InstaDeepAI/ms_ninespecies_benchmark

Dataset Card for Nine-Species excluding Yeast

Dataset used for the baseline comparison of InstaNovo to other models.

Dataset Summary

Dataset used in the original DeepNovo 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 with the identifier MSV000081382.

Please also cite InstaNovo:

@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}
}