InstaDeepAI/ms_proteometools

Dataset Card for High-Confidence ProteomeTools

Dataset used to train, validate and test InstaNovo and InstaNovo+.

Dataset Summary

This dataset consists of the highest-confidence peptide-spectral matches from three parts of the ProteomeTools datasets. The original datasets may be found in the PRIDE repository with identifiers:

• PXD004732 (Part I)
• PXD010595 (Part II)
• PXD021013 (Part III)

The dataset has been split on unique peptides with the following ratio:

• 80% train
• 10% validation
• 10% test

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

MaxQuant additional columns:

• experiment_name (string)
• evidence_index (in64)
• scan_number (in64)
• precursor_recalibrated_mz (float64)

Citation Information

If you use this dataset, please cite the original authors. The original ProteomeTools data is available on PRIDE with identifiers PXD004732 (Part I), PXD010595 (Part II), and PXD021013 (Part III).

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}
}