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