README.md

---
license: cc0-1.0
configs:
- config_name: default
  data_files:
  - split: train
    path: data/train-*
  - split: validation
    path: data/validation-*
  - split: test
    path: data/test-*
dataset_info:
  features:
  - name: sequence
    dtype: string
  - name: modified_sequence
    dtype: string
  - name: precursor_mz
    dtype: float64
  - name: precursor_charge
    dtype: int64
  - name: mz_array
    sequence: float64
  - name: intensity_array
    sequence: float32
  splits:
  - name: train
    num_bytes: 839098224
    num_examples: 499402
  - name: validation
    num_bytes: 49792990
    num_examples: 28572
  - name: test
    num_bytes: 45505134
    num_examples: 27142
  download_size: 1119691599
  dataset_size: 934396348
---


# Dataset Card for Nine-Species excluding Yeast
Dataset used for the baseline comparison of InstaNovo to other models.


## Dataset Description

- **Repository:** [InstaNovo](https://github.com/instadeepai/InstaNovo)
- **Paper:** [De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments](https://www.biorxiv.org/content/10.1101/2023.08.30.555055v1) 

### Dataset Summary

Dataset used in the original [DeepNovo](https://www.pnas.org/doi/full/10.1073/pnas.1705691114) paper. 
- The training set contains 8 species excluding yeast
- The validation/test set contains the yeast species

## Dataset Structure

The dataset is tabular, where each row corresponds to a labelled MS2 spectra.
- `sequence (string)` \
  The target peptide sequence excluding post-translational modifications
- `modified_sequence (string)` \
  The target peptide sequence including post-translational modifications
- `precursor_mz (float64)` \
  The mass-to-charge of the precursor (from MS1)
- `charge (int64)` \
  The charge of the precursor (from MS1)
- `mz_array (list[float64])` \
  The mass-to-charge values of the MS2 spectrum
- `mz_array (list[float32])` \
  The intensity values of the MS2 spectrum

## Citation Information

If you use this dataset, please cite the original authors.
The original data is available on [MASSIVE](https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp) with the identifier `MSV000081382`.

Please also cite InstaNovo:

```bibtex
@article{eloff_kalogeropoulos_2023_instanovo,
	title = {De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments},
	author = {Kevin Eloff and Konstantinos Kalogeropoulos and Oliver Morell and Amandla Mabona and Jakob Berg Jespersen and Wesley Williams and Sam van Beljouw and Marcin Skwark and Andreas Hougaard Laustsen and Stan J. J. Brouns and Anne Ljungars and Erwin Marten Schoof and Jeroen Van Goey and Ulrich auf dem Keller and Karim Beguir and Nicolas Lopez Carranza and Timothy Patrick Jenkins},
	year = {2023},
	doi = {10.1101/2023.08.30.555055},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/10.1101/2023.08.30.555055v1},
	journal = {bioRxiv}
}
```