post-translational modifications |
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- `modified_sequence (string)` \ |
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The target peptide sequence including post-translational modifications |
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- `precursor_mz (float64)` \ |
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The mass-to-charge of the precursor (from MS1) |
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- `charge (int64)` \ |
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The charge of the precursor (from MS1) |
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- `mz_array (list[float64])` \ |
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The mass-to-charge values of the MS2 spectrum |
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- `mz_array (list[float32])` \ |
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The intensity values of the MS2 spectrum |
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## Citation Information |
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If you use this dataset, please cite the original authors. |
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The original data is available on [MASSIVE](https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp) with the identifier `MSV000081382`. |
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Please also cite InstaNovo: |
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```bibtex |
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@article{eloff_kalogeropoulos_2025_instanovo, |
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title = {InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale |
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proteomics experiments}, |
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author = {Eloff, Kevin and Kalogeropoulos, Konstantinos and Mabona, Amandla and Morell, |
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Oliver and Catzel, Rachel and Rivera-de-Torre, Esperanza and Berg Jespersen, |
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Jakob and Williams, Wesley and van Beljouw, Sam P. B. and Skwark, Marcin J. |
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and Laustsen, Andreas Hougaard and Brouns, Stan J. J. and Ljungars, |
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Anne and Schoof, Erwin M. and Van Goey, Jeroen and auf dem Keller, Ulrich and |
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Beguir, Karim and Lopez Carranza, Nicolas and Jenkins, Timothy P.}, |
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year = 2025, |
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month = {Mar}, |
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day = 31, |
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journal = {Nature Machine Intelligence}, |
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doi = {10.1038/s42256-025-01019-5}, |
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issn = {2522-5839}, |
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url = {https://doi.org/10.1038/s42256-025-01019-5} |
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} |
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``` |
